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    khdrbs1b KH domain containing, RNA binding, signal transduction associated 1b [ Danio rerio (zebrafish) ]

    Gene ID: 406516, updated on 9-Dec-2024

    Summary

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    Official Symbol
    khdrbs1bprovided by ZNC
    Official Full Name
    KH domain containing, RNA binding, signal transduction associated 1bprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040426-2344
    See related
    Ensembl:ENSDARG00000070475 AllianceGenome:ZFIN:ZDB-GENE-040426-2344
    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
    sb:cb97; khdrbs1l; zgc:85948; wu:fb07d11; wu:fi43c05
    Summary
    Enables mRNA 3'-UTR binding activity. Predicted to be involved in regulation of alternative mRNA splicing, via spliceosome. Predicted to act upstream of or within mRNA processing. Predicted to be active in nucleus. Is expressed in several structures, including gill; immature eye; nervous system; pleuroperitoneal region; and segmental plate. Orthologous to human KHDRBS1 (KH RNA binding domain containing, signal transduction associated 1). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See khdrbs1b in Genome Data Viewer
    Location:
    chromosome: 19
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 19 NC_007130.7 (30351032..30359046, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 19 NC_007130.6 (30760197..30771764, complement)

    Chromosome 19 - NC_007130.7Genomic Context describing neighboring genes Neighboring gene si:ch73-130a3.4 Neighboring gene karyopherin alpha 6 (importin alpha 7) Neighboring gene uncharacterized LOC137488528 Neighboring gene tetraspanin 13b Neighboring gene anterior gradient 2

    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. Genome wide analysis of 3' UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish. Vejnar CE, et al. Genome Res, 2019 Jul. PMID 31227602, Free PMC Article
    2. Evolutionary and Expression Analyses Show Co-option of khdrbs Genes for Origin of Vertebrate Brain. Wang S, et al. Front Genet, 2017. PMID 29354154, Free PMC Article
    3. Immune gene variation associated with chromosome-scale differences among individual zebrafish genomes. McConnell SC, et al. Sci Rep, 2023 May 13. PMID 37179373, Free PMC Article
    4. Hematopoietic gene expression profile in zebrafish kidney marrow. Song HD, et al. Proc Natl Acad Sci U S A, 2004 Nov 16. PMID 15520368, Free PMC Article
    5. 15000 unique zebrafish EST clusters and their future use in microarray for profiling gene expression patterns during embryogenesis. Lo J, et al. Genome Res, 2003 Mar. PMID 12618376, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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 mRNA 3'-UTR binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables poly(A) binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of alternative mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    KH domain-containing, RNA-binding, signal transduction-associated protein 1b
    Names
    KH domain containing RNA binding signal transduction associated 1 like

    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_213235.1 → NP_998400.1  KH domain-containing, RNA-binding, signal transduction-associated protein 1b

      See identical proteins and their annotated locations for NP_998400.1

      Status: PROVISIONAL

      Source sequence(s)
      BC067711
      UniProtKB/TrEMBL
      A9JT32, Q6NW62
      Related
      ENSDARP00000094247.4, ENSDART00000103471.5
      Conserved Domains (3) summary
      cd02395
      Location:60 → 178
      SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...
      pfam16274
      Location:7 → 56
      Qua1; Qua1 domain
      pfam16568
      Location:269 → 319
      Sam68-YY; Tyrosine-rich domain of Sam68

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007130.7 Reference GRCz11 Primary Assembly

      Range
      30351032..30359046 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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