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Protein

Runt-related transcription factor 3

Gene

RUNX3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

CBF binds to the core site, 5'-PYGPYGGT-3', of a number of enhancers and promoters, including murine leukemia virus, polyomavirus enhancer, T-cell receptor enhancers, lck, IL-3 and GM-CSF promoters.

GO - Molecular functioni

  1. ATP binding Source: UniProtKB
  2. RNA polymerase II regulatory region sequence-specific DNA binding Source: BHF-UCL
  3. sequence-specific DNA binding RNA polymerase II transcription factor activity Source: BHF-UCL
  4. sequence-specific DNA binding transcription factor activity Source: ProtInc

GO - Biological processi

  1. axon guidance Source: Ensembl
  2. cell maturation Source: Ensembl
  3. chondrocyte differentiation Source: Ensembl
  4. hair follicle morphogenesis Source: Ensembl
  5. interferon-gamma production Source: Ensembl
  6. negative regulation of cell cycle Source: UniProtKB
  7. negative regulation of epithelial cell proliferation Source: UniProtKB
  8. negative regulation of transcription from RNA polymerase II promoter Source: BHF-UCL
  9. peripheral nervous system neuron development Source: BHF-UCL
  10. positive regulation of extrinsic apoptotic signaling pathway Source: Ensembl
  11. protein phosphorylation Source: UniProtKB
  12. regulation of transcription, DNA-templated Source: UniProtKB
  13. transcription from RNA polymerase II promoter Source: ProtInc
Complete GO annotation...

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Runt-related transcription factor 3
Alternative name(s):
Acute myeloid leukemia 2 protein
Core-binding factor subunit alpha-3
Short name:
CBF-alpha-3
Oncogene AML-2
Polyomavirus enhancer-binding protein 2 alpha C subunit
Short name:
PEA2-alpha C
Short name:
PEBP2-alpha C
SL3-3 enhancer factor 1 alpha C subunit
SL3/AKV core-binding factor alpha C subunit
Gene namesi
Name:RUNX3
Synonyms:AML2, CBFA3, PEBP2A3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:10473. RUNX3.

Subcellular locationi

Nucleus PROSITE-ProRule annotation1 Publication. Cytoplasm 1 Publication
Note: The tyrosine phosphorylated form localizes to the cytoplasm.

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB
  2. Golgi apparatus Source: HPA
  3. intracellular membrane-bounded organelle Source: HPA
  4. nuclear chromatin Source: BHF-UCL
  5. nucleolus Source: HPA
  6. nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA34886.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 415415Runt-related transcription factor 3PRO_0000174662Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei243 – 2431Phosphoserine1 Publication

Post-translational modificationi

Phosphorylated on tyrosine residues by SRC. Phosphorylated by LCK and FYN.1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ13761.
PaxDbiQ13761.
PRIDEiQ13761.

PTM databases

PhosphoSiteiQ13761.

Expressioni

Gene expression databases

BgeeiQ13761.
CleanExiHS_RUNX3.
ExpressionAtlasiQ13761. baseline and differential.
GenevestigatoriQ13761.

Organism-specific databases

HPAiCAB025416.
HPA004195.
HPA059006.

Interactioni

Subunit structurei

Heterodimer of an alpha and a beta subunit. The alpha subunit binds DNA as a monomer and through the Runt domain. DNA-binding is increased by heterodimerization. Interacts with TLE1 and SUV39H1. The tyrosine phosphorylated form (via runt domain) interacts with SRC (via protein kinase domain). Interacts with FYN and LCK. Interacts with FOXP3.4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
BRD2P254408EBI-925990,EBI-2874802
CTNNB1P3522212EBI-925990,EBI-491549
EP300Q094727EBI-925990,EBI-447295
HDAC4P565249EBI-925990,EBI-308629
HDAC5Q9UQL65EBI-925990,EBI-715576
TCF7L2Q9NQB014EBI-925990,EBI-924724
TLE1Q047243EBI-925990,EBI-711424

Protein-protein interaction databases

BioGridi107312. 27 interactions.
IntActiQ13761. 15 interactions.
MINTiMINT-6774046.
STRINGi9606.ENSP00000343477.

Structurei

3D structure databases

ProteinModelPortaliQ13761.
SMRiQ13761. Positions 56-204.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini54 – 182129RuntPROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi23 – 275Poly-Gly
Compositional biasi191 – 415225Pro/Ser/Thr-richAdd
BLAST

Domaini

A proline/serine/threonine rich region at the C-terminus is necessary for transcriptional activation of target genes.

Sequence similaritiesi

Contains 1 Runt domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiNOG123889.
GeneTreeiENSGT00390000016964.
HOGENOMiHOG000045616.
HOVERGENiHBG060268.
InParanoidiQ13761.
KOiK09279.
OMAiTSRFHHT.
OrthoDBiEOG7WQ7TV.
PhylomeDBiQ13761.
TreeFamiTF321496.

Family and domain databases

Gene3Di2.60.40.720. 1 hit.
4.10.770.10. 1 hit.
InterProiIPR000040. AML1_Runt.
IPR008967. p53-like_TF_DNA-bd.
IPR012346. p53/RUNT-type_TF_DNA-bd.
IPR013524. Runt_dom.
IPR027384. Runx_central_dom.
IPR013711. RunxI_C_dom.
[Graphical view]
PANTHERiPTHR11950. PTHR11950. 1 hit.
PfamiPF00853. Runt. 1 hit.
PF08504. RunxI. 1 hit.
[Graphical view]
PRINTSiPR00967. ONCOGENEAML1.
SUPFAMiSSF49417. SSF49417. 1 hit.
PROSITEiPS51062. RUNT. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q13761-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MRIPVDPSTS RRFTPPSPAF PCGGGGGKMG ENSGALSAQA AVGPGGRARP
60 70 80 90 100
EVRSMVDVLA DHAGELVRTD SPNFLCSVLP SHWRCNKTLP VAFKVVALGD
110 120 130 140 150
VPDGTVVTVM AGNDENYSAE LRNASAVMKN QVARFNDLRF VGRSGRGKSF
160 170 180 190 200
TLTITVFTNP TQVATYHRAI KVTVDGPREP RRHRQKLEDQ TKPFPDRFGD
210 220 230 240 250
LERLRMRVTP STPSPRGSLS TTSHFSSQPQ TPIQGTSELN PFSDPRQFDR
260 270 280 290 300
SFPTLPTLTE SRFPDPRMHY PGAMSAAFPY SATPSGTSIS SLSVAGMPAT
310 320 330 340 350
SRFHHTYLPP PYPGAPQNQS GPFQANPSPY HLYYGTSSGS YQFSMVAGSS
360 370 380 390 400
SGGDRSPTRM LASCTSSAAS VAAGNLMNPS LGGQSDGVEA DGSHSNSPTA
410
LSTPGRMDEA VWRPY
Length:415
Mass (Da):44,356
Last modified:October 31, 1999 - v2
Checksum:i593FBFB3C4639BBD
GO
Isoform 2 (identifier: Q13761-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-5: MRIPV → MASNSIFDSFPTYSPTFIR

Show »
Length:429
Mass (Da):45,922
Checksum:iE9A43E96EDF82389
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti249 – 2491D → V in CAA56093 (PubMed:7835892).Curated
Sequence conflicti253 – 2531P → S in CAA56093 (PubMed:7835892).Curated
Sequence conflicti256 – 2561P → S in CAA56093 (PubMed:7835892).Curated
Sequence conflicti259 – 2591T → S in CAA56093 (PubMed:7835892).Curated
Sequence conflicti268 – 2692MH → IY in CAA56093 (PubMed:7835892).Curated
Sequence conflicti271 – 2711P → T in CAA56093 (PubMed:7835892).Curated
Sequence conflicti297 – 2982MP → IS in CAA56093 (PubMed:7835892).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 55MRIPV → MASNSIFDSFPTYSPTFIR in isoform 2. 1 PublicationVSP_005949

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z35278 mRNA. Translation: CAA84541.1.
X79550 mRNA. Translation: CAA56093.2.
AL023096 Genomic DNA. Translation: CAA18856.1.
AL445471, AL023096 Genomic DNA. Translation: CAC42093.2.
AL023096, AL445471 Genomic DNA. Translation: CAI20422.1.
CH471134 Genomic DNA. Translation: EAW95148.1.
BC013362 mRNA. Translation: AAH13362.1.
U14520 Genomic DNA. Translation: AAA86465.1.
CCDSiCCDS257.1. [Q13761-1]
CCDS30633.1. [Q13761-2]
PIRiB55563.
S60078.
RefSeqiNP_001026850.1. NM_001031680.2. [Q13761-2]
NP_004341.1. NM_004350.2. [Q13761-1]
XP_005246081.1. XM_005246024.2. [Q13761-2]
UniGeneiHs.170019.

Genome annotation databases

EnsembliENST00000308873; ENSP00000308051; ENSG00000020633. [Q13761-1]
ENST00000338888; ENSP00000343477; ENSG00000020633. [Q13761-2]
ENST00000399916; ENSP00000382800; ENSG00000020633. [Q13761-2]
GeneIDi864.
KEGGihsa:864.
UCSCiuc001bjq.3. human. [Q13761-1]
uc001bjr.3. human. [Q13761-2]

Polymorphism databases

DMDMi17368453.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z35278 mRNA. Translation: CAA84541.1.
X79550 mRNA. Translation: CAA56093.2.
AL023096 Genomic DNA. Translation: CAA18856.1.
AL445471, AL023096 Genomic DNA. Translation: CAC42093.2.
AL023096, AL445471 Genomic DNA. Translation: CAI20422.1.
CH471134 Genomic DNA. Translation: EAW95148.1.
BC013362 mRNA. Translation: AAH13362.1.
U14520 Genomic DNA. Translation: AAA86465.1.
CCDSiCCDS257.1. [Q13761-1]
CCDS30633.1. [Q13761-2]
PIRiB55563.
S60078.
RefSeqiNP_001026850.1. NM_001031680.2. [Q13761-2]
NP_004341.1. NM_004350.2. [Q13761-1]
XP_005246081.1. XM_005246024.2. [Q13761-2]
UniGeneiHs.170019.

3D structure databases

ProteinModelPortaliQ13761.
SMRiQ13761. Positions 56-204.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi107312. 27 interactions.
IntActiQ13761. 15 interactions.
MINTiMINT-6774046.
STRINGi9606.ENSP00000343477.

PTM databases

PhosphoSiteiQ13761.

Polymorphism databases

DMDMi17368453.

Proteomic databases

MaxQBiQ13761.
PaxDbiQ13761.
PRIDEiQ13761.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000308873; ENSP00000308051; ENSG00000020633. [Q13761-1]
ENST00000338888; ENSP00000343477; ENSG00000020633. [Q13761-2]
ENST00000399916; ENSP00000382800; ENSG00000020633. [Q13761-2]
GeneIDi864.
KEGGihsa:864.
UCSCiuc001bjq.3. human. [Q13761-1]
uc001bjr.3. human. [Q13761-2]

Organism-specific databases

CTDi864.
GeneCardsiGC01M025226.
HGNCiHGNC:10473. RUNX3.
HPAiCAB025416.
HPA004195.
HPA059006.
MIMi600210. gene.
neXtProtiNX_Q13761.
PharmGKBiPA34886.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG123889.
GeneTreeiENSGT00390000016964.
HOGENOMiHOG000045616.
HOVERGENiHBG060268.
InParanoidiQ13761.
KOiK09279.
OMAiTSRFHHT.
OrthoDBiEOG7WQ7TV.
PhylomeDBiQ13761.
TreeFamiTF321496.

Miscellaneous databases

ChiTaRSiRUNX3. human.
GeneWikiiRUNX3.
GenomeRNAii864.
NextBioi3602.
PROiQ13761.
SOURCEiSearch...

Gene expression databases

BgeeiQ13761.
CleanExiHS_RUNX3.
ExpressionAtlasiQ13761. baseline and differential.
GenevestigatoriQ13761.

Family and domain databases

Gene3Di2.60.40.720. 1 hit.
4.10.770.10. 1 hit.
InterProiIPR000040. AML1_Runt.
IPR008967. p53-like_TF_DNA-bd.
IPR012346. p53/RUNT-type_TF_DNA-bd.
IPR013524. Runt_dom.
IPR027384. Runx_central_dom.
IPR013711. RunxI_C_dom.
[Graphical view]
PANTHERiPTHR11950. PTHR11950. 1 hit.
PfamiPF00853. Runt. 1 hit.
PF08504. RunxI. 1 hit.
[Graphical view]
PRINTSiPR00967. ONCOGENEAML1.
SUPFAMiSSF49417. SSF49417. 1 hit.
PROSITEiPS51062. RUNT. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning, mapping and expression of PEBP2 alpha C, a third gene encoding the mammalian Runt domain."
    Bae S.-C., Takahashi E., Zhang Y.-W., Ogawa E., Shigesada K., Namba Y., Satake M., Ito Y.
    Gene 159:245-248(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
  2. "AML1, AML2, and AML3, the human members of the runt domain gene-family: cDNA structure, expression, and chromosomal localization."
    Levanon D., Negreanu V., Bernstein Y., Bar-Am I., Avivi L., Groner Y.
    Genomics 23:425-432(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
  3. Groner Y.
    Submitted (JAN-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: SEQUENCE REVISION.
  4. "The DNA sequence and biological annotation of human chromosome 1."
    Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.
    , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
    Nature 441:315-321(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  6. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Tissue: Skin.
  7. "Identification of a new murine runt domain-containing gene, Cbfa3, and localization of the human homolog, CBFA3, to chromosome 1p35-pter."
    Wijmenga C., Speck N.A., Dracopoli N.C., Hofker M.H., Liu P., Collins F.S.
    Genomics 26:611-614(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 95-148.
  8. "Transcriptional repression by AML1 and LEF-1 is mediated by the TLE/Groucho corepressors."
    Levanon D., Goldstein R.E., Bernstein Y., Tang H., Goldenberg D., Stifani S., Paroush Z., Groner Y.
    Proc. Natl. Acad. Sci. U.S.A. 95:11590-11595(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH TLE1.
  9. Cited for: INTERACTION WITH SUV39H1.
  10. "Foxp3 controls regulatory T-cell function by interacting with AML1/Runx1."
    Ono M., Yaguchi H., Ohkura N., Kitabayashi I., Nagamura Y., Nomura T., Miyachi Y., Tsukada T., Sakaguchi S.
    Nature 446:685-689(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH FOXP3.
  11. "Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis."
    Cantin G.T., Yi W., Lu B., Park S.K., Xu T., Lee J.-D., Yates J.R. III
    J. Proteome Res. 7:1346-1351(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-243, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  12. "Src kinase phosphorylates RUNX3 at tyrosine residues and localizes the protein in the cytoplasm."
    Goh Y.M., Cinghu S., Hong E.T., Lee Y.S., Kim J.H., Jang J.W., Li Y.H., Chi X.Z., Lee K.S., Wee H., Ito Y., Oh B.C., Bae S.C.
    J. Biol. Chem. 285:10122-10129(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION, PHOSPHORYLATION, INTERACTION WITH SRC; FYN AND LCK.

Entry informationi

Entry nameiRUNX3_HUMAN
AccessioniPrimary (citable) accession number: Q13761
Secondary accession number(s): B1AJV5, Q12969, Q13760
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 2001
Last sequence update: October 31, 1999
Last modified: March 31, 2015
This is version 156 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.