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rbm39a RNA binding motif protein 39a [ Danio rerio (zebrafish) ]

Gene ID: 406251, updated on 27-Mar-2024

Summary

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Official Symbol
rbm39aprovided by ZNC
Official Full Name
RNA binding motif protein 39aprovided by ZNC
Primary source
ZFIN:ZDB-GENE-040426-2852
See related
Ensembl:ENSDARG00000011613 AllianceGenome:ZFIN:ZDB-GENE-040426-2852
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
rnpc2; zgc:55780
Summary
Predicted to enable RNA binding activity. Predicted to act upstream of or within mRNA processing. Predicted to be located in nucleus. Orthologous to human RBM39 (RNA binding motif protein 39). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
human mouse all
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Genomic context

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Location:
chromosome: 11
Exon count:
19
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 11 NC_007122.7 (24339307..24345421)
105 previous assembly GRCz10 (GCF_000002035.5) 11 NC_007122.6 (24101694..24107805)

Chromosome 11 - NC_007122.7Genomic Context describing neighboring genes Neighboring gene si:dkey-76p14.2 Neighboring gene RAS (RAD and GEM)-like GTP-binding 1 Neighboring gene si:ch211-15p9.2 Neighboring gene NFS1 cysteine desulfurase

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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Related articles in PubMed

  1. pnp4a Is the Causal Gene of the Medaka Iridophore Mutant guanineless. Kimura T, et al. G3 (Bethesda), 2017 Apr 3. PMID 28258112, Free PMC Article
  2. Triclosan regulates alternative splicing events of nerve-related genes through RNA-binding protein CELF2 to induce zebrafish neurotoxicity. Wang D, et al. J Hazard Mater, 2021 Jul 5. PMID 33621777
  3. prpf4 is essential for cell survival and posterior lateral line primordium migration in zebrafish. Wang Y, et al. J Genet Genomics, 2018 Aug 20. PMID 30174136
  4. Integrative view of α2,3-sialyltransferases (ST3Gal) molecular and functional evolution in deuterostomes: significance of lineage-specific losses. Petit D, et al. Mol Biol Evol, 2015 Apr. PMID 25534026, Free PMC Article
  5. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article

See all (8) citations in PubMed

GeneRIFs: Gene References Into Functions

Pathways from PubChem

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General gene information

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Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables U1 snRNP binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables nucleic acid binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within mRNA processing IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
RNA-binding protein 39; RNA-binding protein 39a
Names
RNA-binding region (RNP1, RRM) containing 2
rbm39

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001012304.1 → NP_001012304.1  RNA-binding protein 39a

    See identical proteins and their annotated locations for NP_001012304.1

    Status: PROVISIONAL

    Source sequence(s)
    BC044487
    UniProtKB/TrEMBL
    F6P603, F6PC52, Q803H1
    Related
    ENSDARP00000022349.4, ENSDART00000017973.7
    Conserved Domains (5) summary
    cd12284
    Location:248 → 320
    RRM2_RBM23_RBM39; RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins
    cd12285
    Location:416 → 500
    RRM3_RBM39_like; RNA recognition motif 3 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins
    cd12536
    Location:148 → 232
    RRM1_RBM39; RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39)
    TIGR01622
    Location:91 → 511
    SF-CC1; splicing factor, CC1-like family
    pfam15519
    Location:337 → 432
    RBM39linker; linker between RRM2 and RRM3 domains in RBM39 protein

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007122.7 Reference GRCz11 Primary Assembly

    Range
    24339307..24345421
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005169275.3 → XP_005169332.1  RNA-binding protein 39 isoform X1

    See identical proteins and their annotated locations for XP_005169332.1

    UniProtKB/TrEMBL
    F6P603, F6PC52, Q803H1
    Related
    ENSDARP00000116290.1, ENSDART00000135435.3
    Conserved Domains (5) summary
    cd12284
    Location:248 → 320
    RRM2_RBM23_RBM39; RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins
    cd12285
    Location:416 → 500
    RRM3_RBM39_like; RNA recognition motif 3 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins
    cd12536
    Location:148 → 232
    RRM1_RBM39; RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39)
    TIGR01622
    Location:91 → 511
    SF-CC1; splicing factor, CC1-like family
    pfam15519
    Location:337 → 432
    RBM39linker; linker between RRM2 and RRM3 domains in RBM39 protein

  2. XM_009306024.3 → XP_009304299.1  RNA-binding protein 39 isoform X4

    UniProtKB/TrEMBL
    A0A8M3B422
    Conserved Domains (3) summary
    cd12284
    Location:3 → 75
    RRM2_RBM23_RBM39; RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins
    cd12285
    Location:171 → 255
    RRM3_RBM39_like; RNA recognition motif 3 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins
    pfam15519
    Location:92 → 187
    RBM39linker; linker between RRM2 and RRM3 domains in RBM39 protein

  3. XM_005169278.4 → XP_005169335.1  RNA-binding protein 39 isoform X2

    See identical proteins and their annotated locations for XP_005169335.1

    UniProtKB/TrEMBL
    A0A2R8QAM8, A0A8M2BGK8
    Conserved Domains (5) summary
    cd12284
    Location:233 → 305
    RRM2_RBM23_RBM39; RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins
    cd12285
    Location:401 → 485
    RRM3_RBM39_like; RNA recognition motif 3 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins
    cd12536
    Location:133 → 217
    RRM1_RBM39; RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39)
    TIGR01622
    Location:76 → 496
    SF-CC1; splicing factor, CC1-like family
    pfam15519
    Location:322 → 417
    RBM39linker; linker between RRM2 and RRM3 domains in RBM39 protein

  4. XM_005169277.4 → XP_005169334.1  RNA-binding protein 39 isoform X2

    See identical proteins and their annotated locations for XP_005169334.1

    UniProtKB/TrEMBL
    A0A2R8QAM8, A0A8M2BGK8
    Related
    ENSDARP00000150420.1, ENSDART00000186418.1
    Conserved Domains (5) summary
    cd12284
    Location:233 → 305
    RRM2_RBM23_RBM39; RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins
    cd12285
    Location:401 → 485
    RRM3_RBM39_like; RNA recognition motif 3 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins
    cd12536
    Location:133 → 217
    RRM1_RBM39; RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39)
    TIGR01622
    Location:76 → 496
    SF-CC1; splicing factor, CC1-like family
    pfam15519
    Location:322 → 417
    RBM39linker; linker between RRM2 and RRM3 domains in RBM39 protein

  5. XM_021479585.1 → XP_021335260.1  RNA-binding protein 39 isoform X3

    UniProtKB/TrEMBL
    A0A8M9QLK0
    Conserved Domains (1) summary
    TIGR01622
    Location:1 → 358
    SF-CC1; splicing factor, CC1-like family
Nucleotide Protein Strain
Heading Accession and Version

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