runx1 RUNX family transcription factor 1 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: runx1provided by ZNC
Official Full Name: RUNX family transcription factor 1provided by ZNC
Primary source: ZFIN:ZDB-GENE-000605-1
See related: Ensembl:ENSDARG00000087646 AllianceGenome:ZFIN:ZDB-GENE-000605-1
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: runxa
Summary: Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in several processes, including cardiac muscle tissue regeneration; positive regulation of collagen biosynthetic process; and regulation of connective tissue replacement. Acts upstream of or within several processes, including endothelial to hematopoietic transition; hemopoiesis; and regulation of gene expression. Predicted to be located in nucleus. Is expressed in several structures, including cranial ganglion; hematopoietic cell; hematopoietic system; mesoderm; and vasculature. Human ortholog(s) of this gene implicated in acute myeloid leukemia and esophagus squamous cell carcinoma. Orthologous to human RUNX1 (RUNX family transcription factor 1). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 1

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	1	NC_007112.7 (1358644..1496652, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	1	NC_007112.6 (1241703..1253991, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	Unplaced Scaffold	NW_003334029.1 (7866..22130)

Chromosome 1 - NC_007112.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development.
Title: Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development.
Runx1 regulates zebrafish neutrophil maturation via synergistic interaction with c-Myb.
Title: Runx1 regulates zebrafish neutrophil maturation via synergistic interaction with c-Myb.
Dysregulation of NIPBL leads to impaired RUNX1 expression and haematopoietic defects.
Title: Dysregulation of NIPBL leads to impaired RUNX1 expression and haematopoietic defects.
Runx1 promotes scar deposition and inhibits myocardial proliferation and survival during zebrafish heart regeneration.
Title: Runx1 promotes scar deposition and inhibits myocardial proliferation and survival during zebrafish heart regeneration.
Enrichment of hematopoietic stem/progenitor cells in the zebrafish kidney.
Title: Enrichment of hematopoietic stem/progenitor cells in the zebrafish kidney.
Our data suggest that runx1 and cbfb are required at 2 different steps during early hematopoietic stem cell development
Title: CBFβ and RUNX1 are required at 2 different steps during the development of hematopoietic stem cells in zebrafish.
We propose that cohesin and CTCF have distinct functions in the regulation of runx1 during zebrafish embryogenesis.
Title: Cohesin and CTCF differentially regulate spatiotemporal runx1 expression during zebrafish development.
Morpholino knockdown of Myef2 or Runx1 in zebrafish results in reduced numbers of hematopoietic stem cells, suggesting that these two factors also interact in vivo to regulate hematopoiesis.
Title: A novel complex, RUNX1-MYEF2, represses hematopoietic genes in erythroid cells.
Runx1 is induced by high Pu.1 level and in turn transrepresses pu.1 expression, thus constituting a negative feedback loop that fashions a favorable Pu.1 level required for balanced fate commitment to neutrophils versus macrophages.
Title: Runx1 regulates embryonic myeloid fate choice in zebrafish through a negative feedback loop inhibiting Pu.1 expression.
hematopoietic stem cell numbers depended on activity of the transcription factor Runx1, on blood flow, and on proper development of the dorsal aorta
Title: Live imaging of Runx1 expression in the dorsal aorta tracks the emergence of blood progenitors from endothelial cells.

Submit: New GeneRIF Correction See all GeneRIFs (12)

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
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within B cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within blood vessel development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cardiac muscle tissue regeneration	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 definitive hemopoiesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic hemopoiesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within endothelial to hematopoietic transition	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	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within myeloid cell differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within myeloid cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within myeloid leukocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within neutrophil differentiation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in ossification	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of collagen biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of extracellular matrix organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of gene expression	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of neutrophil differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of regulation of cardiac muscle cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of connective tissue replacement	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of hematopoietic progenitor cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of myeloid cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of neutrophil differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of plasminogen activation	IMP Inferred from Mutant Phenotype more info	PubMed
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 1

Names: aml1; runt-related transcription factor a; runx1a

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_131603.3 → NP_571678.1 runt-related transcription factor 1

See identical proteins and their annotated locations for NP_571678.1

Status: VALIDATED

Source sequence(s)

CZQB01066254, CZQB01066256, LO018592

UniProtKB/TrEMBL

A0A8N7XJB6, F1QAL3, Q78BK7, Q9DGB8

Related

ENSDARP00000112019.3, ENSDART00000130697.3

Conserved Domains (3) summary

pfam00853
Location:63 → 184

Runt; Runt domain

pfam08504
Location:359 → 451

RunxI; Runx inhibition domain

cl26464
Location:160 → 426

Atrophin-1; Atrophin-1 family

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_007112.7 Reference GRCz11 Primary Assembly

Range

1358644..1496652 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_068220752.1 → XP_068076853.1 runt-related transcription factor 1 isoform X1
XM_021475832.2 → XP_021331507.1 runt-related transcription factor 1 isoform X2

UniProtKB/TrEMBL

A0A8M9PJ75

Conserved Domains (2) summary

pfam00853
Location:63 → 182

Runt; Runt domain

pfam08504
Location:303 → 395

RunxI; Runx inhibition domain