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Conserved domains on  [gi|1032753998|ref|XP_016838091|]
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arginine-glutamic acid dipeptide repeats protein isoform X12 [Nasonia vitripennis]

Protein Classification

mesoderm induction early response protein( domain architecture ID 10477681)

mesoderm induction early response (MIER) protein such as MIER2 that acts as a transcriptional repressor

Gene Ontology:  GO:0003677|GO:0006355|GO:0003700
PubMed:  28046085|8882580

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SANT_MTA3_like cd11661
Myb-Like Dna-Binding Domain of MTA3 and related proteins; Members in this SANT/myb family ...
 127-172 1.65e-23

Myb-Like Dna-Binding Domain of MTA3 and related proteins; Members in this SANT/myb family include domains found in mouse metastasis-associated protein 3 (MTA3) proteins and arginine-glutamic dipeptide (RERE) repeats proteins. SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domains are a diverse set of proteins that share a common 3 alpha-helix bundle. MTA3 has been shown to interact with nucleosome remodeling and deacetylase (NuRD) proteins CHD4 and HDAC1, and the core cohesin complex protein RAD21 in the ovary, and regulate G2/M progression in proliferating granulosa cells. RERE belongs to the atrophin family and has been identified as a nuclear receptor corepressor; altered expression levels of RERE are associated with cancer in humans while mutations of Rere in mice cause failure in closing the anterior neural tube and fusion of the telencephalic and optic vesicles during embryogenesis.


:

Pssm-ID: 212559 [Multi-domain]  Cd Length: 46  Bit Score: 94.60  E-value: 1.65e-23
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1032753998  127 KWSEEETKRFVKGLRQFGKNFSRIRKDLLPHKDTPDLVEYYYLWKK 172
Cdd:cd11661      1 EWSESEAKLFEEGLRKYGKDFHDIRQDFLPWKSVGELVEFYYMWKK 46
Atrophin-1 super family cl38111
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 1316-1478 5.73e-08

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


The actual alignment was detected with superfamily member pfam03154:

Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 57.85  E-value: 5.73e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032753998 1316 GPSPEPRIEDSECHRSQSAIFLRHWNRGEnNSCTRTDLTFKPVPDSKLARKRDERSRKQAEREREERDRAQQQQQQQQQQ 1395
Cdd:pfam03154  539 SPSPEPTVVNTPSHASQSARFYKHLDRGY-NSCARTDLYFMPLAGSKLAKKREEALEKAKREAEQKAREEKEREKEKEKE 617

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032753998 1396 QAR------------KMTTPEKQPETCKPPSRGPLEPVVS----PYDRYAARPGAYTDTPALRQLSEYARPHAAFSPAR- 1458
Cdd:pfam03154  618 RERererereaeraaKASSSSHEGRMGDPQLAGPAHMRPSfeppPTTIAAVPPYIGPDTPALRTLSEYARPHVMSPTNRn 697

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1032753998 1459 HP-----GPQDAMLHY-MYG-----PAARER 1478
Cdd:pfam03154  698 HPffvplNPTDPLLAYhMPGlynvdPAIRER 728
ELM2 pfam01448
ELM2 domain; The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown ...
 9-71 3.41e-05

ELM2 domain; The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown function. It is found in the MTA1 protein that is part of the NuRD complex. The domain is usually found to the N terminus of a myb-like DNA binding domain pfam00249. ELM2 is also found associated with an ARID DNA binding domain pfam01388 in Swiss:O82364. This suggests that ELM2 may also be involved in DNA binding, or perhaps is a protein-protein interaction domain.


:

Pssm-ID: 460214  Cd Length: 53  Bit Score: 42.99  E-value: 3.41e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1032753998    9 IRVGPSHqdlvscQAHLPEYRpgiPPAELLPDPEfaKDREELRWIPAMTL-DMDLLMYLRAARS 71
Cdd:pfam01448    1 IRVGPRY------QAEIPELL---PPSEEEDRYE--EEDELLVWDPNHNLpDRKLDEYLVVARS 53
 
Name Accession Description Interval E-value
SANT_MTA3_like cd11661
Myb-Like Dna-Binding Domain of MTA3 and related proteins; Members in this SANT/myb family ...
 127-172 1.65e-23

Myb-Like Dna-Binding Domain of MTA3 and related proteins; Members in this SANT/myb family include domains found in mouse metastasis-associated protein 3 (MTA3) proteins and arginine-glutamic dipeptide (RERE) repeats proteins. SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domains are a diverse set of proteins that share a common 3 alpha-helix bundle. MTA3 has been shown to interact with nucleosome remodeling and deacetylase (NuRD) proteins CHD4 and HDAC1, and the core cohesin complex protein RAD21 in the ovary, and regulate G2/M progression in proliferating granulosa cells. RERE belongs to the atrophin family and has been identified as a nuclear receptor corepressor; altered expression levels of RERE are associated with cancer in humans while mutations of Rere in mice cause failure in closing the anterior neural tube and fusion of the telencephalic and optic vesicles during embryogenesis.


Pssm-ID: 212559 [Multi-domain]  Cd Length: 46  Bit Score: 94.60  E-value: 1.65e-23
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1032753998  127 KWSEEETKRFVKGLRQFGKNFSRIRKDLLPHKDTPDLVEYYYLWKK 172
Cdd:cd11661      1 EWSESEAKLFEEGLRKYGKDFHDIRQDFLPWKSVGELVEFYYMWKK 46
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 1316-1478 5.73e-08

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 57.85  E-value: 5.73e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032753998 1316 GPSPEPRIEDSECHRSQSAIFLRHWNRGEnNSCTRTDLTFKPVPDSKLARKRDERSRKQAEREREERDRAQQQQQQQQQQ 1395
Cdd:pfam03154  539 SPSPEPTVVNTPSHASQSARFYKHLDRGY-NSCARTDLYFMPLAGSKLAKKREEALEKAKREAEQKAREEKEREKEKEKE 617

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032753998 1396 QAR------------KMTTPEKQPETCKPPSRGPLEPVVS----PYDRYAARPGAYTDTPALRQLSEYARPHAAFSPAR- 1458
Cdd:pfam03154  618 RERererereaeraaKASSSSHEGRMGDPQLAGPAHMRPSfeppPTTIAAVPPYIGPDTPALRTLSEYARPHVMSPTNRn 697

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1032753998 1459 HP-----GPQDAMLHY-MYG-----PAARER 1478
Cdd:pfam03154  698 HPffvplNPTDPLLAYhMPGlynvdPAIRER 728
Myb_DNA-bind_7 pfam15963
Myb DNA-binding like;
126-163 9.72e-07

Myb DNA-binding like;


Pssm-ID: 464956 [Multi-domain]  Cd Length: 85  Bit Score: 48.30  E-value: 9.72e-07
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1032753998  126 KKWSEEETKRFVKGLRQFGKNFSRIRKdLLPHKDTPDL 163
Cdd:pfam15963    9 KRWSKEETELFYKALSMFGTDFSLIAQ-LFPGRTRRQI 45
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
126-173 9.71e-06

SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 44.14  E-value: 9.71e-06
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 1032753998   126 KKWSEEETKRFVKGLRQFG-KNFSRIRKDlLPHKDTPDLVEYYYLWKKT 173
Cdd:smart00717    2 GEWTEEEDELLIELVKKYGkNNWEKIAKE-LPGRTAEQCRERWRNLLKP 49
ELM2 pfam01448
ELM2 domain; The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown ...
 9-71 3.41e-05

ELM2 domain; The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown function. It is found in the MTA1 protein that is part of the NuRD complex. The domain is usually found to the N terminus of a myb-like DNA binding domain pfam00249. ELM2 is also found associated with an ARID DNA binding domain pfam01388 in Swiss:O82364. This suggests that ELM2 may also be involved in DNA binding, or perhaps is a protein-protein interaction domain.


Pssm-ID: 460214  Cd Length: 53  Bit Score: 42.99  E-value: 3.41e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1032753998    9 IRVGPSHqdlvscQAHLPEYRpgiPPAELLPDPEfaKDREELRWIPAMTL-DMDLLMYLRAARS 71
Cdd:pfam01448    1 IRVGPRY------QAEIPELL---PPSEEEDRYE--EEDELLVWDPNHNLpDRKLDEYLVVARS 53
 
Name Accession Description Interval E-value
SANT_MTA3_like cd11661
Myb-Like Dna-Binding Domain of MTA3 and related proteins; Members in this SANT/myb family ...
 127-172 1.65e-23

Myb-Like Dna-Binding Domain of MTA3 and related proteins; Members in this SANT/myb family include domains found in mouse metastasis-associated protein 3 (MTA3) proteins and arginine-glutamic dipeptide (RERE) repeats proteins. SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domains are a diverse set of proteins that share a common 3 alpha-helix bundle. MTA3 has been shown to interact with nucleosome remodeling and deacetylase (NuRD) proteins CHD4 and HDAC1, and the core cohesin complex protein RAD21 in the ovary, and regulate G2/M progression in proliferating granulosa cells. RERE belongs to the atrophin family and has been identified as a nuclear receptor corepressor; altered expression levels of RERE are associated with cancer in humans while mutations of Rere in mice cause failure in closing the anterior neural tube and fusion of the telencephalic and optic vesicles during embryogenesis.


Pssm-ID: 212559 [Multi-domain]  Cd Length: 46  Bit Score: 94.60  E-value: 1.65e-23
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1032753998  127 KWSEEETKRFVKGLRQFGKNFSRIRKDLLPHKDTPDLVEYYYLWKK 172
Cdd:cd11661      1 EWSESEAKLFEEGLRKYGKDFHDIRQDFLPWKSVGELVEFYYMWKK 46
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 1316-1478 5.73e-08

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 57.85  E-value: 5.73e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032753998 1316 GPSPEPRIEDSECHRSQSAIFLRHWNRGEnNSCTRTDLTFKPVPDSKLARKRDERSRKQAEREREERDRAQQQQQQQQQQ 1395
Cdd:pfam03154  539 SPSPEPTVVNTPSHASQSARFYKHLDRGY-NSCARTDLYFMPLAGSKLAKKREEALEKAKREAEQKAREEKEREKEKEKE 617

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1032753998 1396 QAR------------KMTTPEKQPETCKPPSRGPLEPVVS----PYDRYAARPGAYTDTPALRQLSEYARPHAAFSPAR- 1458
Cdd:pfam03154  618 RERererereaeraaKASSSSHEGRMGDPQLAGPAHMRPSfeppPTTIAAVPPYIGPDTPALRTLSEYARPHVMSPTNRn 697

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1032753998 1459 HP-----GPQDAMLHY-MYG-----PAARER 1478
Cdd:pfam03154  698 HPffvplNPTDPLLAYhMPGlynvdPAIRER 728
Myb_DNA-bind_7 pfam15963
Myb DNA-binding like;
126-163 9.72e-07

Myb DNA-binding like;


Pssm-ID: 464956 [Multi-domain]  Cd Length: 85  Bit Score: 48.30  E-value: 9.72e-07
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1032753998  126 KKWSEEETKRFVKGLRQFGKNFSRIRKdLLPHKDTPDL 163
Cdd:pfam15963    9 KRWSKEETELFYKALSMFGTDFSLIAQ-LFPGRTRRQI 45
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
126-173 9.71e-06

SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 44.14  E-value: 9.71e-06
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*....
gi 1032753998   126 KKWSEEETKRFVKGLRQFG-KNFSRIRKDlLPHKDTPDLVEYYYLWKKT 173
Cdd:smart00717    2 GEWTEEEDELLIELVKKYGkNNWEKIAKE-LPGRTAEQCRERWRNLLKP 49
SANT cd00167
'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric ...
 127-171 1.49e-05

'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.


Pssm-ID: 238096 [Multi-domain]  Cd Length: 45  Bit Score: 43.72  E-value: 1.49e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1032753998  127 KWSEEETKRFVKGLRQFG-KNFSRIRKdLLPHKDTPDLVEYYYLWK 171
Cdd:cd00167      1 PWTEEEDELLLEAVKKYGkNNWEKIAK-ELPGRTPKQCRERWRNLL 45
ELM2 pfam01448
ELM2 domain; The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown ...
 9-71 3.41e-05

ELM2 domain; The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown function. It is found in the MTA1 protein that is part of the NuRD complex. The domain is usually found to the N terminus of a myb-like DNA binding domain pfam00249. ELM2 is also found associated with an ARID DNA binding domain pfam01388 in Swiss:O82364. This suggests that ELM2 may also be involved in DNA binding, or perhaps is a protein-protein interaction domain.


Pssm-ID: 460214  Cd Length: 53  Bit Score: 42.99  E-value: 3.41e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1032753998    9 IRVGPSHqdlvscQAHLPEYRpgiPPAELLPDPEfaKDREELRWIPAMTL-DMDLLMYLRAARS 71
Cdd:pfam01448    1 IRVGPRY------QAEIPELL---PPSEEEDRYE--EEDELLVWDPNHNLpDRKLDEYLVVARS 53
Myb_DNA-binding pfam00249
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 126-171 1.64e-04

Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.


Pssm-ID: 459731 [Multi-domain]  Cd Length: 46  Bit Score: 40.56  E-value: 1.64e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1032753998  126 KKWSEEETKRFVKGLRQFGKNFSRIrKDLLPHKDTPDLVEYYYLWK 171
Cdd:pfam00249    2 GPWTPEEDELLLEAVEKLGNRWKKI-AKLLPGRTDNQCKNRWQNYL 46
SANT_TRF cd11660
Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human ...
 126-159 8.24e-03

Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family; Human telomere repeat binding factors, TRF1 and TRF2, function as part of the 6 component shelterin complex. TRF2 binds DNA and recruits RAP1 (via binding to the RAP1 protein c-terminal (RCT)) and TIN2 in the protection of telomeres from DNA repair machinery. Metazoan shelterin consists of 3 DNA binding proteins (TRF2, TRF1, and POT1) and 3 recruited proteins that bind to one or more of these DNA-binding proteins (RAP1, TIN2, TPP1). Schizosaccharomyces pombe TAZ1 is an orthlog and binds RAP1. Human TRF1 and TRF2 bind double-stranded DNA. hTRF2 consists of a basic N-terminus, a TRF homology domain, the RAP1 binding motif (RBM), the TIN2 binding motif (TBM) and a myb-like DNA binding domain, SANT, named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. Tandem copies of the domain bind telomeric DNA tandem repeats as part of the capping complex. The single myb-like domain of TRF-type proteins is similar to the tandem myb_like domains found in yeast RAP1.


Pssm-ID: 212558 [Multi-domain]  Cd Length: 50  Bit Score: 36.01  E-value: 8.24e-03
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 1032753998  126 KKWSEEETKRFVKGLRQFGK-NFSRIRKDLLPHKD 159
Cdd:cd11660      1 RKWTDEEDEALVEGVEKYGVgNWAKILKDYFFVNN 35
 
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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