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Conserved domains on  [gi|196015763|ref|XP_002117737|]
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uncharacterized protein TRIADDRAFT_33041 [Trichoplax adhaerens]

Protein Classification

RNA-binding protein( domain architecture ID 10188096)

RNA-binding protein recognizes RNA via an RNA recognition motif (RRM)

Gene Ontology:  GO:0003723
PubMed:  15853797|22278943|18515081
SCOP:  3000110

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM_ABT1_like cd12263
RNA recognition motif (RRM) found in activator of basal transcription 1 (ABT1) and similar ...
 6-109 2.82e-44

RNA recognition motif (RRM) found in activator of basal transcription 1 (ABT1) and similar proteins; This subfamily corresponds to the RRM of novel nuclear proteins termed ABT1 and its homologous counterpart, pre-rRNA-processing protein ESF2 (eighteen S factor 2), from yeast. ABT1 associates with the TATA-binding protein (TBP) and enhances basal transcription activity of class II promoters. Meanwhile, ABT1 could be a transcription cofactor that can bind to DNA in a sequence-independent manner. The yeast ABT1 homolog, ESF2, is a component of 90S preribosomes and 5' ETS-based RNPs. It is previously identified as a putative partner of the TATA-element binding protein. However, it is primarily localized to the nucleolus and physically associates with pre-rRNA processing factors. ESF2 may play a role in ribosome biogenesis. It is required for normal pre-rRNA processing, as well as for SSU processome assembly and function. Both ABT1 and ESF2 contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


:

Pssm-ID: 409707 [Multi-domain]  Cd Length: 98  Bit Score: 141.95  E-value: 2.82e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196015763   6 GIVYISRIPPHMNPLKIQRIFSRYGQINRIFLQPIGYSLMINIRnsteivrSKRIHETKLYSEGWIEFKKKKIAKSVAFS 85
Cdd:cd12263    1 GIVYLSRIPPGMNPAKLRQLLSQYGEVGRIYLQPEDPSKRKKRK-------KKGGNKKKKFTEGWVEFEDKKVAKRVAES 73

                         90       100
                 ....*....|....*....|....
gi 196015763  86 LNNTKIGRKNRGYYDHDFWNLKYL 109
Cdd:cd12263   74 LNNTPIGGKKRSRFRDDLWNIKYL 97
 
Name Accession Description Interval E-value
RRM_ABT1_like cd12263
RNA recognition motif (RRM) found in activator of basal transcription 1 (ABT1) and similar ...
 6-109 2.82e-44

RNA recognition motif (RRM) found in activator of basal transcription 1 (ABT1) and similar proteins; This subfamily corresponds to the RRM of novel nuclear proteins termed ABT1 and its homologous counterpart, pre-rRNA-processing protein ESF2 (eighteen S factor 2), from yeast. ABT1 associates with the TATA-binding protein (TBP) and enhances basal transcription activity of class II promoters. Meanwhile, ABT1 could be a transcription cofactor that can bind to DNA in a sequence-independent manner. The yeast ABT1 homolog, ESF2, is a component of 90S preribosomes and 5' ETS-based RNPs. It is previously identified as a putative partner of the TATA-element binding protein. However, it is primarily localized to the nucleolus and physically associates with pre-rRNA processing factors. ESF2 may play a role in ribosome biogenesis. It is required for normal pre-rRNA processing, as well as for SSU processome assembly and function. Both ABT1 and ESF2 contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409707 [Multi-domain]  Cd Length: 98  Bit Score: 141.95  E-value: 2.82e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196015763   6 GIVYISRIPPHMNPLKIQRIFSRYGQINRIFLQPIGYSLMINIRnsteivrSKRIHETKLYSEGWIEFKKKKIAKSVAFS 85
Cdd:cd12263    1 GIVYLSRIPPGMNPAKLRQLLSQYGEVGRIYLQPEDPSKRKKRK-------KKGGNKKKKFTEGWVEFEDKKVAKRVAES 73

                         90       100
                 ....*....|....*....|....
gi 196015763  86 LNNTKIGRKNRGYYDHDFWNLKYL 109
Cdd:cd12263   74 LNNTPIGGKKRSRFRDDLWNIKYL 97
RRM smart00360
RNA recognition motif;
8-92 3.68e-03

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 34.88  E-value: 3.68e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196015763     8 VYISRIPPHMNPLKIQRIFSRYGQINRIFlqpigyslminIRNSTEIVRSKRIhetklyseGWIEFKKKKIAKSVAFSLN 87
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFGKVESVR-----------LVRDKETGKSKGF--------AFVEFESEEDAEKALEALN 62


                   ....*
gi 196015763    88 NTKIG 92
Cdd:smart00360  63 GKELD 67
 
Name Accession Description Interval E-value
RRM_ABT1_like cd12263
RNA recognition motif (RRM) found in activator of basal transcription 1 (ABT1) and similar ...
 6-109 2.82e-44

RNA recognition motif (RRM) found in activator of basal transcription 1 (ABT1) and similar proteins; This subfamily corresponds to the RRM of novel nuclear proteins termed ABT1 and its homologous counterpart, pre-rRNA-processing protein ESF2 (eighteen S factor 2), from yeast. ABT1 associates with the TATA-binding protein (TBP) and enhances basal transcription activity of class II promoters. Meanwhile, ABT1 could be a transcription cofactor that can bind to DNA in a sequence-independent manner. The yeast ABT1 homolog, ESF2, is a component of 90S preribosomes and 5' ETS-based RNPs. It is previously identified as a putative partner of the TATA-element binding protein. However, it is primarily localized to the nucleolus and physically associates with pre-rRNA processing factors. ESF2 may play a role in ribosome biogenesis. It is required for normal pre-rRNA processing, as well as for SSU processome assembly and function. Both ABT1 and ESF2 contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409707 [Multi-domain]  Cd Length: 98  Bit Score: 141.95  E-value: 2.82e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196015763   6 GIVYISRIPPHMNPLKIQRIFSRYGQINRIFLQPIGYSLMINIRnsteivrSKRIHETKLYSEGWIEFKKKKIAKSVAFS 85
Cdd:cd12263    1 GIVYLSRIPPGMNPAKLRQLLSQYGEVGRIYLQPEDPSKRKKRK-------KKGGNKKKKFTEGWVEFEDKKVAKRVAES 73

                         90       100
                 ....*....|....*....|....
gi 196015763  86 LNNTKIGRKNRGYYDHDFWNLKYL 109
Cdd:cd12263   74 LNNTPIGGKKRSRFRDDLWNIKYL 97
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 8-94 1.44e-03

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).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 35.72  E-value: 1.44e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196015763   8 VYISRIPPHMNPLKIQRIFSRYGQINRIFLqpigyslminIRNSTeiVRSKRIhetklyseGWIEFKKKKIAKSVAFSLN 87
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRI----------VRDRD--GKSKGF--------AFVEFESPEDAEKALEALN 60


                 ....*..
gi 196015763  88 NTKIGRK 94
Cdd:cd00590   61 GTELGGR 67
RRM_Nop15p cd12552
RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins; ...
 7-88 1.51e-03

RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins; This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409968 [Multi-domain]  Cd Length: 77  Bit Score: 36.00  E-value: 1.51e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196015763   7 IVYISRIPPHMNPLKIQRIFSRYGQINRIflqpigyslminirnstEIVRSKRIHETKLYseGWIEFKKKKIAKSVAFSL 86
Cdd:cd12552    1 IIYVSHLPHGFHEKELKKYFAQFGDLKNV-----------------RLARSKKTGNSKHY--GFLEFVNPEDAMIAQKSM 61


                 ..
gi 196015763  87 NN 88
Cdd:cd12552   62 NN 63
RRM smart00360
RNA recognition motif;
8-92 3.68e-03

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 34.88  E-value: 3.68e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196015763     8 VYISRIPPHMNPLKIQRIFSRYGQINRIFlqpigyslminIRNSTEIVRSKRIhetklyseGWIEFKKKKIAKSVAFSLN 87
Cdd:smart00360   2 LFVGNLPPDTTEEELRELFSKFGKVESVR-----------LVRDKETGKSKGF--------AFVEFESEEDAEKALEALN 62


                   ....*
gi 196015763    88 NTKIG 92
Cdd:smart00360  63 GKELD 67
RRM_NIFK_like cd12307
RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) ...
 7-88 7.60e-03

RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins; This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409748 [Multi-domain]  Cd Length: 74  Bit Score: 33.70  E-value: 7.60e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 196015763   7 IVYISRIPPHMNPLKIQRIFSRYGQINRIFLqpigyslminirnsteiVRSKRIHETKLYseGWIEFKKKKIAKSVAFSL 86
Cdd:cd12307    1 VVYIGHLPHGFYEPELRKYFSQFGTVTRLRL-----------------SRSKKTGKSKGY--AFVEFEDPEVAKIVAETM 61


                 ..
gi 196015763  87 NN 88
Cdd:cd12307   62 NN 63
 
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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