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Conserved domains on  [gi|1958750351|ref|XP_038958135|]
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ribonuclease 3 isoform X1 [Rattus norvegicus]

Protein Classification

DICER-like protein; ribonuclease III domain-containing protein( domain architecture ID 11535647)

DICER-like (DCL) protein of the RNASE III family; ribonuclease III domain-containing protein similar to Arabidopsis thaliana RNC1 that binds specific group II introns in chloroplasts and facilitates their splicing

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1104-1332 9.63e-64

dsRNA-specific ribonuclease [Transcription];


:

Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 216.50  E-value: 9.63e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351 1104 QKLTEFEEAIGVIFTHVRLLARAFTLRTVGFNHLTLGHNQRMEFLGDSIMQLVATEYLFIHFPDHHEGHLTLLRSSLVNN 1183
Cdd:COG0571      2 EDLEELEERLGYRFKDPELLEQALTHRSYANEHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSE 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351 1184 RTQAKVAEELGMQEY------AITNDKTKRPvalrtKTLADLLESFIAALYIDKDLEYVHTFMNVCFFPRLKEFILNQDW 1257
Cdd:COG0571     82 ETLAEIARELGLGDYlrlgkgEEKSGGRRRP-----SILADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPGGAG 156

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958750351 1258 NDPKSQLQQCcltLRTEGKEPdiPLYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEKYN 1332
Cdd:COG0571    157 KDYKTALQEW---LQARGLPL--PEYEVVEEEGPDHAKTFTVEVLVGGKVLGEGTGRSKKEAEQAAAKAALEKLG 226
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 958-1078 1.80e-40

RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing.


:

Pssm-ID: 238333  Cd Length: 133  Bit Score: 145.83  E-value: 1.80e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351  958 PSRINHNERLEFLGDAVVEFLTSVHLYYLFPSLEEGGLATYRTAIVQNQHLAMLAKKLELDRFMLYAHGPDLCRESDLRH 1037
Cdd:cd00593     15 EHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLGKGEEKSGGRLRPK 94

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1958750351 1038 AMANCFEALIGAVYLEGTLEEAKQLFGRLLFndPDLREVWL 1078
Cdd:cd00593     95 ILADVFEALIGAIYLDGGFEAARKFLLRLLG--PLIEEISL 133
SF-CC1 super family cl36939
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 212-274 8.86e-04

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


The actual alignment was detected with superfamily member TIGR01622:

Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 43.37  E-value: 8.86e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958750351  212 KAQSERRSPERLKHYDDHRHRDHSHGRGERHRSLERRERGRS----PERRRPESRYRSEYDR--GRTPP 274
Cdd:TIGR01622   29 RSRDRSRDRERSRSRRRDRHRDRDYYRGRERRSRSRRPNRRYrpreKRRRRGDSYRRRRDDRrsRREKP 97
 
Name Accession Description Interval E-value
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1104-1332 9.63e-64

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 216.50  E-value: 9.63e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351 1104 QKLTEFEEAIGVIFTHVRLLARAFTLRTVGFNHLTLGHNQRMEFLGDSIMQLVATEYLFIHFPDHHEGHLTLLRSSLVNN 1183
Cdd:COG0571      2 EDLEELEERLGYRFKDPELLEQALTHRSYANEHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSE 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351 1184 RTQAKVAEELGMQEY------AITNDKTKRPvalrtKTLADLLESFIAALYIDKDLEYVHTFMNVCFFPRLKEFILNQDW 1257
Cdd:COG0571     82 ETLAEIARELGLGDYlrlgkgEEKSGGRRRP-----SILADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPGGAG 156

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958750351 1258 NDPKSQLQQCcltLRTEGKEPdiPLYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEKYN 1332
Cdd:COG0571    157 KDYKTALQEW---LQARGLPL--PEYEVVEEEGPDHAKTFTVEVLVGGKVLGEGTGRSKKEAEQAAAKAALEKLG 226
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1109-1330 1.63e-54

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing]


Pssm-ID: 274024 [Multi-domain]  Cd Length: 220  Bit Score: 189.72  E-value: 1.63e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351 1109 FEEAIGVIFTHVRLLARAFTLRTVG-FNHLTLGHNQRMEFLGDSIMQLVATEYLFIHFPDHHEGHLTLLRSSLVNNRTQA 1187
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRSYAnEHHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351 1188 KVAEELGMQEY-AITNDKTKRPVALRTKTLADLLESFIAALYIDKDLEYVHTFMNVCFFPRLKEFILNQDWNDPKSQLQQ 1266
Cdd:TIGR02191   81 EVARELGLGDFlLLGKGEEKSGGRRRDSILADAFEALIGAIYLDSGLEAARKFILKLLIPRIDAIIKEETLKDYKTALQE 160

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958750351 1267 ccLTLRtEGKEPdiPLYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEK 1330
Cdd:TIGR02191  161 --WAQA-RGKPL--PEYRLIKEEGPDHDKEFTVEVSVNGEPYGEGKGKSKKEAEQNAAKAALEK 219
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1121-1253 1.46e-45

RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing.


Pssm-ID: 238333  Cd Length: 133  Bit Score: 160.47  E-value: 1.46e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351 1121 RLLARAFTLRTVGFNHLTLgHNQRMEFLGDSIMQLVATEYLFIHFPDHHEGHLTLLRSSLVNNRTQAKVAEELGMQEYAI 1200
Cdd:cd00593      1 SLLLEALTHPSYANEHGRF-NNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLR 79

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1958750351 1201 TNDK-TKRPVALRTKTLADLLESFIAALYIDKDLEYVHTFMNVCFFPRLKEFIL 1253
Cdd:cd00593     80 LGKGeEKSGGRLRPKILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIEEISL 133
RIBOc smart00535
Ribonuclease III family;
1121-1251 1.84e-43

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 154.30  E-value: 1.84e-43
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351  1121 RLLARAFTLRTVGFNHltlGHNQRMEFLGDSIMQLVATEYLFIHFPDHHEGHLTLLRSSLVNNRTQAKVAEELGMQEY-A 1199
Cdd:smart00535    1 SLLLRALTHASYSNEH---EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFiR 77

                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|..
gi 1958750351  1200 ITNDKTKRPVALRTKTLADLLESFIAALYIDKDLEYVHTFMNVCFFPRLKEF 1251
Cdd:smart00535   78 LGRGEAISGGRDKPKILADVFEALIGAIYLDSGLEAAREFIRDLLGPRLDEL 129
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 958-1078 1.80e-40

RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing.


Pssm-ID: 238333  Cd Length: 133  Bit Score: 145.83  E-value: 1.80e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351  958 PSRINHNERLEFLGDAVVEFLTSVHLYYLFPSLEEGGLATYRTAIVQNQHLAMLAKKLELDRFMLYAHGPDLCRESDLRH 1037
Cdd:cd00593     15 EHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLGKGEEKSGGRLRPK 94

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1958750351 1038 AMANCFEALIGAVYLEGTLEEAKQLFGRLLFndPDLREVWL 1078
Cdd:cd00593     95 ILADVFEALIGAIYLDGGFEAARKFLLRLLG--PLIEEISL 133
RIBOc smart00535
Ribonuclease III family;
942-1074 5.13e-39

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 141.59  E-value: 5.13e-39
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351   942 NTLINIMSRLGQDDPTPsrinHNERLEFLGDAVVEFLTSVHLYYLFPSLEEGGLATYRTAIVQNQHLAMLAKKLELDRFM 1021
Cdd:smart00535    1 SLLLRALTHASYSNEHE----HNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFI 76

                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|...
gi 1958750351  1022 LYAHGPDLCRESDLRHAMANCFEALIGAVYLEGTLEEAKQLFGRLLFNDPDLR 1074
Cdd:smart00535   77 RLGRGEAISGGRDKPKILADVFEALIGAIYLDSGLEAAREFIRDLLGPRLDEL 129
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 878-1089 3.44e-30

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing]


Pssm-ID: 274024 [Multi-domain]  Cd Length: 220  Bit Score: 119.62  E-value: 3.44e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351  878 LDKLIGYTFQDRCLLQLAMTHPSHHlnfgmnpdharnslsncgirqpkygdrKVHHmhmrkkgintlinimsrlgqddpt 957
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRSYA---------------------------NEHH------------------------ 29

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351  958 pSRINHNERLEFLGDAVVEFLTSVHLYYLFPSLEEGGLATYRTAIVQNQHLAMLAKKLELDRFMLYAHGPDLCRESDLRH 1037
Cdd:TIGR02191   30 -KDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAEVARELGLGDFLLLGKGEEKSGGRRRDS 108

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1958750351 1038 AMANCFEALIGAVYLEGTLEEAKQLFGRLLFndPDLREVWLNYPLHPL--QLQE 1089
Cdd:TIGR02191  109 ILADAFEALIGAIYLDSGLEAARKFILKLLI--PRIDAIIKEETLKDYktALQE 160
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 960-1070 8.71e-30

Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA processing. They probably also cleave a stem-loop structure at the 3' end of U2 snRNA to ensure formation of the correct U2 3' end; they are involved in polyadenylation-independent transcription termination. Some members may be mitochondrial ribosomal protein subunit L15, others may be 60S ribosomal protein L3.


Pssm-ID: 434075  Cd Length: 127  Bit Score: 114.96  E-value: 8.71e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351  960 RINHNERLEFLGDAVVEFLTSVHLYYlFPSLEEGGLATYRTAIVQNQHLAMLAKKLELDRFMLYAHGPDLCRESDLRHAM 1039
Cdd:pfam14622   17 RKPYNERLEFLGDAVLELSVSEYLFK-KPDLDEGGLTKLRASIVSEESLAEIAREIGLGKYLRLGKGEEETGGSGRESIL 95

                           90       100       110
                   ....*....|....*....|....*....|.
gi 1958750351 1040 ANCFEALIGAVYLEGTLEEAKQLFGRLLFND 1070
Cdd:pfam14622   96 ADALEALIGAIYLDGGFEVAKEFILKKILPD 126
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1143-1232 5.16e-26

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 103.51  E-value: 5.16e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351 1143 QRMEFLGDSIMQLVATEYLFIHFPDHHEGHLTLLRSSLVNNRTQAKVAEELGMQEYAITNDKTKRPVAL----------- 1211
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDIRRRNNalgkgpkradg 80

                           90       100
                   ....*....|....*....|.
gi 1958750351 1212 RTKTLADLLESFIAALYIDKD 1232
Cdd:pfam00636   81 KEKVLADAFEALIGALYLDGG 101
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 212-274 8.86e-04

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 43.37  E-value: 8.86e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958750351  212 KAQSERRSPERLKHYDDHRHRDHSHGRGERHRSLERRERGRS----PERRRPESRYRSEYDR--GRTPP 274
Cdd:TIGR01622   29 RSRDRSRDRERSRSRRRDRHRDRDYYRGRERRSRSRRPNRRYrpreKRRRRGDSYRRRRDDRrsRREKP 97
PRP38_assoc pfam12871
Pre-mRNA-splicing factor 38-associated hydrophilic C-term; This domain is a hydrophilic region ...
 211-272 2.37e-03

Pre-mRNA-splicing factor 38-associated hydrophilic C-term; This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins. The function is not known.


Pssm-ID: 463734 [Multi-domain]  Cd Length: 98  Bit Score: 38.60  E-value: 2.37e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958750351  211 PKAQSERRSPERLKHYDDHRHRDHSHgrgERHRSLERRERG-RSPERRRPESRYRSEYDRGRT 272
Cdd:pfam12871   29 ERASLSRKRRSRSRRRSSTRDRSRSR---SRSRSRDRRSRGtRDRRRDRDRDRYRSLRSRSRD 88
 
Name Accession Description Interval E-value
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1104-1332 9.63e-64

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 216.50  E-value: 9.63e-64
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351 1104 QKLTEFEEAIGVIFTHVRLLARAFTLRTVGFNHLTLGHNQRMEFLGDSIMQLVATEYLFIHFPDHHEGHLTLLRSSLVNN 1183
Cdd:COG0571      2 EDLEELEERLGYRFKDPELLEQALTHRSYANEHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSE 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351 1184 RTQAKVAEELGMQEY------AITNDKTKRPvalrtKTLADLLESFIAALYIDKDLEYVHTFMNVCFFPRLKEFILNQDW 1257
Cdd:COG0571     82 ETLAEIARELGLGDYlrlgkgEEKSGGRRRP-----SILADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPGGAG 156

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958750351 1258 NDPKSQLQQCcltLRTEGKEPdiPLYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEKYN 1332
Cdd:COG0571    157 KDYKTALQEW---LQARGLPL--PEYEVVEEEGPDHAKTFTVEVLVGGKVLGEGTGRSKKEAEQAAAKAALEKLG 226
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1109-1330 1.63e-54

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing]


Pssm-ID: 274024 [Multi-domain]  Cd Length: 220  Bit Score: 189.72  E-value: 1.63e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351 1109 FEEAIGVIFTHVRLLARAFTLRTVG-FNHLTLGHNQRMEFLGDSIMQLVATEYLFIHFPDHHEGHLTLLRSSLVNNRTQA 1187
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRSYAnEHHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLA 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351 1188 KVAEELGMQEY-AITNDKTKRPVALRTKTLADLLESFIAALYIDKDLEYVHTFMNVCFFPRLKEFILNQDWNDPKSQLQQ 1266
Cdd:TIGR02191   81 EVARELGLGDFlLLGKGEEKSGGRRRDSILADAFEALIGAIYLDSGLEAARKFILKLLIPRIDAIIKEETLKDYKTALQE 160

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958750351 1267 ccLTLRtEGKEPdiPLYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEK 1330
Cdd:TIGR02191  161 --WAQA-RGKPL--PEYRLIKEEGPDHDKEFTVEVSVNGEPYGEGKGKSKKEAEQNAAKAALEK 219
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 1121-1253 1.46e-45

RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing.


Pssm-ID: 238333  Cd Length: 133  Bit Score: 160.47  E-value: 1.46e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351 1121 RLLARAFTLRTVGFNHLTLgHNQRMEFLGDSIMQLVATEYLFIHFPDHHEGHLTLLRSSLVNNRTQAKVAEELGMQEYAI 1200
Cdd:cd00593      1 SLLLEALTHPSYANEHGRF-NNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLR 79

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1958750351 1201 TNDK-TKRPVALRTKTLADLLESFIAALYIDKDLEYVHTFMNVCFFPRLKEFIL 1253
Cdd:cd00593     80 LGKGeEKSGGRLRPKILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIEEISL 133
RIBOc smart00535
Ribonuclease III family;
1121-1251 1.84e-43

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 154.30  E-value: 1.84e-43
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351  1121 RLLARAFTLRTVGFNHltlGHNQRMEFLGDSIMQLVATEYLFIHFPDHHEGHLTLLRSSLVNNRTQAKVAEELGMQEY-A 1199
Cdd:smart00535    1 SLLLRALTHASYSNEH---EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFiR 77

                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|..
gi 1958750351  1200 ITNDKTKRPVALRTKTLADLLESFIAALYIDKDLEYVHTFMNVCFFPRLKEF 1251
Cdd:smart00535   78 LGRGEAISGGRDKPKILADVFEALIGAIYLDSGLEAAREFIRDLLGPRLDEL 129
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 958-1078 1.80e-40

RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing.


Pssm-ID: 238333  Cd Length: 133  Bit Score: 145.83  E-value: 1.80e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351  958 PSRINHNERLEFLGDAVVEFLTSVHLYYLFPSLEEGGLATYRTAIVQNQHLAMLAKKLELDRFMLYAHGPDLCRESDLRH 1037
Cdd:cd00593     15 EHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLGKGEEKSGGRLRPK 94

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1958750351 1038 AMANCFEALIGAVYLEGTLEEAKQLFGRLLFndPDLREVWL 1078
Cdd:cd00593     95 ILADVFEALIGAIYLDGGFEAARKFLLRLLG--PLIEEISL 133
DSRM_RNAse_III_meta_like cd19877
double-stranded RNA binding motif of metazoan ribonuclease III (RNase III) and similar ...
 1258-1331 2.73e-40

double-stranded RNA binding motif of metazoan ribonuclease III (RNase III) and similar proteins; RNase III (EC 3.1.26.3; also known as Drosha, or ribonuclease 3) is a double-stranded RNA (dsRNA)-specific endoribonuclease that is involved in the initial step of microRNA (miRNA) biogenesis. It is a component of the microprocessor complex that is required to process primary miRNA transcripts (pri-miRNAs) to release precursor miRNA (pre-miRNA) in the nucleus. Within the microprocessor complex, RNase III cleaves the 3' and 5' strands of a stem-loop in pri-miRNAs (processing center 11 bp from the dsRNA-ssRNA junction) to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. It is also involved in pre-rRNA processing. Metazoan RNase III is a larger protein than bacterial RNase III. It contains two RNase III domains in the C-terminal half of the protein followed by a double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380706  Cd Length: 75  Bit Score: 143.18  E-value: 2.73e-40
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958750351 1258 NDPKSQLQQCCLTLRTEG-KEPDIPLYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEKY 1331
Cdd:cd19877      1 NDPKSQLQQCCLTLRTEGkKEPDIPEYKVLQKSGPTNTRVYTVAVYFRGERIATGTGSSIQQAEMNAAEKALEKL 75
RIBOc smart00535
Ribonuclease III family;
942-1074 5.13e-39

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 141.59  E-value: 5.13e-39
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351   942 NTLINIMSRLGQDDPTPsrinHNERLEFLGDAVVEFLTSVHLYYLFPSLEEGGLATYRTAIVQNQHLAMLAKKLELDRFM 1021
Cdd:smart00535    1 SLLLRALTHASYSNEHE----HNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFI 76

                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|...
gi 1958750351  1022 LYAHGPDLCRESDLRHAMANCFEALIGAVYLEGTLEEAKQLFGRLLFNDPDLR 1074
Cdd:smart00535   77 RLGRGEAISGGRDKPKILADVFEALIGAIYLDSGLEAAREFIRDLLGPRLDEL 129
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 878-1089 3.44e-30

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing]


Pssm-ID: 274024 [Multi-domain]  Cd Length: 220  Bit Score: 119.62  E-value: 3.44e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351  878 LDKLIGYTFQDRCLLQLAMTHPSHHlnfgmnpdharnslsncgirqpkygdrKVHHmhmrkkgintlinimsrlgqddpt 957
Cdd:TIGR02191    1 LEKRLGYKFKNPELLEQALTHRSYA---------------------------NEHH------------------------ 29

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351  958 pSRINHNERLEFLGDAVVEFLTSVHLYYLFPSLEEGGLATYRTAIVQNQHLAMLAKKLELDRFMLYAHGPDLCRESDLRH 1037
Cdd:TIGR02191   30 -KDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAEVARELGLGDFLLLGKGEEKSGGRRRDS 108

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1958750351 1038 AMANCFEALIGAVYLEGTLEEAKQLFGRLLFndPDLREVWLNYPLHPL--QLQE 1089
Cdd:TIGR02191  109 ILADAFEALIGAIYLDSGLEAARKFILKLLI--PRIDAIIKEETLKDYktALQE 160
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 960-1070 8.71e-30

Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA processing. They probably also cleave a stem-loop structure at the 3' end of U2 snRNA to ensure formation of the correct U2 3' end; they are involved in polyadenylation-independent transcription termination. Some members may be mitochondrial ribosomal protein subunit L15, others may be 60S ribosomal protein L3.


Pssm-ID: 434075  Cd Length: 127  Bit Score: 114.96  E-value: 8.71e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351  960 RINHNERLEFLGDAVVEFLTSVHLYYlFPSLEEGGLATYRTAIVQNQHLAMLAKKLELDRFMLYAHGPDLCRESDLRHAM 1039
Cdd:pfam14622   17 RKPYNERLEFLGDAVLELSVSEYLFK-KPDLDEGGLTKLRASIVSEESLAEIAREIGLGKYLRLGKGEEETGGSGRESIL 95

                           90       100       110
                   ....*....|....*....|....*....|.
gi 1958750351 1040 ANCFEALIGAVYLEGTLEEAKQLFGRLLFND 1070
Cdd:pfam14622   96 ADALEALIGAIYLDGGFEVAKEFILKKILPD 126
Ribonuclease_3 pfam00636
Ribonuclease III domain;
1143-1232 5.16e-26

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 103.51  E-value: 5.16e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351 1143 QRMEFLGDSIMQLVATEYLFIHFPDHHEGHLTLLRSSLVNNRTQAKVAEELGMQEYAITNDKTKRPVAL----------- 1211
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDIRRRNNalgkgpkradg 80

                           90       100
                   ....*....|....*....|.
gi 1958750351 1212 RTKTLADLLESFIAALYIDKD 1232
Cdd:pfam00636   81 KEKVLADAFEALIGALYLDGG 101
Ribonuclease_3 pfam00636
Ribonuclease III domain;
965-1054 2.59e-23

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 95.80  E-value: 2.59e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351  965 ERLEFLGDAVVEFLTSVHLYYLFPSLEEGGLATYRTAIVQNQHLAMLAKKLELDRFMLYAHGPDLCRESDLRHA------ 1038
Cdd:pfam00636    1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDIRRRNNALGKGpkradg 80

                           90       100
                   ....*....|....*....|
gi 1958750351 1039 ----MANCFEALIGAVYLEG 1054
Cdd:pfam00636   81 kekvLADAFEALIGALYLDG 100
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 1122-1248 1.52e-20

Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA processing. They probably also cleave a stem-loop structure at the 3' end of U2 snRNA to ensure formation of the correct U2 3' end; they are involved in polyadenylation-independent transcription termination. Some members may be mitochondrial ribosomal protein subunit L15, others may be 60S ribosomal protein L3.


Pssm-ID: 434075  Cd Length: 127  Bit Score: 88.77  E-value: 1.52e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958750351 1122 LLARAFTLRTvgFNHLTLGHNQRMEFLGDSIMQLVATEYLFiHFPDHHEGHLTLLRSSLVNNRTQAKVAEELGMQEYAIT 1201
Cdd:pfam14622    3 LLLQALTHKS--YANGRKPYNERLEFLGDAVLELSVSEYLF-KKPDLDEGGLTKLRASIVSEESLAEIAREIGLGKYLRL 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 1958750351 1202 NDKTKRPVAL-RTKTLADLLESFIAALYIDKDLEYVHTFMNVCFFPRL 1248
Cdd:pfam14622   80 GKGEEETGGSgRESILADALEALIGAIYLDGGFEVAKEFILKKILPDL 127
DSRM smart00358
Double-stranded RNA binding motif;
1260-1331 3.36e-18

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 80.00  E-value: 3.36e-18
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958750351  1260 PKSQLQQCCltlRTEGKEPDiplYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEKY 1331
Cdd:smart00358    1 PKSLLQELA---QKRKLPPE---YELVKEEGPDHAPRFTVTVKVGGKRTGEGEGSSKKEAKQRAAEAALRSL 66
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 1259-1330 4.04e-18

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: 79.84  E-value: 4.04e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958750351 1259 DPKSQLQQCCltlrtEGKEPDIPLYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEK 1330
Cdd:cd10845      2 DYKTALQEYL-----QKRGLPLPEYELVEEEGPDHNKTFTVEVKVNGKVIGEGTGRSKKEAEQAAAKAALEK 68
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 1260-1331 3.39e-15

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: 71.49  E-value: 3.39e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958750351 1260 PKSQLQQCCLTLRTEgkepdiPLYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEKY 1331
Cdd:pfam00035    1 PKSLLQEYAQKNGKP------PPYEYVSEEGPPHSPKFTVTVKVDGKLYGSGTGSSKKEAEQLAAEKALEKL 66
DSRM_MRPL3_like cd19873
double-stranded RNA binding motif of Saccharomyces cerevisiae mitochondrial 54S ribosomal ...
 1258-1331 3.21e-09

double-stranded RNA binding motif of Saccharomyces cerevisiae mitochondrial 54S ribosomal protein L3 (MRPL3) and similar proteins; MRPL3 (also called mitochondrial large ribosomal subunit protein mL44) is a component of the mitochondrial ribosome (mitoribosome), a dedicated translation machinery responsible for the synthesis of mitochondrial genome-encoded proteins, including at least some of the essential transmembrane subunits of the mitochondrial respiratory chain. MRPL3 contains a RNase III-like domain and a double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380702  Cd Length: 84  Bit Score: 54.92  E-value: 3.21e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958750351 1258 NDPKSQLQQCCltlRTEGKEPdiPLYKTLQTVG-PSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEKY 1331
Cdd:cd19873     12 ENPKRTLSALL---KREGLEP--PVSRLLKESGrASHTPTFVVGVYSGSQKLGEGAGSSIKMAEIRAARDALRKH 81
DSRM_RNT1p-like cd19876
double-stranded RNA binding motif of Saccharomyces cerevisiae ribonuclease 3 (RNT1p) and ...
 1275-1330 2.22e-05

double-stranded RNA binding motif of Saccharomyces cerevisiae ribonuclease 3 (RNT1p) and similar proteins; RNT1p (EC 3.1.26.3; also known as ribonuclease III (RNase III)) is a dsRNA-specific nuclease that cleaves eukaryotic pre-ribosomal RNA at the U3 snoRNP-dependent A0 site in the 5'-external transcribed spacer (ETS) and in the 3'-ETS. RNT1p contains 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: 380705  Cd Length: 69  Bit Score: 43.48  E-value: 2.22e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958750351 1275 GKEPDIPLYKTLQTVGPsHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEK 1330
Cdd:cd19876     13 GPASLKPEYVVVKKEGG-NDPNYTVACRINGEVLGTGVGRSIKKAGQRAAMSALSN 67
DSRM_STRBP_RED-like_rpt1 cd19865
first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 1283-1329 5.44e-04

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: 39.64  E-value: 5.44e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1958750351 1283 YKTLQTVGPSHARTYTVAVYFKGeRIGCGKGPSIQQAEMGAAMDALE 1329
Cdd:cd19865     16 YKLTSQTGPVHAPVFTMSVEVNG-QTFEGTGRSKKKAKLEAAEKALR 61
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 212-274 8.86e-04

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 43.37  E-value: 8.86e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958750351  212 KAQSERRSPERLKHYDDHRHRDHSHGRGERHRSLERRERGRS----PERRRPESRYRSEYDR--GRTPP 274
Cdd:TIGR01622   29 RSRDRSRDRERSRSRRRDRHRDRDYYRGRERRSRSRRPNRRYrpreKRRRRGDSYRRRRDDRrsRREKP 97
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 1281-1328 2.28e-03

double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 amino acid domain that adopts an alpha-beta-beta-beta-alpha fold. It is not sequence specific, but highly specific for double-stranded RNAs (dsRNAs) of various origin and structure. The DSRM domains are found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila Staufen protein, E. coli RNase III, RNase H1, and dsRNA dependent adenosine deaminases. They are involved in numerous cellular mechanisms ranging from localization and transport of messenger RNAs, through maturation and degradation of RNAs, to viral response and signal transduction. Some members harbor tandem DSRMs that act in small RNA biogenesis.


Pssm-ID: 380679 [Multi-domain]  Cd Length: 57  Bit Score: 37.65  E-value: 2.28e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1958750351 1281 PLYKTLQtVGPSHARTYTVAVYFKGERiGCGKGPSIQQAEMGAAMDAL 1328
Cdd:cd00048     12 PEYETVE-EGGPHNPRFTCTVTVNGQT-FEGEGKSKKEAKQAAAEKAL 57
PRP38_assoc pfam12871
Pre-mRNA-splicing factor 38-associated hydrophilic C-term; This domain is a hydrophilic region ...
 211-272 2.37e-03

Pre-mRNA-splicing factor 38-associated hydrophilic C-term; This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins. The function is not known.


Pssm-ID: 463734 [Multi-domain]  Cd Length: 98  Bit Score: 38.60  E-value: 2.37e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958750351  211 PKAQSERRSPERLKHYDDHRHRDHSHgrgERHRSLERRERG-RSPERRRPESRYRSEYDRGRT 272
Cdd:pfam12871   29 ERASLSRKRRSRSRRRSSTRDRSRSR---SRSRSRDRRSRGtRDRRRDRDRDRYRSLRSRSRD 88
DSRM_EIF2AK2_rpt1 cd19903
first double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha ...
 1283-1329 2.96e-03

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: 2.96e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1958750351 1283 YKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALE 1329
Cdd:cd19903     20 YVEVPTSGPSHDPRFTFQVVIDGKEYPEGEGKSKKEAKQAAAKLALE 66
DSRM_AtDRB-like_rpt2 cd19908
second double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...
 1279-1328 6.26e-03

second double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRBs)and similar proteins; This family includes a group of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRB1-5). They bind double-stranded RNA (dsRNA) and may be involved in RNA-mediated silencing. Members of this family contain two to 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: 380737 [Multi-domain]  Cd Length: 69  Bit Score: 36.69  E-value: 6.26e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1958750351 1279 DIPLYKTlQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDAL 1328
Cdd:cd19908     17 PLPLYTT-VRSGPGHVPTFTCTVEIAGITFTGEAAKTKKQAEKSAARTAW 65
seadorna_dsRNA TIGR04238
seadornavirus double-stranded RNA-binding protein; This protein family occurs in the ...
 1259-1330 6.84e-03

seadornavirus double-stranded RNA-binding protein; This protein family occurs in the seadornavirus virus group, with an N-terminal domain for binding double-stranded RNA, is designated VP12 in Banna virus, VP8 in Kadipiro virus, and VP11 in Liao ning virus.


Pssm-ID: 275074 [Multi-domain]  Cd Length: 201  Bit Score: 39.54  E-value: 6.84e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958750351 1259 DPKSQLQQCCLTLRTEgkepdIPLYKTLQTVGPSHARTYTVAVYFKGERIGCgKGPSIQQAEMGAAMDALEK 1330
Cdd:TIGR04238    1 NVVGMLQELAVKRGLE-----LPVYEKVGKEGPDHAPTFTIKLTANDIEVIE-AASSKKQAEKLAAATIYED 66
Transformer pfam06495
Fruit fly transformer protein; This family consists of transformer proteins from several ...
 199-262 7.05e-03

Fruit fly transformer protein; This family consists of transformer proteins from several Drosophila species and also from Ceratitis capitata (Mediterranean fruit fly). The transformer locus (tra) produces an RNA processing protein that alternatively splices the doublesex pre-mRNA in the sex determination hierarchy of Drosophila melanogaster.


Pssm-ID: 253769 [Multi-domain]  Cd Length: 182  Bit Score: 39.25  E-value: 7.05e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958750351  199 TPHFRHLPPYSLPKAQSERRSPERLKHYDDHRHRDHSHGRGERHRSLERRERGRSPERRRPESR 262
Cdd:pfam06495   50 TTSHRGRRTRSRSRSQSAERNSCQRRHRSRSRSRNRSDSRHRSTSSTERRRRSRSRSRYSRTPR 113
 
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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