runx3 RUNX family transcription factor 3 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: runx3provided by ZNC
Official Full Name: RUNX family transcription factor 3provided by ZNC
Primary source: ZFIN:ZDB-GENE-000605-2
See related: Ensembl:ENSDARG00000052826 AllianceGenome:ZFIN:ZDB-GENE-000605-2
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: runxb
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within cartilage development; embryonic viscerocranium morphogenesis; and hemopoiesis. Predicted to be located in nucleus. Is expressed in several structures, including Rohon-Beard neurons; digestive system; ganglia; oral epithelium; and skeletal element. Human ortholog(s) of this gene implicated in several diseases, including breast cancer (multiple); female reproductive organ cancer (multiple); lung non-small cell carcinoma; pancreatic cancer; and urinary bladder cancer. Orthologous to human RUNX3 (RUNX family transcription factor 3). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 13

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	13	NC_007124.7 (45092766..45201055, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	13	NC_007124.6 (44955862..45018380, complement)

Chromosome 13 - NC_007124.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages 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?

In neuronal fate determination, Runx co-factor Cbfbeta is essential for its function, but the high level of Runx3 expression can overcome the loss of Cbfbeta, demonstrating that Cbfbeta in this context serves solely as a signal amplifier of Runx3 activity.
Title: An ancient neurotrophin receptor code; a single Runx/Cbfβ complex determines somatosensory neuron fate specification in zebrafish.
successive induction of the transcription factors Runx3, Egr1 and Sox9b constitutes a regulatory cascade that controls expression of Follistatin A in pharyngeal endoderm, the latter modulating BMP signaling in developing cranial cartilage in zebrafish
Title: RUNX3, EGR1 and SOX9B form a regulatory cascade required to modulate BMP-signaling during cranial cartilage development in zebrafish.
Zebrafish embryos lacking Rad21, or cohesin subunit Smc3, fail to express runx3 and lose hematopoietic runx1 expression in early embryonic development.
Title: Cohesin-dependent regulation of Runx genes.
Runx3 expression leads to an increase in primitive blood cell numbers, together with an increase in runx1-expressing cells in the ventral wall of the dorsal aorta.
Title: Runx3 is required for hematopoietic development in zebrafish.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within cartilage development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chondrocyte differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within embryonic viscerocranium morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in epithelium development	IEA Inferred from Electronic Annotation more info
involved_in hemopoiesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within hemopoiesis	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within hemopoiesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in ossification	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: runt-related transcription factor 3

Names: runt-related transcription factor b

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_001362344.1 → NP_001349273.1 runt-related transcription factor 3 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

CABZ01078998, CABZ01083960, CT025744

Related

ENSDARP00000146778.1, ENSDART00000180265.1

Conserved Domains (2) summary

pfam00853
Location:69 → 190

Runt; Runt domain

pfam08504
Location:334 → 438

RunxI; Runx inhibition domain
NM_131604.3 → NP_571679.2 runt-related transcription factor 3 isoform 2

See identical proteins and their annotated locations for NP_571679.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.

Source sequence(s)

CABZ01083960, CT025744

UniProtKB/TrEMBL

A0A0R4ISE9, A0A0R4IYN7, Q9DEA0

Related

ENSDARP00000141377.2, ENSDART00000163556.2

Conserved Domains (2) summary

pfam00853
Location:55 → 176

Runt; Runt domain

pfam08504
Location:320 → 424

RunxI; Runx inhibition domain