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Conserved domains on  [gi|33585614|gb|AAH55696|]
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Rnasen protein, partial [Mus musculus]

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];
511-739 5.48e-64

dsRNA-specific ribonuclease [Transcription];


:

Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 213.42  E-value: 5.48e-64
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614 511 QKLTEFEEAIGVIFTHVRLLARAFTLRTVGFNHLTLGHNQRMEFLGDSIMQLVATEYLFIHFPDHHEGHLTLLRSSLVNN 590
Cdd:COG0571   2 EDLEELEERLGYRFKDPELLEQALTHRSYANEHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSE 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614 591 RTQAKVAEELGMQEY------AITNDKTKRPvalrtKTLADLLESFIAALYIDKDLEYVHTFMNVCFFPRLKEFILNQDW 664
Cdd:COG0571  82 ETLAEIARELGLGDYlrlgkgEEKSGGRRRP-----SILADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPGGAG 156

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 33585614 665 NDPKSQLQQCcltLRTEGKEPdiPLYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEKYN 739
Cdd:COG0571 157 KDYKTALQEW---LQARGLPL--PEYEVVEEEGPDHAKTFTVEVLVGGKVLGEGTGRSKKEAEQAAAKAALEKLG 226
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 365-479 4.46e-39

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: 141.21  E-value: 4.46e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614 365 PSRINHNERLEFLGDAVVEFLTSVHLYYLFPSLEEGGLATYRTAIVQNQHLAMLAKKLELDRFMLYAHGPDLCRESDLRH 444
Cdd:cd00593  15 EHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLGKGEEKSGGRLRPK 94

                        90       100       110
                ....*....|....*....|....*....|....*
gi 33585614 445 AMANCFEALIGAVYLEGSLEEAKQLFGRLLFNDPD 479
Cdd:cd00593  95 ILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIE 129
 
Name Accession Description Interval E-value
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
511-739 5.48e-64

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 213.42  E-value: 5.48e-64
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614 511 QKLTEFEEAIGVIFTHVRLLARAFTLRTVGFNHLTLGHNQRMEFLGDSIMQLVATEYLFIHFPDHHEGHLTLLRSSLVNN 590
Cdd:COG0571   2 EDLEELEERLGYRFKDPELLEQALTHRSYANEHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSE 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614 591 RTQAKVAEELGMQEY------AITNDKTKRPvalrtKTLADLLESFIAALYIDKDLEYVHTFMNVCFFPRLKEFILNQDW 664
Cdd:COG0571  82 ETLAEIARELGLGDYlrlgkgEEKSGGRRRP-----SILADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPGGAG 156

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 33585614 665 NDPKSQLQQCcltLRTEGKEPdiPLYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEKYN 739
Cdd:COG0571 157 KDYKTALQEW---LQARGLPL--PEYEVVEEEGPDHAKTFTVEVLVGGKVLGEGTGRSKKEAEQAAAKAALEKLG 226
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 516-737 1.13e-53

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: 185.10  E-value: 1.13e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614   516 FEEAIGVIFTHVRLLARAFTLRTVG-FNHLTLGHNQRMEFLGDSIMQLVATEYLFIHFPDHHEGHLTLLRSSLVNNRTQA 594
Cdd:TIGR02191   1 LEKRLGYKFKNPELLEQALTHRSYAnEHHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614   595 KVAEELGMQEY-AITNDKTKRPVALRTKTLADLLESFIAALYIDKDLEYVHTFMNVCFFPRLKEFILNQDWNDPKSQLQQ 673
Cdd:TIGR02191  81 EVARELGLGDFlLLGKGEEKSGGRRRDSILADAFEALIGAIYLDSGLEAARKFILKLLIPRIDAIIKEETLKDYKTALQE 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 33585614   674 ccLTLRtEGKEPdiPLYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEK 737
Cdd:TIGR02191 161 --WAQA-RGKPL--PEYRLIKEEGPDHDKEFTVEVSVNGEPYGEGKGKSKKEAEQNAAKAALEK 219
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 528-660 8.63e-44

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: 154.31  E-value: 8.63e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614 528 RLLARAFTLRTVGFNHLTLgHNQRMEFLGDSIMQLVATEYLFIHFPDHHEGHLTLLRSSLVNNRTQAKVAEELGMQEYAI 607
Cdd:cd00593   1 SLLLEALTHPSYANEHGRF-NNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLR 79

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 33585614 608 TNDK-TKRPVALRTKTLADLLESFIAALYIDKDLEYVHTFMNVCFFPRLKEFIL 660
Cdd:cd00593  80 LGKGeEKSGGRLRPKILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIEEISL 133
RIBOc smart00535
Ribonuclease III family;
528-658 6.79e-42

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 148.91  E-value: 6.79e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614    528 RLLARAFTLRTVGFNHltlGHNQRMEFLGDSIMQLVATEYLFIHFPDHHEGHLTLLRSSLVNNRTQAKVAEELGMQEY-A 606
Cdd:smart00535   1 SLLLRALTHASYSNEH---EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFiR 77

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 33585614    607 ITNDKTKRPVALRTKTLADLLESFIAALYIDKDLEYVHTFMNVCFFPRLKEF 658
Cdd:smart00535  78 LGRGEAISGGRDKPKILADVFEALIGAIYLDSGLEAAREFIRDLLGPRLDEL 129
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 365-479 4.46e-39

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: 141.21  E-value: 4.46e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614 365 PSRINHNERLEFLGDAVVEFLTSVHLYYLFPSLEEGGLATYRTAIVQNQHLAMLAKKLELDRFMLYAHGPDLCRESDLRH 444
Cdd:cd00593  15 EHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLGKGEEKSGGRLRPK 94

                        90       100       110
                ....*....|....*....|....*....|....*
gi 33585614 445 AMANCFEALIGAVYLEGSLEEAKQLFGRLLFNDPD 479
Cdd:cd00593  95 ILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIE 129
RIBOc smart00535
Ribonuclease III family;
349-481 4.37e-38

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 138.12  E-value: 4.37e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614    349 NTLINIMSRLGQDDPTPsrinHNERLEFLGDAVVEFLTSVHLYYLFPSLEEGGLATYRTAIVQNQHLAMLAKKLELDRFM 428
Cdd:smart00535   1 SLLLRALTHASYSNEHE----HNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFI 76

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 33585614    429 LYAHGPDLCRESDLRHAMANCFEALIGAVYLEGSLEEAKQLFGRLLFNDPDLR 481
Cdd:smart00535  77 RLGRGEAISGGRDKPKILADVFEALIGAIYLDSGLEAAREFIRDLLGPRLDEL 129
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 285-496 1.08e-29

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: 117.30  E-value: 1.08e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614   285 LDKLIGYTFQDRCLLQLAMTHPSHHlnfgmnpdharnslsncgirqpkygdrKVHHmhmrkkgintlinimsrlgqddpt 364
Cdd:TIGR02191   1 LEKRLGYKFKNPELLEQALTHRSYA---------------------------NEHH------------------------ 29

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614   365 pSRINHNERLEFLGDAVVEFLTSVHLYYLFPSLEEGGLATYRTAIVQNQHLAMLAKKLELDRFMLYAHGPDLCRESDLRH 444
Cdd:TIGR02191  30 -KDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAEVARELGLGDFLLLGKGEEKSGGRRRDS 108

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 33585614   445 AMANCFEALIGAVYLEGSLEEAKQLFGRLLFndPDLREVWLNYPLHPL--QLQE 496
Cdd:TIGR02191 109 ILADAFEALIGAIYLDSGLEAARKFILKLLI--PRIDAIIKEETLKDYktALQE 160
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 367-477 7.67e-29

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: 111.50  E-value: 7.67e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614   367 RINHNERLEFLGDAVVEFLTSVHLYYlFPSLEEGGLATYRTAIVQNQHLAMLAKKLELDRFMLYAHGPDLCRESDLRHAM 446
Cdd:pfam14622  17 RKPYNERLEFLGDAVLELSVSEYLFK-KPDLDEGGLTKLRASIVSEESLAEIAREIGLGKYLRLGKGEEETGGSGRESIL 95

                          90       100       110
                  ....*....|....*....|....*....|.
gi 33585614   447 ANCFEALIGAVYLEGSLEEAKQLFGRLLFND 477
Cdd:pfam14622  96 ADALEALIGAIYLDGGFEVAKEFILKKILPD 126
Ribonuclease_3 pfam00636
Ribonuclease III domain;
550-639 2.97e-25

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 100.43  E-value: 2.97e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614   550 QRMEFLGDSIMQLVATEYLFIHFPDHHEGHLTLLRSSLVNNRTQAKVAEELGMQEYAITNDKTKRPVAL----------- 618
Cdd:pfam00636   1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDIRRRNNalgkgpkradg 80

                          90       100
                  ....*....|....*....|.
gi 33585614   619 RTKTLADLLESFIAALYIDKD 639
Cdd:pfam00636  81 KEKVLADAFEALIGALYLDGG 101
 
Name Accession Description Interval E-value
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
511-739 5.48e-64

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 213.42  E-value: 5.48e-64
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614 511 QKLTEFEEAIGVIFTHVRLLARAFTLRTVGFNHLTLGHNQRMEFLGDSIMQLVATEYLFIHFPDHHEGHLTLLRSSLVNN 590
Cdd:COG0571   2 EDLEELEERLGYRFKDPELLEQALTHRSYANEHGGLENNERLEFLGDAVLGLVVAEYLYRRFPDAPEGELSKLRAALVSE 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614 591 RTQAKVAEELGMQEY------AITNDKTKRPvalrtKTLADLLESFIAALYIDKDLEYVHTFMNVCFFPRLKEFILNQDW 664
Cdd:COG0571  82 ETLAEIARELGLGDYlrlgkgEEKSGGRRRP-----SILADAFEALIGAIYLDGGLEAARKFVLRLFEPRLEEIAPGGAG 156

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 33585614 665 NDPKSQLQQCcltLRTEGKEPdiPLYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEKYN 739
Cdd:COG0571 157 KDYKTALQEW---LQARGLPL--PEYEVVEEEGPDHAKTFTVEVLVGGKVLGEGTGRSKKEAEQAAAKAALEKLG 226
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 516-737 1.13e-53

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: 185.10  E-value: 1.13e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614   516 FEEAIGVIFTHVRLLARAFTLRTVG-FNHLTLGHNQRMEFLGDSIMQLVATEYLFIHFPDHHEGHLTLLRSSLVNNRTQA 594
Cdd:TIGR02191   1 LEKRLGYKFKNPELLEQALTHRSYAnEHHKDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614   595 KVAEELGMQEY-AITNDKTKRPVALRTKTLADLLESFIAALYIDKDLEYVHTFMNVCFFPRLKEFILNQDWNDPKSQLQQ 673
Cdd:TIGR02191  81 EVARELGLGDFlLLGKGEEKSGGRRRDSILADAFEALIGAIYLDSGLEAARKFILKLLIPRIDAIIKEETLKDYKTALQE 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 33585614   674 ccLTLRtEGKEPdiPLYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEK 737
Cdd:TIGR02191 161 --WAQA-RGKPL--PEYRLIKEEGPDHDKEFTVEVSVNGEPYGEGKGKSKKEAEQNAAKAALEK 219
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 528-660 8.63e-44

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: 154.31  E-value: 8.63e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614 528 RLLARAFTLRTVGFNHLTLgHNQRMEFLGDSIMQLVATEYLFIHFPDHHEGHLTLLRSSLVNNRTQAKVAEELGMQEYAI 607
Cdd:cd00593   1 SLLLEALTHPSYANEHGRF-NNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLR 79

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 33585614 608 TNDK-TKRPVALRTKTLADLLESFIAALYIDKDLEYVHTFMNVCFFPRLKEFIL 660
Cdd:cd00593  80 LGKGeEKSGGRLRPKILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIEEISL 133
RIBOc smart00535
Ribonuclease III family;
528-658 6.79e-42

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 148.91  E-value: 6.79e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614    528 RLLARAFTLRTVGFNHltlGHNQRMEFLGDSIMQLVATEYLFIHFPDHHEGHLTLLRSSLVNNRTQAKVAEELGMQEY-A 606
Cdd:smart00535   1 SLLLRALTHASYSNEH---EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFiR 77

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 33585614    607 ITNDKTKRPVALRTKTLADLLESFIAALYIDKDLEYVHTFMNVCFFPRLKEF 658
Cdd:smart00535  78 LGRGEAISGGRDKPKILADVFEALIGAIYLDSGLEAAREFIRDLLGPRLDEL 129
DSRM_RNAse_III_meta_like cd19877
double-stranded RNA binding motif of metazoan ribonuclease III (RNase III) and similar ...
 665-738 1.35e-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: 1.35e-40
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 33585614 665 NDPKSQLQQCCLTLRTEG-KEPDIPLYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEKY 738
Cdd:cd19877   1 NDPKSQLQQCCLTLRTEGkKEPDIPEYKVLQKSGPTNTRVYTVAVYFRGERIATGTGSSIQQAEMNAAEKALEKL 75
RIBOc cd00593
RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and ...
 365-479 4.46e-39

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: 141.21  E-value: 4.46e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614 365 PSRINHNERLEFLGDAVVEFLTSVHLYYLFPSLEEGGLATYRTAIVQNQHLAMLAKKLELDRFMLYAHGPDLCRESDLRH 444
Cdd:cd00593  15 EHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRLGKGEEKSGGRLRPK 94

                        90       100       110
                ....*....|....*....|....*....|....*
gi 33585614 445 AMANCFEALIGAVYLEGSLEEAKQLFGRLLFNDPD 479
Cdd:cd00593  95 ILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIE 129
RIBOc smart00535
Ribonuclease III family;
349-481 4.37e-38

Ribonuclease III family;


Pssm-ID: 197778  Cd Length: 129  Bit Score: 138.12  E-value: 4.37e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614    349 NTLINIMSRLGQDDPTPsrinHNERLEFLGDAVVEFLTSVHLYYLFPSLEEGGLATYRTAIVQNQHLAMLAKKLELDRFM 428
Cdd:smart00535   1 SLLLRALTHASYSNEHE----HNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFI 76

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 33585614    429 LYAHGPDLCRESDLRHAMANCFEALIGAVYLEGSLEEAKQLFGRLLFNDPDLR 481
Cdd:smart00535  77 RLGRGEAISGGRDKPKILADVFEALIGAIYLDSGLEAAREFIRDLLGPRLDEL 129
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 285-496 1.08e-29

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: 117.30  E-value: 1.08e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614   285 LDKLIGYTFQDRCLLQLAMTHPSHHlnfgmnpdharnslsncgirqpkygdrKVHHmhmrkkgintlinimsrlgqddpt 364
Cdd:TIGR02191   1 LEKRLGYKFKNPELLEQALTHRSYA---------------------------NEHH------------------------ 29

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614   365 pSRINHNERLEFLGDAVVEFLTSVHLYYLFPSLEEGGLATYRTAIVQNQHLAMLAKKLELDRFMLYAHGPDLCRESDLRH 444
Cdd:TIGR02191  30 -KDVKNNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSRLRAALVSEESLAEVARELGLGDFLLLGKGEEKSGGRRRDS 108

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 33585614   445 AMANCFEALIGAVYLEGSLEEAKQLFGRLLFndPDLREVWLNYPLHPL--QLQE 496
Cdd:TIGR02191 109 ILADAFEALIGAIYLDSGLEAARKFILKLLI--PRIDAIIKEETLKDYktALQE 160
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 367-477 7.67e-29

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: 111.50  E-value: 7.67e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614   367 RINHNERLEFLGDAVVEFLTSVHLYYlFPSLEEGGLATYRTAIVQNQHLAMLAKKLELDRFMLYAHGPDLCRESDLRHAM 446
Cdd:pfam14622  17 RKPYNERLEFLGDAVLELSVSEYLFK-KPDLDEGGLTKLRASIVSEESLAEIAREIGLGKYLRLGKGEEETGGSGRESIL 95

                          90       100       110
                  ....*....|....*....|....*....|.
gi 33585614   447 ANCFEALIGAVYLEGSLEEAKQLFGRLLFND 477
Cdd:pfam14622  96 ADALEALIGAIYLDGGFEVAKEFILKKILPD 126
Ribonuclease_3 pfam00636
Ribonuclease III domain;
550-639 2.97e-25

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 100.43  E-value: 2.97e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614   550 QRMEFLGDSIMQLVATEYLFIHFPDHHEGHLTLLRSSLVNNRTQAKVAEELGMQEYAITNDKTKRPVAL----------- 618
Cdd:pfam00636   1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDIRRRNNalgkgpkradg 80

                          90       100
                  ....*....|....*....|.
gi 33585614   619 RTKTLADLLESFIAALYIDKD 639
Cdd:pfam00636  81 KEKVLADAFEALIGALYLDGG 101
Ribonuclease_3 pfam00636
Ribonuclease III domain;
372-461 1.25e-22

Ribonuclease III domain;


Pssm-ID: 459883  Cd Length: 101  Bit Score: 93.11  E-value: 1.25e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614   372 ERLEFLGDAVVEFLTSVHLYYLFPSLEEGGLATYRTAIVQNQHLAMLAKKLELDRFMLYAHGPDLCRESDLRHA------ 445
Cdd:pfam00636   1 ERLEFLGDAVLELYVREYLFEKFPDLREGDLHRLRSALVSNEALAKLARKLGLEKFLTEEELDIRRRNNALGKGpkradg 80

                          90       100
                  ....*....|....*....|
gi 33585614   446 ----MANCFEALIGAVYLEG 461
Cdd:pfam00636  81 kekvLADAFEALIGALYLDG 100
Ribonucleas_3_3 pfam14622
Ribonuclease-III-like; Members of this family are involved in rDNA transcription and rRNA ...
 529-655 9.46e-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: 85.69  E-value: 9.46e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 33585614   529 LLARAFTLRTvgFNHLTLGHNQRMEFLGDSIMQLVATEYLFiHFPDHHEGHLTLLRSSLVNNRTQAKVAEELGMQEYAIT 608
Cdd:pfam14622   3 LLLQALTHKS--YANGRKPYNERLEFLGDAVLELSVSEYLF-KKPDLDEGGLTKLRASIVSEESLAEIAREIGLGKYLRL 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 33585614   609 NDKTKRPVAL-RTKTLADLLESFIAALYIDKDLEYVHTFMNVCFFPRL 655
Cdd:pfam14622  80 GKGEEETGGSgRESILADALEALIGAIYLDGGFEVAKEFILKKILPDL 127
DSRM smart00358
Double-stranded RNA binding motif;
667-738 1.89e-18

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 80.00  E-value: 1.89e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 33585614    667 PKSQLQQCCltlRTEGKEPDiplYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEKY 738
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 ...
 666-737 3.73e-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: 79.07  E-value: 3.73e-18
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 33585614 666 DPKSQLQQCCltlrtEGKEPDIPLYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEK 737
Cdd:cd10845   2 DYKTALQEYL-----QKRGLPLPEYELVEEEGPDHNKTFTVEVKVNGKVIGEGTGRSKKEAEQAAAKAALEK 68
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 667-738 2.49e-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: 71.11  E-value: 2.49e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 33585614   667 PKSQLQQCCLTLRTEgkepdiPLYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEKY 738
Cdd:pfam00035   1 PKSLLQEYAQKNGKP------PPYEYVSEEGPPHSPKFTVTVKVDGKLYGSGTGSSKKEAEQLAAEKALEKL 66
DSRM_MRPL3_like cd19873
double-stranded RNA binding motif of Saccharomyces cerevisiae mitochondrial 54S ribosomal ...
 665-738 1.79e-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: 1.79e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 33585614 665 NDPKSQLQQCCltlRTEGKEPdiPLYKTLQTVG-PSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEKY 738
Cdd:cd19873  12 ENPKRTLSALL---KREGLEP--PVSRLLKESGrASHTPTFVVGVYSGSQKLGEGAGSSIKMAEIRAARDALRKH 81
DSRM_RNT1p-like cd19876
double-stranded RNA binding motif of Saccharomyces cerevisiae ribonuclease 3 (RNT1p) and ...
 682-737 1.25e-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: 1.25e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 33585614 682 GKEPDIPLYKTLQTVGPsHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALEK 737
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 ...
 690-736 3.06e-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: 3.06e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 33585614 690 YKTLQTVGPSHARTYTVAVYFKGeRIGCGKGPSIQQAEMGAAMDALE 736
Cdd:cd19865  16 YKLTSQTGPVHAPVFTMSVEVNG-QTFEGTGRSKKKAKLEAAEKALR 61
DSRM_STAU2_rpt1 cd19880
first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 688-735 6.29e-04

first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 2 (Staufen 2) and similar proteins; Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen 2 contains five 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: 380709  Cd Length: 68  Bit Score: 38.93  E-value: 6.29e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 33585614 688 PLYKTLQTVGPSHARTYTVAVYFkGERIGCGKGPSIQQAEMGAAMDAL 735
Cdd:cd19880  22 PQYKLLNERGPAHAKIFTVQLTL-GEQTWEAEGSSIKKAQHAAASKAL 68
DSRM_EIF2AK2_rpt1 cd19903
first double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha ...
 690-736 1.23e-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: 38.14  E-value: 1.23e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 33585614 690 YKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDALE 736
Cdd:cd19903  20 YVEVPTSGPSHDPRFTFQVVIDGKEYPEGEGKSKKEAKQAAAKLALE 66
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 688-735 1.29e-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: 1.29e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 33585614 688 PLYKTLQtVGPSHARTYTVAVYFKGERiGCGKGPSIQQAEMGAAMDAL 735
Cdd:cd00048  12 PEYETVE-EGGPHNPRFTCTVTVNGQT-FEGEGKSKKEAKQAAAEKAL 57
DSRM_AtDRB-like_rpt2 cd19908
second double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...
 686-735 3.51e-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: 3.51e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 33585614 686 DIPLYKTlQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDAL 735
Cdd:cd19908  17 PLPLYTT-VRSGPGHVPTFTCTVEIAGITFTGEAAKTKKQAEKSAARTAW 65
seadorna_dsRNA TIGR04238
seadornavirus double-stranded RNA-binding protein; This protein family occurs in the ...
 666-737 6.09e-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: 38.77  E-value: 6.09e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 33585614   666 DPKSQLQQCCLTLRTEgkepdIPLYKTLQTVGPSHARTYTVAVYFKGERIGCgKGPSIQQAEMGAAMDALEK 737
Cdd:TIGR04238   1 NVVGMLQELAVKRGLE-----LPVYEKVGKEGPDHAPTFTIKLTANDIEVIE-AASSKKQAEKLAAATIYED 66
DSRM_STAU_rpt1 cd19857
first double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 688-735 8.29e-03

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


Pssm-ID: 380686  Cd Length: 64  Bit Score: 35.32  E-value: 8.29e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 33585614 688 PLYKTLQTVGPSHARTYTVAVYFKGERIGCGKGPSIQQAEMGAAMDAL 735
Cdd:cd19857  17 PQYTLVDEEGPAHKKTFTVKLTLGDEEEYEASGSSIKKAQHAAAEKAL 64
 
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.
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