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Conserved domains on  [gi|386768926|ref|NP_001245831|]
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uncharacterized protein Dmel_CG4896, isoform G [Drosophila melanogaster]

Protein Classification

RNA-binding protein( domain architecture ID 106745)

RNA-binding protein containing an RNA recognition motif (RRM)

CATH:  3.30.70.330
Gene Ontology:  GO:0003723
PubMed:  15853797
SCOP:  3000110

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 211-252 6.07e-12

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


The actual alignment was detected with superfamily member cd12561:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 81  Bit Score: 60.07  E-value: 6.07e-12
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 386768926 211 PLNNIILFGLKKHVTEADIMGELIKVDLEPTSIRVMRKQQTG 252
Cdd:cd12561    1 PNNTIMLRGLPLSVTEEDIRNALVSHGVQPKDVRLMRRKTTG 42
U2AF_lg super family cl36941
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 74-158 4.93e-03

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


The actual alignment was detected with superfamily member TIGR01642:

Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 37.95  E-value: 4.93e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386768926   74 EDYEDQGNYNSRQNLDQRHGEDKYDRRHADSQGRRDHDSNYDKSGQDMDKDRDHRwkNYDrvSRERNHDDFDrgSERSSR 153
Cdd:TIGR01642   2 DEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRR--RYD--SRSPRSLRYS--SVRRSR 75


                  ....*
gi 386768926  154 SNDQR 158
Cdd:TIGR01642  76 DRPRR 80
 
Name Accession Description Interval E-value
RRM1_RBM5_like cd12561
RNA recognition motif 1 (RRM1) found in RNA-binding protein 5 (RBM5) and similar proteins; ...
 211-252 6.07e-12

RNA recognition motif 1 (RRM1) found in RNA-binding protein 5 (RBM5) and similar proteins; This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 409977 [Multi-domain]  Cd Length: 81  Bit Score: 60.07  E-value: 6.07e-12
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 386768926 211 PLNNIILFGLKKHVTEADIMGELIKVDLEPTSIRVMRKQQTG 252
Cdd:cd12561    1 PNNTIMLRGLPLSVTEEDIRNALVSHGVQPKDVRLMRRKTTG 42
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 74-158 4.93e-03

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 37.95  E-value: 4.93e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386768926   74 EDYEDQGNYNSRQNLDQRHGEDKYDRRHADSQGRRDHDSNYDKSGQDMDKDRDHRwkNYDrvSRERNHDDFDrgSERSSR 153
Cdd:TIGR01642   2 DEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRR--RYD--SRSPRSLRYS--SVRRSR 75


                  ....*
gi 386768926  154 SNDQR 158
Cdd:TIGR01642  76 DRPRR 80
 
Name Accession Description Interval E-value
RRM1_RBM5_like cd12561
RNA recognition motif 1 (RRM1) found in RNA-binding protein 5 (RBM5) and similar proteins; ...
 211-252 6.07e-12

RNA recognition motif 1 (RRM1) found in RNA-binding protein 5 (RBM5) and similar proteins; This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 409977 [Multi-domain]  Cd Length: 81  Bit Score: 60.07  E-value: 6.07e-12
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 386768926 211 PLNNIILFGLKKHVTEADIMGELIKVDLEPTSIRVMRKQQTG 252
Cdd:cd12561    1 PNNTIMLRGLPLSVTEEDIRNALVSHGVQPKDVRLMRRKTTG 42
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 74-158 4.93e-03

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 37.95  E-value: 4.93e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386768926   74 EDYEDQGNYNSRQNLDQRHGEDKYDRRHADSQGRRDHDSNYDKSGQDMDKDRDHRwkNYDrvSRERNHDDFDrgSERSSR 153
Cdd:TIGR01642   2 DEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRR--RYD--SRSPRSLRYS--SVRRSR 75


                  ....*
gi 386768926  154 SNDQR 158
Cdd:TIGR01642  76 DRPRR 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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