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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

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
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Genomic context

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

Expression

  • 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

General gene information

Markers

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

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_001362251.1NP_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:70190
    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:1765
    Qua1; Qua1 domain
    pfam16568
    Location:289339
    Sam68-YY; Tyrosine-rich domain of Sam68
  2. NM_001362252.1NP_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:70190
    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:1765
    Qua1; Qua1 domain
    pfam16568
    Location:289314
    Sam68-YY; Tyrosine-rich domain of Sam68
  3. NM_130925.2NP_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:70190
    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:1765
    Qua1; Qua1 domain
    pfam16568
    Location:289340
    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_009307570.4XP_009305845.1  KH domain-containing, RNA-binding, signal transduction-associated protein 1a isoform X1

    UniProtKB/TrEMBL
    A0A8M6Z928
    Conserved Domains (3) summary
    cd02395
    Location:70190
    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:252291
    CDV3; Carnitine deficiency-associated protein 3
    pfam16274
    Location:1765
    Qua1; Qua1 domain
  2. XM_017358677.3XP_017214166.1  KH domain-containing, RNA-binding, signal transduction-associated protein 1a isoform X1

    UniProtKB/TrEMBL
    A0A8M6Z928
    Conserved Domains (3) summary
    cd02395
    Location:70190
    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:252291
    CDV3; Carnitine deficiency-associated protein 3
    pfam16274
    Location:1765
    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.