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Conserved domains on  [gi|30678641|ref|NP_849275|]
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Double-stranded RNA-binding domain (DsRBD)-containing protein [Arabidopsis thaliana]

Protein Classification

dsRNA-binding motif domain-containing protein( domain architecture ID 855)

dsRNA-binding motif (DSRM) domain-containing protein may be involved in posttranscriptional gene regulation, for example by preventing the expression of proteins or by mediating RNA localization

Gene Ontology:  GO:0003725
PubMed:  1438302

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DSRM_SF super family cl00054
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 91-159 1.71e-09

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.


The actual alignment was detected with superfamily member cd19869:

Pssm-ID: 444671  Cd Length: 70  Bit Score: 51.98  E-value: 1.71e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30678641  91 NLCSVRHWKAPLYE-YIAEGPCHMKIFTGKVTVEMKEdsRITVLECFGNPQYKKKIAAEQAAEAALWYLK 159
Cdd:cd19869   2 EICLKRRWPMPVYRcVEEEGPAHAKRFTYMVRVKIPE--RGWTIECEGEPMRSKKRAKDSAALLLLEYLK 69
 
Name Accession Description Interval E-value
DSRM_DCL_plant cd19869
double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant ...
 91-159 1.71e-09

double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant Dicer-like (DCL) proteins and other ribonuclease (RNase) III-like (RTL) proteins. DCLs are endoribonucleases involved in RNA-mediated post-transcriptional gene silencing (PTGS). They function in the microRNA (miRNA) biogenesis pathway by cleaving primary miRNAs (pri-miRNAs) and precursor miRNAs (pre-miRNAs). Family members contain 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: 380698  Cd Length: 70  Bit Score: 51.98  E-value: 1.71e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30678641  91 NLCSVRHWKAPLYE-YIAEGPCHMKIFTGKVTVEMKEdsRITVLECFGNPQYKKKIAAEQAAEAALWYLK 159
Cdd:cd19869   2 EICLKRRWPMPVYRcVEEEGPAHAKRFTYMVRVKIPE--RGWTIECEGEPMRSKKRAKDSAALLLLEYLK 69
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 85-126 7.29e-04

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: 36.44  E-value: 7.29e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 30678641    85 AKSQLYNLCSVRHWKAPLYEYIAEGPCHMKIFTGKVTVEMKE 126
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKL 42
 
Name Accession Description Interval E-value
DSRM_DCL_plant cd19869
double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant ...
 91-159 1.71e-09

double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant Dicer-like (DCL) proteins and other ribonuclease (RNase) III-like (RTL) proteins. DCLs are endoribonucleases involved in RNA-mediated post-transcriptional gene silencing (PTGS). They function in the microRNA (miRNA) biogenesis pathway by cleaving primary miRNAs (pri-miRNAs) and precursor miRNAs (pre-miRNAs). Family members contain 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: 380698  Cd Length: 70  Bit Score: 51.98  E-value: 1.71e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30678641  91 NLCSVRHWKAPLYE-YIAEGPCHMKIFTGKVTVEMKEdsRITVLECFGNPQYKKKIAAEQAAEAALWYLK 159
Cdd:cd19869   2 EICLKRRWPMPVYRcVEEEGPAHAKRFTYMVRVKIPE--RGWTIECEGEPMRSKKRAKDSAALLLLEYLK 69
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 85-126 7.29e-04

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: 36.44  E-value: 7.29e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 30678641    85 AKSQLYNLCSVRHWKAPLYEYIAEGPCHMKIFTGKVTVEMKE 126
Cdd:pfam00035   1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKL 42
DSRM_SON-like cd19870
double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...
 87-122 8.88e-04

double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known as Bax antagonist selected in saccharomyces 1 (BASS1), negative regulatory element-binding protein (NRE-binding protein), or protein DBP-5, or SON3) is an RNA-binding protein which acts as an mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. It specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Members of this group contain 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: 380699  Cd Length: 75  Bit Score: 36.49  E-value: 8.88e-04
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 30678641  87 SQLYNLCSVRHWKAPLYEYIAE-GPCHMKIFTGKVTV 122
Cdd:cd19870   6 SALMELCNKRKWGPPEFRLVEEsGPPHRKHFLFKVVV 42
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 85-126 1.41e-03

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: 35.93  E-value: 1.41e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 30678641  85 AKSQLYNLCSVRHWKAPLYEYIAE-GPCHMKIFTGKVTVEMKE 126
Cdd:cd10845   3 YKTALQEYLQKRGLPLPEYELVEEeGPDHNKTFTVEVKVNGKV 45
DSRM_AtDRB-like_rpt1 cd19907
first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...
 86-141 4.02e-03

first 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 first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380736 [Multi-domain]  Cd Length: 69  Bit Score: 34.76  E-value: 4.02e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 30678641  86 KSQLYNLCSVRHWKAPLYEYIAEGPCHMKIFTGKVTVemkeDSRItvlecFGNPQY 141
Cdd:cd19907   3 KSQLQEYAQKSCLNLPVYACIREGPDHAPRFRATVTF----NGVI-----FESPPG 49
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 90-126 5.51e-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: 33.80  E-value: 5.51e-03
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 30678641  90 YNLCSVRHWKAPLYEYIAEGPCHMKIFTGKVTVEMKE 126
Cdd:cd00048   1 NELCQKNKWPPPEYETVEEGGPHNPRFTCTVTVNGQT 37
DND1_DSRM pfam14709
double strand RNA binding domain from DEAD END PROTEIN 1; A C-terminal domain in human dead ...
 83-159 7.10e-03

double strand RNA binding domain from DEAD END PROTEIN 1; A C-terminal domain in human dead end protein 1 (DND1_HUMAN) homologous to double strand RNA binding domains (PF00035, PF00333)


Pssm-ID: 405408  Cd Length: 80  Bit Score: 34.24  E-value: 7.10e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30678641    83 SSAKSQLYNLCSVRHWKAPLYE-YIAEGPCHMKIFTGKVTVEMKEDSRITVLECF--GNPQYKKKIAAEQAAEAALWYLK 159
Cdd:pfam14709   1 TSAVSHLEELCQKNKWGSPVYElHSTAGPDGKQLFTYKVVIPGIETPFPGVIWIFmpGKLCSTKEEAKEAAAEQVLEALG 80
 
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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