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

Summary

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, Dec 2024]
Orthologs: human mouse all
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Genomic context

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_007127.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Markers

AI415764 (e-PCR)
- UniSTS:206646

fi17g09.x1 (e-PCR)
- UniSTS:196940

fb82h10.x1 (e-PCR)
- UniSTS:191700

fb82h10.x1 (e-PCR)
- UniSTS:191701

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)

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

NC_007127.7 Reference GRCz11 Primary Assembly

Range

54785264..54800202 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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 ...
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 ...
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 ...
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 ...
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 ...