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khdc4 KH domain containing 4, pre-mRNA splicing factor [ Danio rerio (zebrafish) ]

Gene ID: 321686, updated on 2-Nov-2024

Summary

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Official Symbol
khdc4provided by ZNC
Official Full Name
KH domain containing 4, pre-mRNA splicing factorprovided by ZNC
Primary source
ZFIN:ZDB-GENE-030131-405
See related
Ensembl:ENSDARG00000035023 AllianceGenome:ZFIN:ZDB-GENE-030131-405
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
kiaa0907; wu:fb26g02; si:zfos-1192g2.2
Summary
Predicted to enable RNA binding activity. Predicted to be involved in mRNA splice site recognition. Predicted to act upstream of or within RNA splicing and mRNA processing. Predicted to be located in cytoplasm. Predicted to be part of spliceosomal complex. Predicted to be active in nucleus. Orthologous to human KHDC4 (KH domain containing 4, pre-mRNA splicing factor). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs
human mouse all
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Genomic context

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See khdc4 in Genome Data Viewer
Location:
chromosome: 16
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 16 NC_007127.7 (54785264..54800202, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 16 NC_007127.6 (54911225..54926163, complement)

Chromosome 16 - NC_007127.7Genomic Context describing neighboring genes Neighboring gene serine/threonine-protein kinase pim-2 Neighboring gene mitochondrial assembly of ribosomal large subunit 1 Neighboring gene uncharacterized LOC137488000 Neighboring gene zinc finger and BTB domain containing 7B

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. A cellular retinoic acid-binding protein from zebrafish (Danio rerio): cDNA sequence, phylogenetic analysis, mRNA expression, and gene linkage mapping. Sharma MK, et al. Gene, 2003 Jun 5. PMID 12853146
  2. The zebrafish gene map defines ancestral vertebrate chromosomes. Woods IG, et al. Genome Res, 2005 Sep. PMID 16109975, Free PMC Article
  3. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
  5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

See all (6) 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 IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables RNA binding ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within RNA splicing IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA splice site recognition ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  
part_of spliceosomal complex ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
KH homology domain-containing protein 4
Names
brings lots of money 7
pre-mRNA splicing factor protein khdc4
protein BLOM7

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_212593.1 → NP_997758.1  KH homology domain-containing protein 4

    See identical proteins and their annotated locations for NP_997758.1

    Status: PROVISIONAL

    Source sequence(s)
    BC045375
    UniProtKB/Swiss-Prot
    Q6NZ18, Q7ZVX3
    Related
    ENSDARP00000134042.2, ENSDART00000161833.3
    Conserved Domains (2) summary
    PHA03249
    Location:407 → 525
    PHA03249; DNA packaging tegument protein UL25; Provisional
    cl00098
    Location:207 → 311
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

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_007127.7 Reference GRCz11 Primary Assembly

    Range
    54785264..54800202 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005169775.5 → XP_005169832.1  KH homology domain-containing protein 4 isoform X4

    UniProtKB/Swiss-Prot
    Q6NZ18, Q7ZVX3
    UniProtKB/TrEMBL
    A0A8M2BH11, F1QQM1
    Related
    ENSDARP00000059559.5, ENSDART00000059560.8
    Conserved Domains (2) summary
    PHA03249
    Location:407 → 526
    PHA03249; DNA packaging tegument protein UL25; Provisional
    cl00098
    Location:207 → 311
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

  2. XM_005169774.5 → XP_005169831.1  KH homology domain-containing protein 4 isoform X2

    UniProtKB/Swiss-Prot
    Q6NZ18, Q7ZVX3
    UniProtKB/TrEMBL
    A0A8M2BH01
    Conserved Domains (2) summary
    PHA03249
    Location:407 → 527
    PHA03249; DNA packaging tegument protein UL25; Provisional
    cl00098
    Location:207 → 311
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

  3. XM_009292749.4 → XP_009291024.1  KH homology domain-containing protein 4 isoform X5

    UniProtKB/Swiss-Prot
    Q6NZ18, Q7ZVX3
    UniProtKB/TrEMBL
    A0A8M3AR35
    Conserved Domains (2) summary
    PHA03249
    Location:408 → 526
    PHA03249; DNA packaging tegument protein UL25; Provisional
    cl00098
    Location:208 → 312
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

  4. XM_009292748.4 → XP_009291023.1  KH homology domain-containing protein 4 isoform X3

    UniProtKB/Swiss-Prot
    Q6NZ18, Q7ZVX3
    UniProtKB/TrEMBL
    A0A8M3ATY7
    Conserved Domains (2) summary
    PHA03249
    Location:408 → 527
    PHA03249; DNA packaging tegument protein UL25; Provisional
    cl00098
    Location:208 → 312
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

  5. XM_009292747.4 → XP_009291022.1  KH homology domain-containing protein 4 isoform X1

    UniProtKB/Swiss-Prot
    Q6NZ18, Q7ZVX3
    UniProtKB/TrEMBL
    A0A8M3AJJ6
    Conserved Domains (2) summary
    PHA03249
    Location:408 → 528
    PHA03249; DNA packaging tegument protein UL25; Provisional
    cl00098
    Location:208 → 312
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6NZ18.1 GenPept UniProtKB/Swiss-Prot:Q6NZ18

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