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    khdrbs1a KH domain containing, RNA binding, signal transduction associated 1a [ Danio rerio (zebrafish) ]

    Gene ID: 30082, updated on 9-Dec-2024

    Summary

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    Official Symbol
    khdrbs1aprovided by ZNC
    Official Full Name
    KH domain containing, RNA binding, signal transduction associated 1aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-000210-25
    See related
    Ensembl:ENSDARG00000052856 AllianceGenome:ZFIN:ZDB-GENE-000210-25
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    p62; fa18g12; fa56c01; fc91b01; fj90g10; khdrbs1; wu:fa18g12; wu:fa56c01; wu:fc91b01; wu:fj90g10; zgc:113899
    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 digestive system; fin; integument; nervous system; and pleuroperitoneal region. Orthologous to human KHDRBS1 (KH RNA binding domain containing, signal transduction associated 1). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See khdrbs1a in Genome Data Viewer
    Location:
    chromosome: 13
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 13 NC_007124.7 (45009957..45022319, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 13 NC_007124.6 (44873052..44885470, complement)

    Chromosome 13 - NC_007124.7Genomic Context describing neighboring genes Neighboring gene si:dkeyp-2e4.2 Neighboring gene zinc finger and BTB domain containing 8 opposite strand Neighboring gene V-set domain-containing T-cell activation inhibitor 1 Neighboring gene calcineurin-like EF-hand protein 1 Neighboring gene RUNX family transcription factor 3

    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. The tissue-specific RNA binding protein T-STAR controls regional splicing patterns of neurexin pre-mRNAs in the brain. Ehrmann I, et al. PLoS Genet, 2013 Apr. PMID 23637638, Free PMC Article
    2. mRNA localization patterns in zebrafish oocytes. Howley C, et al. Mech Dev, 2000 Apr. PMID 10727871
    3. 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine induced Parkinson's disease in zebrafish. Sarath Babu N, et al. Proteomics, 2016 May. PMID 26959078
    4. Detection of biomarkers to differentiate endocrine disruption from hepatotoxicity in zebrafish (Danio rerio) using proteomics. Ayobahan SU, et al. Chemosphere, 2020 Feb. PMID 31726584
    5. 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

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC113899

    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 1a
    Names
    GAP-associated phosphoprotein p62
    KH domain containing, RNA binding, signal transduction associated 1

    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_001362251.1 → NP_001349180.1  KH domain-containing, RNA-binding, signal transduction-associated protein 1a isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice junction in the 3' end compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is 1 aa shorter compared to isoform 1.
      Source sequence(s)
      CR376783
      UniProtKB/TrEMBL
      A0A8M3AZE9, A2CE73
      Related
      ENSDARP00000145957.1, ENSDART00000183589.1
      Conserved Domains (3) summary
      cd02395
      Location:70 → 190
      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:17 → 65
      Qua1; Qua1 domain
      pfam16568
      Location:289 → 339
      Sam68-YY; Tyrosine-rich domain of Sam68

    2. NM_001362252.1 → NP_001349181.1  KH domain-containing, RNA-binding, signal transduction-associated protein 1a isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus compard to isoform 1.
      Source sequence(s)
      CR376783
      Related
      ENSDARP00000138873.1, ENSDART00000159021.2
      Conserved Domains (3) summary
      cd02395
      Location:70 → 190
      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:17 → 65
      Qua1; Qua1 domain
      pfam16568
      Location:289 → 314
      Sam68-YY; Tyrosine-rich domain of Sam68

    3. NM_130925.2 → NP_571000.1  KH domain-containing, RNA-binding, signal transduction-associated protein 1a isoform 1

      See identical proteins and their annotated locations for NP_571000.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      CR376783
      UniProtKB/TrEMBL
      A0A8N7UZE2, Q6NW56
      Related
      ENSDARP00000069273.3, ENSDART00000074787.4
      Conserved Domains (3) summary
      cd02395
      Location:70 → 190
      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:17 → 65
      Qua1; Qua1 domain
      pfam16568
      Location:289 → 340
      Sam68-YY; Tyrosine-rich domain of Sam68

    RNA

    1. NR_155504.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      CR376783

    2. NR_155505.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      CR376783

    3. NR_155506.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      CR376783

    4. NR_155507.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      CR376783

    5. NR_155508.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      CR376783

    6. NR_155509.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      CR376783

    7. NR_155510.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      CR376783

    8. NR_155512.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      CR376783

    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_007124.7 Reference GRCz11 Primary Assembly

      Range
      45009957..45022319 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_009307570.4 → XP_009305845.1  KH domain-containing, RNA-binding, signal transduction-associated protein 1a isoform X1

      UniProtKB/TrEMBL
      A0A8M6Z928
      Conserved Domains (3) summary
      cd02395
      Location:70 → 190
      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 ...
      pfam15359
      Location:252 → 291
      CDV3; Carnitine deficiency-associated protein 3
      pfam16274
      Location:17 → 65
      Qua1; Qua1 domain

    2. XM_017358677.3 → XP_017214166.1  KH domain-containing, RNA-binding, signal transduction-associated protein 1a isoform X1

      UniProtKB/TrEMBL
      A0A8M6Z928
      Conserved Domains (3) summary
      cd02395
      Location:70 → 190
      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 ...
      pfam15359
      Location:252 → 291
      CDV3; Carnitine deficiency-associated protein 3
      pfam16274
      Location:17 → 65
      Qua1; Qua1 domain

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001030142.1: Suppressed sequence

      Description
      NM_001030142.1: This RefSeq was permanently suppressed because it is based on a chimeric sequence.
    Nucleotide Protein
    Heading Accession and Version

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