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Conserved domains on  [gi|675269448|ref|NP_001288579|]
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R3H and coiled-coil domain-containing protein 1 isoform b [Homo sapiens]

Protein Classification

R3H_unknown_1 and RRM_SF domain-containing protein( domain architecture ID 10119042)

R3H_unknown_1 and RRM_SF domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
R3H_unknown_1 cd02638
R3H domain of a group of eukaryotic proteins with unknown function. The name of the R3H domain ...
 19-80 2.70e-33

R3H domain of a group of eukaryotic proteins with unknown function. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


:

Pssm-ID: 100067  Cd Length: 62  Bit Score: 118.71  E-value: 2.70e-33
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 675269448  19 VHRIQEELDRFLLQKQLSKVLLFPPLSSRLRYLIHRTAENFDLLSSFSVGEGWKRRTVICHQ 80
Cdd:cd02638    1 VHRVSEELEIFLLSFQRYRVLLFPPLNSRRRYLIHQTVENRFLLSTFSVGEGWARRTVVCYK 62
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 276-340 7.69e-12

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


The actual alignment was detected with superfamily member cd12428:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 66  Bit Score: 60.40  E-value: 7.69e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 675269448 276 HVVEIYDFEPALKTEDLLATFSEFqeKGFRIQWVDDTHALGIF--PCLASAAEALTREFSVLKIRPL 340
Cdd:cd12428    2 DHVFHLTFPKEWKTSDLYQLFSPF--GGIQVSWIDDTSAFVALsdPEQVNIALKTITYHPSYRIRSY 66
 
Name Accession Description Interval E-value
R3H_unknown_1 cd02638
R3H domain of a group of eukaryotic proteins with unknown function. The name of the R3H domain ...
 19-80 2.70e-33

R3H domain of a group of eukaryotic proteins with unknown function. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100067  Cd Length: 62  Bit Score: 118.71  E-value: 2.70e-33
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 675269448  19 VHRIQEELDRFLLQKQLSKVLLFPPLSSRLRYLIHRTAENFDLLSSFSVGEGWKRRTVICHQ 80
Cdd:cd02638    1 VHRVSEELEIFLLSFQRYRVLLFPPLNSRRRYLIHQTVENRFLLSTFSVGEGWARRTVVCYK 62
R3H smart00393
Putative single-stranded nucleic acids-binding domain;
7-80 1.95e-16

Putative single-stranded nucleic acids-binding domain;


Pssm-ID: 214647  Cd Length: 79  Bit Score: 73.49  E-value: 1.95e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 675269448     7 DGVFLSSAENDFVHRIQEELDRFLLQ-----KQLSKVLLFPPLSSRLRYLIHRTAENFDlLSSFSVGEGWKRRTVICHQ 80
Cdd:smart00393   2 DFLPVTLDALSYRPRRREELIELELEiarfvKSTKESVELPPMNSYERKIVHELAEKYG-LESESFGEGPKRRVVISKK 79
R3H pfam01424
R3H domain; The name of the R3H domain comes from the characteriztic spacing of the most ...
 17-78 4.09e-12

R3H domain; The name of the R3H domain comes from the characteriztic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to be binding ssDNA.


Pssm-ID: 460206  Cd Length: 60  Bit Score: 60.97  E-value: 4.09e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 675269448   17 DFVHRIQEELDRFLLQKQlsKVLLFPPLSSRLRYLIHRTAENFDlLSSFSVGEGWKRRTVIC 78
Cdd:pfam01424   1 EFLEQLAEKLAEFVKDTG--KSLELPPMSSYERRIIHELAQKYG-LESESEGEEPNRRVVVY 59
RRM_PARN cd12428
RNA recognition motif (RRM) found in poly(A)-specific ribonuclease PARN and similar proteins; ...
 276-340 7.69e-12

RNA recognition motif (RRM) found in poly(A)-specific ribonuclease PARN and similar proteins; The subfamily corresponds to the RRM of PARN, also termed deadenylating nuclease, or deadenylation nuclease, or polyadenylate-specific ribonuclease, a processive poly(A)-specific 3'-exoribonuclease involved in the decay of eukaryotic mRNAs. It specifically binds both, the poly(A) tail at the 3' end and the 7-methylguanosine (m7G) cap located at the 5' end of eukaryotic mRNAs, and catalyzes the 3'- to 5'-end deadenylation of single-stranded mRNA with a free 3' hydroxyl group both in the nucleus and in the cytoplasm. PARN belongs to the DEDD superfamily of exonucleases. It contains a nuclease domain, an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and an R3H domain. PARN exists as a homodimer. The nuclease domain is involved in the dimerization. RRM and R3H domains are essential for the RNA-binding.


Pssm-ID: 409862 [Multi-domain]  Cd Length: 66  Bit Score: 60.40  E-value: 7.69e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 675269448 276 HVVEIYDFEPALKTEDLLATFSEFqeKGFRIQWVDDTHALGIF--PCLASAAEALTREFSVLKIRPL 340
Cdd:cd12428    2 DHVFHLTFPKEWKTSDLYQLFSPF--GGIQVSWIDDTSAFVALsdPEQVNIALKTITYHPSYRIRSY 66
NCBP3 pfam10309
Nuclear cap-binding protein subunit 3; NCBP3 and NCBP1 form an alternative cap-binding complex ...
 287-328 8.57e-04

Nuclear cap-binding protein subunit 3; NCBP3 and NCBP1 form an alternative cap-binding complex in higher eukaryotes. NCBP3 binds mRNA, associates with components of the mRNA processing machinery and contributes to polyA RNA export.


Pssm-ID: 463048  Cd Length: 59  Bit Score: 37.13  E-value: 8.57e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 675269448  287 LKTEDLLATFSEF--QEKGFRIQWVDDTHALGIFPCLASAAEAL 328
Cdd:pfam10309  14 LSTDDIKAYASEYfnYEPPFRIEWIDDTSANLVFKSEEDALAAL 57
Jag COG1847
Predicted RNA-binding protein Jag (SpoIIIJ-associated), conains KH and R3H domains [General ...
 41-78 1.10e-03

Predicted RNA-binding protein Jag (SpoIIIJ-associated), conains KH and R3H domains [General function prediction only];


Pssm-ID: 441452 [Multi-domain]  Cd Length: 143  Bit Score: 38.94  E-value: 1.10e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 675269448  41 FPPLSSRLRYLIHRTAENFDLLSSFSVGEGWKRRTVIC 78
Cdd:COG1847  103 LEPMSPYERRIIHDALADDPGVETESEGEEPYRRVVIS 140
 
Name Accession Description Interval E-value
R3H_unknown_1 cd02638
R3H domain of a group of eukaryotic proteins with unknown function. The name of the R3H domain ...
 19-80 2.70e-33

R3H domain of a group of eukaryotic proteins with unknown function. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100067  Cd Length: 62  Bit Score: 118.71  E-value: 2.70e-33
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 675269448  19 VHRIQEELDRFLLQKQLSKVLLFPPLSSRLRYLIHRTAENFDLLSSFSVGEGWKRRTVICHQ 80
Cdd:cd02638    1 VHRVSEELEIFLLSFQRYRVLLFPPLNSRRRYLIHQTVENRFLLSTFSVGEGWARRTVVCYK 62
R3H smart00393
Putative single-stranded nucleic acids-binding domain;
7-80 1.95e-16

Putative single-stranded nucleic acids-binding domain;


Pssm-ID: 214647  Cd Length: 79  Bit Score: 73.49  E-value: 1.95e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 675269448     7 DGVFLSSAENDFVHRIQEELDRFLLQ-----KQLSKVLLFPPLSSRLRYLIHRTAENFDlLSSFSVGEGWKRRTVICHQ 80
Cdd:smart00393   2 DFLPVTLDALSYRPRRREELIELELEiarfvKSTKESVELPPMNSYERKIVHELAEKYG-LESESFGEGPKRRVVISKK 79
R3H pfam01424
R3H domain; The name of the R3H domain comes from the characteriztic spacing of the most ...
 17-78 4.09e-12

R3H domain; The name of the R3H domain comes from the characteriztic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to be binding ssDNA.


Pssm-ID: 460206  Cd Length: 60  Bit Score: 60.97  E-value: 4.09e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 675269448   17 DFVHRIQEELDRFLLQKQlsKVLLFPPLSSRLRYLIHRTAENFDlLSSFSVGEGWKRRTVIC 78
Cdd:pfam01424   1 EFLEQLAEKLAEFVKDTG--KSLELPPMSSYERRIIHELAQKYG-LESESEGEEPNRRVVVY 59
RRM_PARN cd12428
RNA recognition motif (RRM) found in poly(A)-specific ribonuclease PARN and similar proteins; ...
 276-340 7.69e-12

RNA recognition motif (RRM) found in poly(A)-specific ribonuclease PARN and similar proteins; The subfamily corresponds to the RRM of PARN, also termed deadenylating nuclease, or deadenylation nuclease, or polyadenylate-specific ribonuclease, a processive poly(A)-specific 3'-exoribonuclease involved in the decay of eukaryotic mRNAs. It specifically binds both, the poly(A) tail at the 3' end and the 7-methylguanosine (m7G) cap located at the 5' end of eukaryotic mRNAs, and catalyzes the 3'- to 5'-end deadenylation of single-stranded mRNA with a free 3' hydroxyl group both in the nucleus and in the cytoplasm. PARN belongs to the DEDD superfamily of exonucleases. It contains a nuclease domain, an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and an R3H domain. PARN exists as a homodimer. The nuclease domain is involved in the dimerization. RRM and R3H domains are essential for the RNA-binding.


Pssm-ID: 409862 [Multi-domain]  Cd Length: 66  Bit Score: 60.40  E-value: 7.69e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 675269448 276 HVVEIYDFEPALKTEDLLATFSEFqeKGFRIQWVDDTHALGIF--PCLASAAEALTREFSVLKIRPL 340
Cdd:cd12428    2 DHVFHLTFPKEWKTSDLYQLFSPF--GGIQVSWIDDTSAFVALsdPEQVNIALKTITYHPSYRIRSY 66
R3H cd02325
R3H domain. The name of the R3H domain comes from the characteristic spacing of the most ...
 19-78 2.43e-11

R3H domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. R3H domains are found in proteins together with ATPase domains, SF1 helicase domains, SF2 DEAH helicase domains, Cys-rich repeats, ring-type zinc fingers, and KH domains. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100064  Cd Length: 59  Bit Score: 58.39  E-value: 2.43e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 675269448  19 VHRIQEELDRFLLQKQlSKVLLFPPLSSRLRYLIHRTAENFDlLSSFSVGEGWKRRTVIC 78
Cdd:cd02325    1 REEREEELEAFAKDAA-GKSLELPPMNSYERKLIHDLAEYYG-LKSESEGEGPNRRVVIT 58
R3H_jag cd02644
R3H domain found in proteins homologous to Bacillus subtilus Jag, which is associated with ...
 37-78 1.30e-04

R3H domain found in proteins homologous to Bacillus subtilus Jag, which is associated with SpoIIIJ. SpoIIIJ is necessary for the third stage of sporulation. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100073  Cd Length: 67  Bit Score: 39.76  E-value: 1.30e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 675269448  37 KVLLFPPLSSRLRYLIHRTAENFDLLSSFSVGEGWKRRTVIC 78
Cdd:cd02644   24 KPVKLEPMNAYERRIIHDALANDEDVETESEGEGPYRRVVIS 65
R3H_G-patch cd02646
R3H domain of a group of fungal and plant proteins with unknown function, who also contain a ...
 22-77 5.54e-04

R3H domain of a group of fungal and plant proteins with unknown function, who also contain a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the R3H domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100075  Cd Length: 58  Bit Score: 37.94  E-value: 5.54e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 675269448  22 IQEELDRFLLQKqlSKVLLFPPLSSRLRYLIHRTAENFDLLSSfSVGEGWKRRTVI 77
Cdd:cd02646    4 IKDEIEAFLLDS--RDSLSFPPMDKHGRKTIHKLANCYNLKSK-SRGKGKKRFVTV 56
NCBP3 pfam10309
Nuclear cap-binding protein subunit 3; NCBP3 and NCBP1 form an alternative cap-binding complex ...
 287-328 8.57e-04

Nuclear cap-binding protein subunit 3; NCBP3 and NCBP1 form an alternative cap-binding complex in higher eukaryotes. NCBP3 binds mRNA, associates with components of the mRNA processing machinery and contributes to polyA RNA export.


Pssm-ID: 463048  Cd Length: 59  Bit Score: 37.13  E-value: 8.57e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 675269448  287 LKTEDLLATFSEF--QEKGFRIQWVDDTHALGIFPCLASAAEAL 328
Cdd:pfam10309  14 LSTDDIKAYASEYfnYEPPFRIEWIDDTSANLVFKSEEDALAAL 57
Jag COG1847
Predicted RNA-binding protein Jag (SpoIIIJ-associated), conains KH and R3H domains [General ...
 41-78 1.10e-03

Predicted RNA-binding protein Jag (SpoIIIJ-associated), conains KH and R3H domains [General function prediction only];


Pssm-ID: 441452 [Multi-domain]  Cd Length: 143  Bit Score: 38.94  E-value: 1.10e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 675269448  41 FPPLSSRLRYLIHRTAENFDLLSSFSVGEGWKRRTVIC 78
Cdd:COG1847  103 LEPMSPYERRIIHDALADDPGVETESEGEEPYRRVVIS 140
R3H_encore_like cd02642
R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the ...
 18-61 7.61e-03

R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H domain is a potential regulator of DBF1 activity in stress responses. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.


Pssm-ID: 100071  Cd Length: 63  Bit Score: 34.89  E-value: 7.61e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 675269448  18 FVHRIQEELDRFLlQKQLSKVLLFPPLSSRLRYLIHRTAENFDL 61
Cdd:cd02642    4 FVLKLEKDLLAFI-KDSTRQSLELPPMNSYYRLLAHRVAQYYGL 46
 
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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