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Conserved domains on  [gi|315583578]
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Chain A, Interleukin enhancer-binding factor 3

Protein Classification

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List of domain hits

 Name Accession Description Interval E-value
DSRM_ILF3_rpt2 cd19912
second double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and ...
 1-72 1.59e-40

second double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and similar proteins; ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. ILF3 contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


:

Pssm-ID: 380741  Cd Length: 72  Bit Score: 127.07  E-value: 1.59e-40
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 315583578  1 ILTKHGKNPV*ELNEKRRGLKYELISETGGSHDKRFV*EVEVDGQKFQGAGSNKKVAKAYAALAALEKLFPD 72
Cdd:cd19912   1 ILTKHGKNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKAYAALAALEKLFPD 72
 
Name Accession Description Interval E-value
DSRM_ILF3_rpt2 cd19912
second double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and ...
 1-72 1.59e-40

second double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and similar proteins; ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. ILF3 contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380741  Cd Length: 72  Bit Score: 127.07  E-value: 1.59e-40
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 315583578  1 ILTKHGKNPV*ELNEKRRGLKYELISETGGSHDKRFV*EVEVDGQKFQGAGSNKKVAKAYAALAALEKLFPD 72
Cdd:cd19912   1 ILTKHGKNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKAYAALAALEKLFPD 72
DSRM smart00358
Double-stranded RNA binding motif;
7-53 4.90e-10

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 49.95  E-value: 4.90e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 315583578    7 KNPV*ELNEKRR-GLKYELISETGGSHDKRFV*EVEVDG-QKFQGAGSN 53
Cdd:smart00358  2 KSLLQELAQKRKlPPEYELVKEEGPDHAPRFTVTVKVGGkRTGEGEGSS 50
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 9-53 2.23e-06

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 40.68  E-value: 2.23e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 315583578   9 PV*ELNE----KRRGLKYELISETGGSHDKRFV*EVEVDGQKF-QGAGSN 53
Cdd:pfam00035  1 PKSLLQEyaqkNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYgSGTGSS 50
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
4-53 2.84e-06

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 42.39  E-value: 2.84e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 315583578   4 KHGKNPV*ELNEK--RRGL---KYELISETGGSHDKRFV*EVEVDGQKF-QGAGSN 53
Cdd:COG0571  154 GAGKDYKTALQEWlqARGLplpEYEVVEEEGPDHAKTFTVEVLVGGKVLgEGTGRS 209
 
Name Accession Description Interval E-value
DSRM_ILF3_rpt2 cd19912
second double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and ...
 1-72 1.59e-40

second double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and similar proteins; ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. ILF3 contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380741  Cd Length: 72  Bit Score: 127.07  E-value: 1.59e-40
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 315583578  1 ILTKHGKNPV*ELNEKRRGLKYELISETGGSHDKRFV*EVEVDGQKFQGAGSNKKVAKAYAALAALEKLFPD 72
Cdd:cd19912   1 ILTKHGKNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKAYAALAALEKLFPD 72
DSRM_STRBP-like_rpt2 cd19897
second double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family ...
 7-53 2.30e-26

second double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3). STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. Members of this STRBP/ILF3 group contain an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380726  Cd Length: 64  Bit Score: 91.27  E-value: 2.30e-26
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 315583578  7 KNPV*ELNEKRRGLKYELISETGGSHDKRFV*EVEVDGQKFQGAGSN 53
Cdd:cd19897   1 KNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFQGAGSN 47
DSRM_STRBP_RED-like_rpt2 cd19866
second double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 7-53 6.54e-24

second double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3), as well as two RNA-editing deaminases, RED1 and RED2. STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. RED1 (EC 3.5.4.37; also called double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. RED2 (also called double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA but also to ssRNA. RED2 lacks editing activity for currently known substrate RNAs. Members of this group contain two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380695  Cd Length: 63  Bit Score: 84.91  E-value: 6.54e-24
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 315583578  7 KNPV*ELNEKRRGLKYELISETGGSHDKRFV*EVEVDGQKFQGAGSN 53
Cdd:cd19866   1 KNPVMLLNELRPGLKYKCLSESGESHAKSFVMSVTVDGQTFEGTGRS 47
DSRM_STRBP_rpt2 cd19911
second double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) ...
 7-53 1.20e-22

second double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) and similar proteins; STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. STRBP contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380740  Cd Length: 64  Bit Score: 81.72  E-value: 1.20e-22
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 315583578  7 KNPV*ELNEKRRGLKYELISETGGSHDKRFV*EVEVDGQKFQGAGSN 53
Cdd:cd19911   1 KNPVMELNEKRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPN 47
DSRM_RED1_rpt2 cd19898
second double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar ...
 6-53 2.97e-19

second double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins; RED1 (EC 3.5.4.37; also known as double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. It contains two double-stranded RNA binding motifs (DSRMs) and a C-terminal RNA-specific adenosine-deaminase (editase) domain. This model describes the second DSRM. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380727  Cd Length: 70  Bit Score: 73.30  E-value: 2.97e-19
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 315583578  6 GKNPV*ELNEKRRGLKYELISETGGSHDKRFV*EVEVDGQKFQGAGSN 53
Cdd:cd19898   2 GKNPVMILNELRPGLKYEFVSESGESHAKNFVMSVTVDGQTFEGSGRN 49
DSRM_STRBP_RED-like_rpt1 cd19865
first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 7-52 1.13e-14

first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3), as well as two RNA-editing deaminases, RED1 and RED2. STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. RED1 (EC 3.5.4.37; also called double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. RED2 (also called double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA, but also to ssRNA. RED2 lacks editing activity for currently known substrate RNAs. Members of this group contain two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380694  Cd Length: 63  Bit Score: 61.59  E-value: 1.13e-14
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 315583578  7 KNPV*ELNEKRRGLKYELISETGGSHDKRFV*EVEVDGQKFQGAGS 52
Cdd:cd19865   1 KNALMQLNELRPGLQYKLTSQTGPVHAPVFTMSVEVNGQTFEGTGR 46
DSRM_RED2_rpt2 cd19899
second double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar ...
 7-51 2.02e-10

second double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar proteins; RED2 (also known as double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA but also to ssRNA. RED2 contains two double-stranded RNA binding motifs (DSRMs) and a C-terminal RNA-specific adenosine-deaminase (editase) domain. This model describes the second DSRM. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. RED2 lacks editing activity for currently known substrate RNAs, and may have an inactive editase domain.


Pssm-ID: 380728  Cd Length: 74  Bit Score: 51.03  E-value: 2.02e-10
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 315583578  7 KNPV*ELNEKRRGLKYELISETGGS-HDKRFV*EVEVDGQKFQGAG 51
Cdd:cd19899   7 KNPVVLLNELRPGLRYVCLSETAEKqHIKSFVMAVRVDGRTFEGSG 52
DSRM_RED1_rpt1 cd19895
first double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins; ...
 7-51 3.36e-10

first double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins; RED1 (EC 3.5.4.37; also known as double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. It contains two double-stranded RNA binding motifs (DSRMs) and a C-terminal RNA-specific adenosine-deaminase (editase) domain. This model describes the first DSRM. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380724  Cd Length: 72  Bit Score: 50.46  E-value: 3.36e-10
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 315583578  7 KNPV*ELNEKRRGLKYELISETGGSHDKRFV*EVEVDGQKFQGAG 51
Cdd:cd19895   6 KNALMQLNEIKPGLQYKLLSQTGPVHAPVFVMSVEVNGQVFEGSG 50
DSRM smart00358
Double-stranded RNA binding motif;
7-53 4.90e-10

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 49.95  E-value: 4.90e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 315583578    7 KNPV*ELNEKRR-GLKYELISETGGSHDKRFV*EVEVDG-QKFQGAGSN 53
Cdd:smart00358  2 KSLLQELAQKRKlPPEYELVKEEGPDHAPRFTVTVKVGGkRTGEGEGSS 50
DSRM_RED2_rpt1 cd19896
first double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar proteins; ...
 7-51 1.57e-09

first double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar proteins; RED2 (also known as double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA but also to ssRNA. RED2 contains two double-stranded RNA binding motifs (DSRMs) and a C-terminal RNA-specific adenosine-deaminase (editase) domain. This model describes the first DSRM. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. RED2 lacks editing activity for currently known substrate RNAs, and may have an inactive editase domain.


Pssm-ID: 380725  Cd Length: 74  Bit Score: 48.94  E-value: 1.57e-09
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 315583578  7 KNPV*ELNEKRRGLKYELISETGGSHDKRFV*EVEVDGQKFQGAG 51
Cdd:cd19896   6 KNALVQLNELKPGLQYRMVSQTGPVHAPVFAVAVEVNGLTFEGTG 50
DSRM_STRBP-like_rpt1 cd19894
first double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family ...
 8-51 3.67e-09

first double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3). STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. Members of this STRBP/ILF3 group contain an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380723  Cd Length: 63  Bit Score: 47.76  E-value: 3.67e-09
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 315583578  8 NPV*ELNEKRRGLKYELISETGGSHDKRFV*EVEVDGQKFQGAG 51
Cdd:cd19894   2 NALMRLNQLRPGLQYKLASQTGPVHAPQFTMSVEVDGVTYEASG 45
DSRM_ILF3_rpt1 cd19910
first double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and ...
 8-51 1.82e-08

first double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and similar proteins; ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. ILF3 contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380739  Cd Length: 73  Bit Score: 46.29  E-value: 1.82e-08
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 315583578  8 NPV*ELNEKRRGLKYELISETGGSHDKRFV*EVEVDGQKFQGAG 51
Cdd:cd19910   7 NALMRLNQLKPGLQYKLISQTGPVHAPVFTMSVEVDGKTFEASG 50
DSRM_STRBP_rpt1 cd19909
first double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) ...
 8-53 4.36e-07

first double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) and similar proteins; STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. STRBP contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380738  Cd Length: 84  Bit Score: 43.10  E-value: 4.36e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 315583578  8 NPV*ELNEKRRGLKYELISETGGSHDKRFV*EVEVDGQKFQGAGSN 53
Cdd:cd19909   7 NALMRLNQIRPGLQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPS 52
DSRM_SON-like cd19870
double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...
 6-48 6.03e-07

double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known as Bax antagonist selected in saccharomyces 1 (BASS1), negative regulatory element-binding protein (NRE-binding protein), or protein DBP-5, or SON3) is an RNA-binding protein which acts as an mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. It specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Members of this group contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380699  Cd Length: 75  Bit Score: 42.27  E-value: 6.03e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 315583578  6 GKNPV*ELNE---KRR--GLKYELISETGGSHDKRFV*EVEVDGQKFQ 48
Cdd:cd19870   1 GKHPVSALMElcnKRKwgPPEFRLVEESGPPHRKHFLFKVVVNGVEYQ 48
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 9-53 2.23e-06

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 40.68  E-value: 2.23e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 315583578   9 PV*ELNE----KRRGLKYELISETGGSHDKRFV*EVEVDGQKF-QGAGSN 53
Cdd:pfam00035  1 PKSLLQEyaqkNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYgSGTGSS 50
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
4-53 2.84e-06

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 42.39  E-value: 2.84e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 315583578   4 KHGKNPV*ELNEK--RRGL---KYELISETGGSHDKRFV*EVEVDGQKF-QGAGSN 53
Cdd:COG0571  154 GAGKDYKTALQEWlqARGLplpEYEVVEEEGPDHAKTFTVEVLVGGKVLgEGTGRS 209
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 7-53 1.09e-05

double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase III (EC 3.1.26.3; also known as ribonuclease 3) digests double-stranded RNA formed within single-strand substrates, but not RNA-DNA hybrids. It is involved in the processing of rRNA precursors, viral transcripts, some mRNAs, and at least 1 tRNA (metY, a minor form of tRNA-init-Met). It cleaves the 30S primary rRNA transcript to yield the immediate precursors to the 16S and 23S rRNAs. The cleavage can occur in assembled 30S, 50S, and even 70S subunits and is influenced by the presence of ribosomal proteins. The RNase III family also includes the mitochondrion-specific ribosomal protein mL44 subfamily, which is composed of mitochondrial 54S ribosomal protein L3 (MRPL3) and mitochondrial 39S ribosomal protein L44 (MRPL44). Members of this family contain an RNase III domain and a C-terminal double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380682 [Multi-domain]  Cd Length: 69  Bit Score: 39.01  E-value: 1.09e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 315583578  7 KNPV*ELNE--KRRGL---KYELISETGGSHDKRFV*EVEVDGQKF-QGAGSN 53
Cdd:cd10845   1 KDYKTALQEylQKRGLplpEYELVEEEGPDHNKTFTVEVKVNGKVIgEGTGRS 53
DSRM_PRKRA-like_rpt1 cd19862
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 7-52 1.24e-05

first double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; This family includes protein activator of the interferon-induced protein kinase (PRKRA) and the RISC-loading complex subunit TARBP2. PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. TARBP2 (also called TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)), participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. This family also includes Drosophila melanogaster Loquacious and similar proteins. Loquacious (Loqs) is a double-stranded RNA-binding domain (dsRBD) protein, a homolog of human TAR RNA binding protein (TRBP) that is a protein first identified as binding the HIV trans-activator RNA (TAR). Loqs interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. PRKRA family proteins contain three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380691 [Multi-domain]  Cd Length: 70  Bit Score: 38.78  E-value: 1.24e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 315583578  7 KNPV*ELNEK--RRGL--KYELISETGGSHDKRFV*EVEVDGQKFQGAGS 52
Cdd:cd19862   1 KTPISVLQELcaKRGItpKYELISSEGAVHEPTFTFRVTVGDITATGSGT 50
DSRM_EIF2AK2_rpt1 cd19903
first double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha ...
 8-47 2.76e-05

first double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. EIF2AK2 proteins contain two to three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380732  Cd Length: 68  Bit Score: 37.75  E-value: 2.76e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 315583578  8 NPV*ELNE----KRRGLKYELISETGGSHDKRFV*EVEVDGQKF 47
Cdd:cd19903   2 NYMGKLNEycqkQKVVLDYVEVPTSGPSHDPRFTFQVVIDGKEY 45
DSRM_DRADA cd19902
double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) ...
 7-47 5.07e-05

double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) and similar proteins; DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. DRADA family members contain at least one double-stranded RNA binding motifs (DSRM); vertebrate proteins contain three. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380731  Cd Length: 71  Bit Score: 37.27  E-value: 5.07e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 315583578  7 KNPV*ELNE----KRRGLKYELISETGGSHDKRFV*EVEVDGQKF 47
Cdd:cd19902   1 KNPVSALMEyaqsRGVTAEIEVLSQSGPPHNPRFKAAVFVGGRRF 45
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 7-56 1.06e-03

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; The family includes EIF2AK2 and adenosine deaminase domain-containing proteins, ADAD1 and ADAD2. EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. ADAD1 (also called testis nuclear RNA-binding protein (TENR)) and ADAD2 (also called testis nuclear RNA-binding protein-like (TENRL)) are phylogenetically related to a family of adenosine deaminases involved in RNA editing. ADAD1 plays an essential function in spermatid morphogenesis. It may be involved in testis-specific nuclear post-transcriptional processes such as heterogeneous nuclear RNA (hnRNA) packaging, alternative splicing, or nuclear/cytoplasmic transport of mRNAs. ADAD2 is a double-stranded RNA binding protein with unclear biological function. Members of this group contains varying numbers of double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380704  Cd Length: 67  Bit Score: 33.78  E-value: 1.06e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 315583578  7 KNPV*ELNE----KRRGLKYElISETGGSHDKRFV*EVEVDGQKF-QGAGSNKKV 56
Cdd:cd19875   1 KNPVSALNEycqkRGLSLEFV-DVSVGPDHCPGFTASATIDGIVFaSATGTSKKE 54
DSRM_DRADA_rpt2 cd19914
second double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase ...
 7-53 1.52e-03

second double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) and similar proteins; DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. Vertebrate DRADA contains three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380743  Cd Length: 71  Bit Score: 33.67  E-value: 1.52e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 315583578  7 KNPV*ELNE--KRRG--LKYELISETGGSHDKRFV*EVEVDGQKFQGAGSN 53
Cdd:cd19914   1 KNPISVLMEhsQKSGnmCEFQLLSQEGPPHDPKFTYCVKVGEQTFPSVVAN 51
DSRM_DRADA_rpt1 cd19913
first double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase ...
 7-50 1.72e-03

first double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA); DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. Vertebrate DRADA contains three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380742  Cd Length: 71  Bit Score: 33.31  E-value: 1.72e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 315583578  7 KNPV*ELNEKRRGLKYE----LISETGGSHDKRFV*EVEVDGQKFQGA 50
Cdd:cd19913   1 KNPVSGLMEYAQFLGQTceflLLEQSGPSHDPRFKFQAVIDGRRFPPA 48
DSRM_DRADA_rpt3 cd19915
third double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase ...
 7-47 3.87e-03

third double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) and similar proteins; DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. Vertebrate DRADA contains three double-stranded RNA binding motifs (DSRMs). This model describes the third motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380744  Cd Length: 71  Bit Score: 32.61  E-value: 3.87e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 315583578  7 KNPV*ELNEKRR----GLKYELISETGGSHDKRFV*EVEVDGQKF 47
Cdd:cd19915   1 TNPVSGLLEYARskgfAAEFKLVDQSGPPHEPKFVYQAKVGGRWF 45
DSRM_STAU_rpt4 cd19860
fourth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 3-53 4.47e-03

fourth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein Staufen and similar proteins; Staufen is a double-stranded RNA binding protein required both for the localization of maternal determinants to the posterior pole of the egg, oskar (osk) RNA, and for correct localization to the anterior pole, anchoring bicoid (bcd) RNA. The family also includes two Staufen homologs from vertebrates, Staufen 1 and Staufen 2. They are present in distinct ribonucleoprotein complexes and associate with different mRNAs. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen proteins contain five double-stranded RNA binding motifs (DSRMs). This model describes the fourth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380689  Cd Length: 68  Bit Score: 32.30  E-value: 4.47e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 315583578  3 TKHGKNPV*elnekrrglkYELISETGGSHDKRFV*EVEVDGQKFQGAGSN 53
Cdd:cd19860  12 ARKEKEPV-----------YSLVAERGTPRRREFVMQVTVGDKTATGTGPN 51
DSRM_STAU1_rpt4 cd19885
fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 5-53 5.78e-03

fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the fourth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380714  Cd Length: 86  Bit Score: 32.37  E-value: 5.78e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 315583578  5 HGKNPV*ELNE-----KRRGLKYELISETGGSHDKRFV*EVEVDGQKFQGAGSN 53
Cdd:cd19885   8 QGMNPISRLAQiqqakKEKEPEYTLITERGLPRRREFVMQVKVGNQTAEGMGPN 61
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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