RUNX1 RUNX family transcription factor 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: RUNX1provided by HGNC
Official Full Name: RUNX family transcription factor 1provided by HGNC
Primary source: HGNC:HGNC:10471
See related: Ensembl:ENSG00000159216 MIM:151385; AllianceGenome:HGNC:10471
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: AML1; CBFA2; EVI-1; AMLCR1; PEBP2aB; CBF2alpha; AML1-EVI-1; PEBP2alpha
Summary: Core binding factor (CBF) is a heterodimeric transcription factor that binds to the core element of many enhancers and promoters. The protein encoded by this gene represents the alpha subunit of CBF and is thought to be involved in the development of normal hematopoiesis. Chromosomal translocations involving this gene are well-documented and have been associated with several types of leukemia. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression: Broad expression in appendix (RPKM 7.9), bone marrow (RPKM 7.3) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 21q22.12

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	21	NC_000021.9 (34787801..35049302, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	21	NC_060945.1 (33170406..33432142, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	21	NC_000021.8 (36160098..36421599, complement)

Chromosome 21 - NC_000021.9 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: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CDK9 phosphorylates RUNX1 to promote megakaryocytic fate in megakaryocytic-erythroid progenitors.
Title: CDK9 phosphorylates RUNX1 to promote megakaryocytic fate in megakaryocytic-erythroid progenitors.
RUNX1-PDIA5 Axis Promotes Malignant Progression of Glioblastoma by Regulating CCAR1 Protein Expression.
Title: RUNX1-PDIA5 Axis Promotes Malignant Progression of Glioblastoma by Regulating CCAR1 Protein Expression.
RUNX1 interacts with lncRNA SMANTIS to regulate monocytic cell functions.
Title: RUNX1 interacts with lncRNA SMANTIS to regulate monocytic cell functions.
RUNX1/miR-429 feedback loop promotes growth, metastasis, and epithelial-mesenchymal transition in oral squamous cell carcinoma by targeting ITGB1.
Title: RUNX1/miR-429 feedback loop promotes growth, metastasis, and epithelial-mesenchymal transition in oral squamous cell carcinoma by targeting ITGB1.
[Acute myeloid leukemia with mutated RUNX1 at the university hospitals of Strasbourg].
Title: [Acute myeloid leukemia with mutated RUNX1 at the university hospitals of Strasbourg].
RUNX1 regulates promoter activity in the absence of cognate DNA binding motifs.
Title: RUNX1 regulates promoter activity in the absence of cognate DNA binding motifs.
RUNX1-induced upregulation of PTGS2 enhances cell growth, migration and invasion in colorectal cancer cells.
Title: RUNX1-induced upregulation of PTGS2 enhances cell growth, migration and invasion in colorectal cancer cells.
A novel t(X;21)(p11.4;q22.12) translocation adds to the role of BCOR and RUNX1 in myelodysplastic syndromes and acute myeloid leukemias.
Title: A novel t(X;21)(p11.4;q22.12) translocation adds to the role of BCOR and RUNX1 in myelodysplastic syndromes and acute myeloid leukemias.
The role of RUNX1/NF-kappaB in regulating PVAT inflammation in aortic dissection.
Title: The role of RUNX1/NF-κB in regulating PVAT inflammation in aortic dissection.
RUNX1-BMP2 promotes vasculogenic mimicry in laryngeal squamous cell carcinoma via activation of the PI3K-AKT signaling pathway.
Title: RUNX1-BMP2 promotes vasculogenic mimicry in laryngeal squamous cell carcinoma via activation of the PI3K-AKT signaling pathway.

Submit: New GeneRIF Correction See all GeneRIFs (761)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Acute myeloid leukemia MedGen: C0023467 OMIM: 601626 GeneReviews: CEBPA-Associated Familial Acute Myeloid Leukemia (AML), ETV6 Thrombocytopenia and Predisposition to Leukemia, RUNX1 Familial Platelet Disorder with Associated Myeloid Malignancies, DDX41-Associated Familial Myelodysplastic Syndrome and Acute Myeloid Leukemia	Compare labs
Hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1 MedGen: C1832388 OMIM: 601399 GeneReviews: RUNX1 Familial Platelet Disorder with Associated Myeloid Malignancies	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2023-06-14) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2023-06-14) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Genetic loci associated with plasma phospholipid n-3 fatty acids: a meta-analysis of genome-wide association studies from the CHARGE Consortium. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetics of rheumatoid arthritis contributes to biology and drug discovery. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies three new susceptibility loci for esophageal squamous-cell carcinoma in Chinese populations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of antibody response to smallpox vaccine. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of pre-eclampsia detects novel maternal single nucleotide polymorphisms and copy-number variants in subsets of the Hyperglycemia and Adverse Pregnancy Outcome (HAPO) study cohort. EBI GWAS Catalog EBI GWAS CatalogPubMed
Joint analysis of three genome-wide association studies of esophageal squamous cell carcinoma in Chinese populations. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Vif	vif	HIV-1 Vif inhibits RUNX1 transcriptional activator by binding CBFB, which can be disrupted by mutating residue F68 in CBFB	PubMed
	vif	The binding of HIV-1 Vif to CBF-beta is mutually exclusive of endogenous RUNX transcriptional factors in cells. Vif inhibits transcription of a RUNX1 reporter gene by competition with CBF-beta	PubMed
	vif	HIV-1 Vif modulates cellular gene expression with RUNX1-associated regulatory domains	PubMed
	vif	The C-terminal tail (residues 131-182) of CBFbeta is dispensable for both Vif-induced A3G degradation and RUNX1-mediated gene transcription	PubMed
	vif	CBFbeta1-130, but not CBFbeta1-126, can fully support RUNX1-mediated gene transcription, indicating CBFbeta acts through different domains in its interaction with Vif and RUNX1	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-52097 (e-PCR)
- UniSTS:82695

GDB:185177 (e-PCR)
- UniSTS:155432

D21S1895 (e-PCR)
- UniSTS:16185

Runx1 (e-PCR), detects polymorphism
- UniSTS:259137

RUNX1_4181 (e-PCR)
- UniSTS:462924

SHGC-6907 (e-PCR)
- UniSTS:66893

SHGC-52137 (e-PCR)
- UniSTS:69218

RH92717 (e-PCR)
- UniSTS:92530

SHGC-82960 (e-PCR)
- UniSTS:96117

D21S1969 (e-PCR)
- UniSTS:38282

RH118473 (e-PCR)
- UniSTS:137868

D21S1921 (e-PCR)
- UniSTS:39573

D21S393 (e-PCR)
- UniSTS:147862

D21S1706 (e-PCR)
- UniSTS:150422

PMC19472P9 (e-PCR)
- UniSTS:271783

G34720 (e-PCR)
- UniSTS:37033

SHGC-170125 (e-PCR)
- UniSTS:173751

Runx1 (e-PCR), detects polymorphism
- UniSTS:141241

SHGC-6871 (e-PCR)
- UniSTS:86717

SHGC-51918 (e-PCR)
- UniSTS:70847

G34658 (e-PCR)
- UniSTS:48589

RH27207 (e-PCR)
- UniSTS:84944

SHGC-87612 (e-PCR)
- UniSTS:24787

RH98631 (e-PCR)
- UniSTS:92121

Runx1 (e-PCR), detects polymorphism
- UniSTS:547547

SHGC-87606 (e-PCR)
- UniSTS:56027

Runx1 (e-PCR), detects polymorphism
- UniSTS:547548

RH81059 (e-PCR)
- UniSTS:92392

SHGC-78899 (e-PCR)
- UniSTS:95730

D21S326 (e-PCR)
- UniSTS:147710

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables calcium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein heterodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables transcription cis-regulatory region binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription coactivator binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription corepressor binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cardiac muscle tissue regeneration	ISS Inferred from Sequence or Structural Similarity more info
involved_in chondrocyte differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in hematopoietic stem cell proliferation	TAS Traceable Author Statement more info	PubMed
involved_in hemopoiesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in hemopoiesis	IDA Inferred from Direct Assay more info	PubMed
involved_in hemopoiesis	TAS Traceable Author Statement more info	PubMed
involved_in myeloid cell differentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in myeloid leukocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of CD4-positive, alpha-beta T cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of granulocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity 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 peripheral nervous system neuron development	TAS Traceable Author Statement more info	PubMed
involved_in positive regulation of CD8-positive, alpha-beta T cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of angiogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of collagen biosynthetic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of extracellular matrix organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of granulocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of interleukin-2 production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of regulation of cardiac muscle cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of connective tissue replacement	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within regulation of plasminogen activation	ISS Inferred from Sequence or Structural Similarity 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 chromatin	ISA Inferred from Sequence Alignment more info
part_of core-binding factor complex	TAS Traceable Author Statement more info	PubMed
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	TAS Traceable Author Statement more info	PubMed

General protein information

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Preferred Names: runt-related transcription factor 1

Names: AML1-ETO fusion; AML1-ETO fusion protein; AML1-EVI-1 fusion protein; PEA2-alpha B; PEBP2-alpha B; SL3-3 enhancer factor 1 alpha B subunit; SL3/AKV core-binding factor alpha B subunit; acute myeloid leukemia 1 protein; core-binding factor, runt domain, alpha subunit 2; mutant RUNX1; oncogene AML-1; polyomavirus enhancer-binding protein 2 alpha B subunit; runt related transcription factor 1

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.

Genomic

NG_011402.2 RefSeqGene

Range

940414..1201911

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_482

mRNA and Protein(s)

NM_001001890.3 → NP_001001890.1 runt-related transcription factor 1 isoform AML1b

See identical proteins and their annotated locations for NP_001001890.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and coding region compared to variant 1. The resulting isoform (AML1b) is shorter and has a distinct N-terminus compared to isoform AML1c.

Source sequence(s)

AP000330, AP000331, D43968

Consensus CDS

CCDS42922.1

UniProtKB/Swiss-Prot

A8MV94, B2RMS4, D3DSG1, O60472, O60473, O76047, O76089, Q01196, Q13081, Q13755, Q13756, Q13757, Q13758, Q13759, Q15341, Q15343, Q16284, Q16285, Q16286

UniProtKB/TrEMBL

H9KVB1

Related

ENSP00000340690.4, ENST00000344691.8

Conserved Domains (2) summary

pfam00853
Location:58 → 179

Runt; Runt domain

pfam08504
Location:362 → 453

RunxI; Runx inhibition domain
NM_001122607.2 → NP_001116079.1 runt-related transcription factor 1 isoform AML1a

See identical proteins and their annotated locations for NP_001116079.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and coding region as well as the 3' UTR and coding region compared to variant 1. The resulting isoform (AML1a) is shorter and has distinct N- and C-termini compared to isoform AML1c.

Source sequence(s)

AP000331, D43967

Consensus CDS

CCDS46646.1

UniProtKB/TrEMBL

A8MZI9

Related

ENSP00000351123.5, ENST00000358356.9

Conserved Domains (1) summary

pfam00853
Location:58 → 179

Runt; Runt domain
NM_001754.5 → NP_001745.2 runt-related transcription factor 1 isoform AML1c

See identical proteins and their annotated locations for NP_001745.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest isoform (AML1c).

Source sequence(s)

AF015262, AP000330, U19601

Consensus CDS

CCDS13639.1

UniProtKB/TrEMBL

H9KVB1

Related

ENSP00000501943.1, ENST00000675419.1

Conserved Domains (2) summary

pfam00853
Location:81 → 207

Runt; Runt domain

pfam08504
Location:389 → 480

RunxI; Runx inhibition domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000021.9 Reference GRCh38.p14 Primary Assembly

Range

34787801..35049302 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011529768.3 → XP_011528070.1 runt-related transcription factor 1 isoform X6

UniProtKB/TrEMBL

H9KVB1

Conserved Domains (2) summary

pfam00853
Location:72 → 192

Runt; Runt domain

pfam08504
Location:312 → 403

RunxI; Runx inhibition domain
XM_011529767.3 → XP_011528069.1 runt-related transcription factor 1 isoform X3

See identical proteins and their annotated locations for XP_011528069.1

UniProtKB/TrEMBL

H9KVB1

Conserved Domains (2) summary

pfam00853
Location:68 → 194

Runt; Runt domain

pfam08504
Location:376 → 467

RunxI; Runx inhibition domain
XM_005261069.5 → XP_005261126.1 runt-related transcription factor 1 isoform X4

UniProtKB/TrEMBL

H9KVB1

Conserved Domains (2) summary

pfam00853
Location:81 → 207

Runt; Runt domain

pfam08504
Location:325 → 416

RunxI; Runx inhibition domain
XM_047441015.1 → XP_047296971.1 runt-related transcription factor 1 isoform X6

UniProtKB/TrEMBL

H9KVB1
XM_047441010.1 → XP_047296966.1 runt-related transcription factor 1 isoform X3

UniProtKB/TrEMBL

H9KVB1
XM_047441012.1 → XP_047296968.1 runt-related transcription factor 1 isoform X4

UniProtKB/TrEMBL

H9KVB1
XM_011529766.3 → XP_011528068.1 runt-related transcription factor 1 isoform X1

See identical proteins and their annotated locations for XP_011528068.1

UniProtKB/TrEMBL

H9KVB1

Conserved Domains (2) summary

pfam00853
Location:81 → 207

Runt; Runt domain

pfam08504
Location:389 → 480

RunxI; Runx inhibition domain
XM_047441014.1 → XP_047296970.1 runt-related transcription factor 1 isoform X6

UniProtKB/TrEMBL

H9KVB1
XM_047441009.1 → XP_047296965.1 runt-related transcription factor 1 isoform X3

UniProtKB/TrEMBL

H9KVB1
XM_047441011.1 → XP_047296967.1 runt-related transcription factor 1 isoform X4

UniProtKB/TrEMBL

H9KVB1
XM_047441007.1 → XP_047296963.1 runt-related transcription factor 1 isoform X1

UniProtKB/TrEMBL

H9KVB1

Related

ENSP00000300305.3, ENST00000300305.7
XM_047441013.1 → XP_047296969.1 runt-related transcription factor 1 isoform X5

UniProtKB/TrEMBL

H9KVB1

Related

ENSP00000382184.1, ENST00000399240.5
XM_005261068.4 → XP_005261125.1 runt-related transcription factor 1 isoform X2

See identical proteins and their annotated locations for XP_005261125.1

UniProtKB/TrEMBL

H9KVB1

Conserved Domains (2) summary

pfam00853
Location:73 → 194

Runt; Runt domain

pfam08504
Location:377 → 468

RunxI; Runx inhibition domain
XM_011529770.3 → XP_011528072.1 runt-related transcription factor 1 isoform X8

UniProtKB/TrEMBL

A8MZI9

Conserved Domains (1) summary

pfam00853
Location:85 → 206

Runt; Runt domain
XM_047441016.1 → XP_047296972.1 runt-related transcription factor 1 isoform X7

Alternate T2T-CHM13v2.0

Genomic

NC_060945.1 Alternate T2T-CHM13v2.0

Range

33170406..33432142 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054324898.1 → XP_054180873.1 runt-related transcription factor 1 isoform X3

UniProtKB/TrEMBL

H9KVB1
XM_054324899.1 → XP_054180874.1 runt-related transcription factor 1 isoform X3

UniProtKB/TrEMBL

H9KVB1
XM_054324901.1 → XP_054180876.1 runt-related transcription factor 1 isoform X4

UniProtKB/TrEMBL

H9KVB1
XM_054324894.1 → XP_054180869.1 runt-related transcription factor 1 isoform X1

UniProtKB/TrEMBL

H9KVB1
XM_054324905.1 → XP_054180880.1 runt-related transcription factor 1 isoform X6

UniProtKB/TrEMBL

H9KVB1
XM_054324902.1 → XP_054180877.1 runt-related transcription factor 1 isoform X4

UniProtKB/TrEMBL

H9KVB1
XM_054324895.1 → XP_054180870.1 runt-related transcription factor 1 isoform X1

UniProtKB/TrEMBL

H9KVB1
XM_054324904.1 → XP_054180879.1 runt-related transcription factor 1 isoform X6

UniProtKB/TrEMBL

H9KVB1
XM_054324897.1 → XP_054180872.1 runt-related transcription factor 1 isoform X3

UniProtKB/TrEMBL

H9KVB1
XM_054324900.1 → XP_054180875.1 runt-related transcription factor 1 isoform X4

UniProtKB/TrEMBL

H9KVB1
XM_054324903.1 → XP_054180878.1 runt-related transcription factor 1 isoform X5

UniProtKB/TrEMBL

H9KVB1
XM_054324896.1 → XP_054180871.1 runt-related transcription factor 1 isoform X2

UniProtKB/TrEMBL

H9KVB1
XM_054324907.1 → XP_054180882.1 runt-related transcription factor 1 isoform X8

UniProtKB/TrEMBL

A8MZI9
XM_054324906.1 → XP_054180881.1 runt-related transcription factor 1 isoform X9