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

Gene ID: 58127, updated on 6-Jul-2026
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, Jul 2025]
Orthologs
all
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Try the new Transcripts and proteins table
See runx3 in Genome Data Viewer
Location:
chromosome: 13
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2025_04 current GRCz12tu (GCF_049306965.1) 13 NC_133188.1 (48688697..48957705, complement)
RS_2024_08 previous assembly GRCz11 (GCF_000002035.6) 13 NC_007124.7 (45092766..45201055, complement)

Chromosome 13 - NC_133188.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC141377064 Neighboring gene calcineurin-like EF-hand protein 1 Neighboring gene uncharacterized LOC141377065 Neighboring gene uncharacterized LOC108191951 Neighboring gene uncharacterized LOC141377015 Neighboring gene SYF2 pre-mRNA-splicing factor Neighboring gene arginine/serine-rich protein 1

Go to nucleotide: Graphics FASTA GenBank

  • 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

Related articles in PubMed

  1. Pathways in blood and vessel development revealed through zebrafish genetics. Crosier PS, et al. Int J Dev Biol, 2002. PMID 12141436
  2. RAD21 mutations cause a human cohesinopathy. Deardorff MA, et al. Am J Hum Genet, 2012 Jun 8. PMID 22633399, Free PMC Article
  3. A hierarchy of Runx transcription factors modulate the onset of chondrogenesis in craniofacial endochondral bones in zebrafish. Flores MV, et al. Dev Dyn, 2006 Nov. PMID 17013873
  4. Transcriptional regulation of gilthead seabream bone morphogenetic protein (BMP) 2 gene by bone- and cartilage-related transcription factors. Marques CL, et al. Gene, 2016 Jan 15. PMID 26456102
  5. Runx1 is required for zebrafish blood and vessel development and expression of a human RUNX1-CBF2T1 transgene advances a model for studies of leukemogenesis. Kalev-Zylinska ML, et al. Development, 2002 Apr. PMID 11934867

See all (36) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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

Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
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
involved_in chondrocyte differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in hemopoiesis IBA
Inferred from Biological aspect of Ancestor
more info
  
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 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
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
Preferred Names
runt-related transcription factor 3
Names
runt-related transcription factor b

NEW Try the new Transcript table

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_001362344.2 → 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)
    JBMGRA010000013
    UniProtKB/TrEMBL
    A0AB32T1U3, A0AC58H1Y8, A0AC58H1Z1, A0AC58H1Z3, A0AC58H1Z5, A0AC58H1Z7, A0AC58H1Z8, A0AC58H201, A0AC58H202, A0AC58H203, A0AC58H210, A0AC58H211, A0AC58H215, A0AC58H216
    Related
    ENSDARP00000146778.1, ENSDART00000180265.1
    Conserved Domains (2) summary
    pfam00853
    Location:69 → 190
    Runt; Runt domain
    pfam08504
    Location:334 → 438
    RunxI; Runx inhibition domain

  2. NM_131604.4 → 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)
    JBMGRA010000013
    UniProtKB/TrEMBL
    A0A0R4ISE9, A0A0R4IYN7, A0A8M1PCD6, 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

RefSeqs of Annotated Genomes: GCF_049306965.1-RS_2025_04

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCz12tu Primary Assembly

Genomic

  1. NC_133188.1 Reference GRCz12tu Primary Assembly

    Range
    48688697..48957705 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_073919902.1 → XP_073776003.1  runt-related transcription factor 3 isoform X1

    UniProtKB/TrEMBL
    A0AB32T1U3, A0AC58H1Y8, A0AC58H1Z1, A0AC58H1Z3, A0AC58H1Z5, A0AC58H1Z7, A0AC58H1Z8, A0AC58H201, A0AC58H202, A0AC58H203, A0AC58H210, A0AC58H211, A0AC58H215, A0AC58H216

  2. XM_073919909.1 → XP_073776010.1  runt-related transcription factor 3 isoform X1

    UniProtKB/TrEMBL
    A0AB32T1U3, A0AC58H1Y8, A0AC58H1Z1, A0AC58H1Z3, A0AC58H1Z5, A0AC58H1Z7, A0AC58H1Z8, A0AC58H201, A0AC58H202, A0AC58H203, A0AC58H210, A0AC58H211, A0AC58H215, A0AC58H216

  3. XM_073919900.1 → XP_073776001.1  runt-related transcription factor 3 isoform X1

    UniProtKB/TrEMBL
    A0AB32T1U3, A0AC58H1Y8, A0AC58H1Z1, A0AC58H1Z3, A0AC58H1Z5, A0AC58H1Z7, A0AC58H1Z8, A0AC58H201, A0AC58H202, A0AC58H203, A0AC58H210, A0AC58H211, A0AC58H215, A0AC58H216

  4. XM_073919907.1 → XP_073776008.1  runt-related transcription factor 3 isoform X1

    UniProtKB/TrEMBL
    A0AB32T1U3, A0AC58H1Y8, A0AC58H1Z1, A0AC58H1Z3, A0AC58H1Z5, A0AC58H1Z7, A0AC58H1Z8, A0AC58H201, A0AC58H202, A0AC58H203, A0AC58H210, A0AC58H211, A0AC58H215, A0AC58H216

  5. XM_073919912.1 → XP_073776013.1  runt-related transcription factor 3 isoform X1

    UniProtKB/TrEMBL
    A0AB32T1U3, A0AC58H1Y8, A0AC58H1Z1, A0AC58H1Z3, A0AC58H1Z5, A0AC58H1Z7, A0AC58H1Z8, A0AC58H201, A0AC58H202, A0AC58H203, A0AC58H210, A0AC58H211, A0AC58H215, A0AC58H216

  6. XM_073919906.1 → XP_073776007.1  runt-related transcription factor 3 isoform X1

    UniProtKB/TrEMBL
    A0AB32T1U3, A0AC58H1Y8, A0AC58H1Z1, A0AC58H1Z3, A0AC58H1Z5, A0AC58H1Z7, A0AC58H1Z8, A0AC58H201, A0AC58H202, A0AC58H203, A0AC58H210, A0AC58H211, A0AC58H215, A0AC58H216

  7. XM_073919905.1 → XP_073776006.1  runt-related transcription factor 3 isoform X1

    UniProtKB/TrEMBL
    A0AB32T1U3, A0AC58H1Y8, A0AC58H1Z1, A0AC58H1Z3, A0AC58H1Z5, A0AC58H1Z7, A0AC58H1Z8, A0AC58H201, A0AC58H202, A0AC58H203, A0AC58H210, A0AC58H211, A0AC58H215, A0AC58H216

  8. XM_073919911.1 → XP_073776012.1  runt-related transcription factor 3 isoform X1

    UniProtKB/TrEMBL
    A0AB32T1U3, A0AC58H1Y8, A0AC58H1Z1, A0AC58H1Z3, A0AC58H1Z5, A0AC58H1Z7, A0AC58H1Z8, A0AC58H201, A0AC58H202, A0AC58H203, A0AC58H210, A0AC58H211, A0AC58H215, A0AC58H216

  9. XM_073919903.1 → XP_073776004.1  runt-related transcription factor 3 isoform X1

    UniProtKB/TrEMBL
    A0AB32T1U3, A0AC58H1Y8, A0AC58H1Z1, A0AC58H1Z3, A0AC58H1Z5, A0AC58H1Z7, A0AC58H1Z8, A0AC58H201, A0AC58H202, A0AC58H203, A0AC58H210, A0AC58H211, A0AC58H215, A0AC58H216

  10. XM_073919901.1 → XP_073776002.1  runt-related transcription factor 3 isoform X1

    UniProtKB/TrEMBL
    A0AB32T1U3, A0AC58H1Y8, A0AC58H1Z1, A0AC58H1Z3, A0AC58H1Z5, A0AC58H1Z7, A0AC58H1Z8, A0AC58H201, A0AC58H202, A0AC58H203, A0AC58H210, A0AC58H211, A0AC58H215, A0AC58H216

  11. XM_073919904.1 → XP_073776005.1  runt-related transcription factor 3 isoform X1

    UniProtKB/TrEMBL
    A0AB32T1U3, A0AC58H1Y8, A0AC58H1Z1, A0AC58H1Z3, A0AC58H1Z5, A0AC58H1Z7, A0AC58H1Z8, A0AC58H201, A0AC58H202, A0AC58H203, A0AC58H210, A0AC58H211, A0AC58H215, A0AC58H216

  12. XM_073919910.1 → XP_073776011.1  runt-related transcription factor 3 isoform X1

    UniProtKB/TrEMBL
    A0AB32T1U3, A0AC58H1Y8, A0AC58H1Z1, A0AC58H1Z3, A0AC58H1Z5, A0AC58H1Z7, A0AC58H1Z8, A0AC58H201, A0AC58H202, A0AC58H203, A0AC58H210, A0AC58H211, A0AC58H215, A0AC58H216

  13. XM_073919908.1 → XP_073776009.1  runt-related transcription factor 3 isoform X1

    UniProtKB/TrEMBL
    A0AB32T1U3, A0AC58H1Y8, A0AC58H1Z1, A0AC58H1Z3, A0AC58H1Z5, A0AC58H1Z7, A0AC58H1Z8, A0AC58H201, A0AC58H202, A0AC58H203, A0AC58H210, A0AC58H211, A0AC58H215, A0AC58H216

  14. XM_073919913.1 → XP_073776014.1  runt-related transcription factor 3 isoform X2

    UniProtKB/TrEMBL
    A0AC58H200, A0AC58H204, A0AC58H205

  15. XM_073919914.1 → XP_073776015.1  runt-related transcription factor 3 isoform X2

    UniProtKB/TrEMBL
    A0AC58H200, A0AC58H204, A0AC58H205

  16. XM_073919915.1 → XP_073776016.1  runt-related transcription factor 3 isoform X2

    UniProtKB/TrEMBL
    A0AC58H200, A0AC58H204, A0AC58H205
Nucleotide Protein Strain
Heading Accession and Version

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