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Conserved domains on  [gi|1229772171|ref|XP_022139032|]
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protein RDM16 isoform X3 [Momordica charantia]

Protein Classification

pre-mRNA processing factor 3 family protein( domain architecture ID 10554148)

pre-mRNA processing factor 3 (PRP3) family protein similar to Saccharomyces cerevisiae U4/U6 small nuclear ribonucleoprotein PRP3, which participates in pre-mRNA splicing as part of the U4/U5/U6 tri-snRNP complex, one of the building blocks of the spliceosome

Gene Ontology:  GO:0006397|GO:0000398

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRP3 pfam08572
pre-mRNA processing factor 3 (PRP3); Pre-mRNA processing factor 3 (PRP3) is a U4/U6-associated ...
 255-484 2.03e-67

pre-mRNA processing factor 3 (PRP3); Pre-mRNA processing factor 3 (PRP3) is a U4/U6-associated splicing factor. The human PRP3 has been implicated in autosomal retinitis pigmentosa.


:

Pssm-ID: 462524  Cd Length: 219  Bit Score: 219.39  E-value: 2.03e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1229772171 255 NPHFDERMGInktKLLRPKRMNFQFVEEGKWSKEAETIKLRSKFGEAQAKERREKQAQ-LAKAKAAPDINPNLIEVserv 333
Cdd:pfam08572   1 NPYFDPRLSA---KPKRRKRRSLKFNEKGKYIKQAERLRRKAQLEELKKRIAEEARKAgLLPDTDLAEKAPKKFKD---- 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1229772171 334 ivkektkEPIPEIEWWDVSLLHSGTYDDVGDGFVANDKIRKD--KITIYVEHPRPIEPPVEPAPPPPQPLKLTKKEQKKL 411
Cdd:pfam08572  74 -------EVPPDIEWWDEPYLPDGSYYDDLIDDKYNLDIEDEdsPITNYVQHPVPIKPPQEKNKPPPKPLYLTKKEQKKL 146

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1229772171 412 RTQRRLAKEKDRQEMIRQGLIEPPKPKVKMSNLMKVLGSEATQDPTKLEKEIRAAAAEREQAHIDRNIARKLT 484
Cdd:pfam08572 147 RRQRRKEALKEKQDKIRLGLEPPPPPKVKLSNLMRVLGNEAVQDPTKVEARVRRQMAERKQKHEEANEERKLT 219
DUF1115 pfam06544
Protein of unknown function (DUF1115); This family represents the C-terminus of hypothetical ...
 508-632 1.34e-49

Protein of unknown function (DUF1115); This family represents the C-terminus of hypothetical eukaryotic proteins of unknown function.


:

Pssm-ID: 461943  Cd Length: 135  Bit Score: 169.01  E-value: 1.34e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1229772171 508 SVYKIYDLSHPQARFKVDVNARENRLTGCAVICDGISVLVVEGGSKSIKRYGKLMLRRINWAASVKEEEEADESD----- 582
Cdd:pfam06544   1 AVFRIKSLSNPKHRFKIDKNAKQLGLTGFCILGPPFGLVVVEGGEKSIKKYKKLMLRRIKWTENPHEDFEAMKEItfewd 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1229772171 583 -----DKPVNKCSLVWQGSVAKSSFNKFFIQECMTEAAARKIFADAGVGHYWDLA 632
Cdd:pfam06544  81 ndednEGEDNKCELVWEGEVKERAFRKWKFKVCETEGEAREFLKKHGVEHYWDLA 135
 
Name Accession Description Interval E-value
PRP3 pfam08572
pre-mRNA processing factor 3 (PRP3); Pre-mRNA processing factor 3 (PRP3) is a U4/U6-associated ...
 255-484 2.03e-67

pre-mRNA processing factor 3 (PRP3); Pre-mRNA processing factor 3 (PRP3) is a U4/U6-associated splicing factor. The human PRP3 has been implicated in autosomal retinitis pigmentosa.


Pssm-ID: 462524  Cd Length: 219  Bit Score: 219.39  E-value: 2.03e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1229772171 255 NPHFDERMGInktKLLRPKRMNFQFVEEGKWSKEAETIKLRSKFGEAQAKERREKQAQ-LAKAKAAPDINPNLIEVserv 333
Cdd:pfam08572   1 NPYFDPRLSA---KPKRRKRRSLKFNEKGKYIKQAERLRRKAQLEELKKRIAEEARKAgLLPDTDLAEKAPKKFKD---- 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1229772171 334 ivkektkEPIPEIEWWDVSLLHSGTYDDVGDGFVANDKIRKD--KITIYVEHPRPIEPPVEPAPPPPQPLKLTKKEQKKL 411
Cdd:pfam08572  74 -------EVPPDIEWWDEPYLPDGSYYDDLIDDKYNLDIEDEdsPITNYVQHPVPIKPPQEKNKPPPKPLYLTKKEQKKL 146

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1229772171 412 RTQRRLAKEKDRQEMIRQGLIEPPKPKVKMSNLMKVLGSEATQDPTKLEKEIRAAAAEREQAHIDRNIARKLT 484
Cdd:pfam08572 147 RRQRRKEALKEKQDKIRLGLEPPPPPKVKLSNLMRVLGNEAVQDPTKVEARVRRQMAERKQKHEEANEERKLT 219
DUF1115 pfam06544
Protein of unknown function (DUF1115); This family represents the C-terminus of hypothetical ...
 508-632 1.34e-49

Protein of unknown function (DUF1115); This family represents the C-terminus of hypothetical eukaryotic proteins of unknown function.


Pssm-ID: 461943  Cd Length: 135  Bit Score: 169.01  E-value: 1.34e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1229772171 508 SVYKIYDLSHPQARFKVDVNARENRLTGCAVICDGISVLVVEGGSKSIKRYGKLMLRRINWAASVKEEEEADESD----- 582
Cdd:pfam06544   1 AVFRIKSLSNPKHRFKIDKNAKQLGLTGFCILGPPFGLVVVEGGEKSIKKYKKLMLRRIKWTENPHEDFEAMKEItfewd 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1229772171 583 -----DKPVNKCSLVWQGSVAKSSFNKFFIQECMTEAAARKIFADAGVGHYWDLA 632
Cdd:pfam06544  81 ndednEGEDNKCELVWEGEVKERAFRKWKFKVCETEGEAREFLKKHGVEHYWDLA 135
Prp3_C cd24162
C-terminal domain of U4/U6 small nuclear ribonucleoprotein Prp3; Prp3 is an essential U4/U6 ...
 507-620 6.05e-47

C-terminal domain of U4/U6 small nuclear ribonucleoprotein Prp3; Prp3 is an essential U4/U6 di-snRNP-associated protein which plays a role in pre-mRNA splicing. It may be involved in U4/U6 reassembly after splicing. The C-terminal domain of Prp3 is a single-stranded RNA-binding domain.


Pssm-ID: 467813  Cd Length: 122  Bit Score: 161.20  E-value: 6.05e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1229772171 507 VSVYKIYDLSHPQARFKVDVNARENRLTGCAVICDGISVLVVEGGSKSIKRYGKLMLRRINWAASVKEEEEADESDD--- 583
Cdd:cd24162     3 VAVFRVKDLSNPKHRFKVDTNAQQLHLTGVCILHPDFNLVVVEGGPKSIKKYKKLMLRRIKWNEDEEPEDDDDGEEEeee 82

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1229772171 584 --KPVNKCSLVWQGSVAKSSFNKFFIQECMTEAAARKIF 620
Cdd:cd24162    83 edLSDNKCVLVWEGTVKKRAFKKFKFKVCPTEAEAREFL 121
 
Name Accession Description Interval E-value
PRP3 pfam08572
pre-mRNA processing factor 3 (PRP3); Pre-mRNA processing factor 3 (PRP3) is a U4/U6-associated ...
 255-484 2.03e-67

pre-mRNA processing factor 3 (PRP3); Pre-mRNA processing factor 3 (PRP3) is a U4/U6-associated splicing factor. The human PRP3 has been implicated in autosomal retinitis pigmentosa.


Pssm-ID: 462524  Cd Length: 219  Bit Score: 219.39  E-value: 2.03e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1229772171 255 NPHFDERMGInktKLLRPKRMNFQFVEEGKWSKEAETIKLRSKFGEAQAKERREKQAQ-LAKAKAAPDINPNLIEVserv 333
Cdd:pfam08572   1 NPYFDPRLSA---KPKRRKRRSLKFNEKGKYIKQAERLRRKAQLEELKKRIAEEARKAgLLPDTDLAEKAPKKFKD---- 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1229772171 334 ivkektkEPIPEIEWWDVSLLHSGTYDDVGDGFVANDKIRKD--KITIYVEHPRPIEPPVEPAPPPPQPLKLTKKEQKKL 411
Cdd:pfam08572  74 -------EVPPDIEWWDEPYLPDGSYYDDLIDDKYNLDIEDEdsPITNYVQHPVPIKPPQEKNKPPPKPLYLTKKEQKKL 146

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1229772171 412 RTQRRLAKEKDRQEMIRQGLIEPPKPKVKMSNLMKVLGSEATQDPTKLEKEIRAAAAEREQAHIDRNIARKLT 484
Cdd:pfam08572 147 RRQRRKEALKEKQDKIRLGLEPPPPPKVKLSNLMRVLGNEAVQDPTKVEARVRRQMAERKQKHEEANEERKLT 219
DUF1115 pfam06544
Protein of unknown function (DUF1115); This family represents the C-terminus of hypothetical ...
 508-632 1.34e-49

Protein of unknown function (DUF1115); This family represents the C-terminus of hypothetical eukaryotic proteins of unknown function.


Pssm-ID: 461943  Cd Length: 135  Bit Score: 169.01  E-value: 1.34e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1229772171 508 SVYKIYDLSHPQARFKVDVNARENRLTGCAVICDGISVLVVEGGSKSIKRYGKLMLRRINWAASVKEEEEADESD----- 582
Cdd:pfam06544   1 AVFRIKSLSNPKHRFKIDKNAKQLGLTGFCILGPPFGLVVVEGGEKSIKKYKKLMLRRIKWTENPHEDFEAMKEItfewd 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1229772171 583 -----DKPVNKCSLVWQGSVAKSSFNKFFIQECMTEAAARKIFADAGVGHYWDLA 632
Cdd:pfam06544  81 ndednEGEDNKCELVWEGEVKERAFRKWKFKVCETEGEAREFLKKHGVEHYWDLA 135
Prp3_C cd24162
C-terminal domain of U4/U6 small nuclear ribonucleoprotein Prp3; Prp3 is an essential U4/U6 ...
 507-620 6.05e-47

C-terminal domain of U4/U6 small nuclear ribonucleoprotein Prp3; Prp3 is an essential U4/U6 di-snRNP-associated protein which plays a role in pre-mRNA splicing. It may be involved in U4/U6 reassembly after splicing. The C-terminal domain of Prp3 is a single-stranded RNA-binding domain.


Pssm-ID: 467813  Cd Length: 122  Bit Score: 161.20  E-value: 6.05e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1229772171 507 VSVYKIYDLSHPQARFKVDVNARENRLTGCAVICDGISVLVVEGGSKSIKRYGKLMLRRINWAASVKEEEEADESDD--- 583
Cdd:cd24162     3 VAVFRVKDLSNPKHRFKVDTNAQQLHLTGVCILHPDFNLVVVEGGPKSIKKYKKLMLRRIKWNEDEEPEDDDDGEEEeee 82

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1229772171 584 --KPVNKCSLVWQGSVAKSSFNKFFIQECMTEAAARKIF 620
Cdd:cd24162    83 edLSDNKCVLVWEGTVKKRAFKKFKFKVCPTEAEAREFL 121
Prp3_C-like cd24140
C-terminal domain of Prp3 and related proteins; This group contains the C-terminal domains of ...
 509-613 3.01e-03

C-terminal domain of Prp3 and related proteins; This group contains the C-terminal domains of Prp3 and RWD domain-containing proteins 2/3. Predicted structures (by AlphaFold) of the C-terminal domains of RWDD2 and RWDD3 reveal similarity to the C-terminal domain of Prp3, an essential U4/U6 di-snRNP-associated protein which plays a role in pre-mRNA splicing. The Prp3 C-terminal domain is a single-stranded RNA-binding domain.


Pssm-ID: 467812  Cd Length: 117  Bit Score: 38.01  E-value: 3.01e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1229772171 509 VYKIYDLSHPQARFKVDVNARENRLTGCAVICDGISVLVVEGGSKSIKRYGKLmLRRINWAASVKEEEEADESDDKPVNK 588
Cdd:cd24140     5 VFHFKHLQNKKKRFKIKENSKELSLKGLCMRIRDPGIIIVVGNEKSCKEYENL-VKKRKWNEDFELHTNTGDIKEKCHNN 83

                          90       100
                  ....*....|....*....|....*.
gi 1229772171 589 CSLV-WQGSVAKSSFNKFFIQECMTE 613
Cdd:cd24140    84 SISKtWEGYLQDCKFKGWFLKVCNDQ 109
 
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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