JARID1A (Jumonji, AT rich interactive domain 1A (RBBP2-like))

Identity

Other names	RBBP2
	RBP2
HGNC	JARID1A
Location	12p13
Location_base_pair	Starts at 259484 and ends at 368881 bp from pter ( according to hg18-Mar_2006).
Local_order	very telomeric side of 12p13

DNA/RNA

Description	31 exons over 105 kb
Transcription	from centromere to telomere, yielding mRNA of 6,5 kb

Protein

Description	JARID1A (Jumonji, AT-rich interactive domain 1A) encodes the 196 kDa retinoblastoma binding protein 2 (1722 amino acids). It contains several motifs, including a leucine-X-cysteine-X-glutamic acid (LXCXE) motif, which is important for association with the T/E1A pocket domain of the retinoblastoma protein. Additionally, the protein contains ARID, Jumonji, and 3 PHD (LAP) domains, which are frequent in proteins regulating transcription through changes in chromatin structure.
Expression	Widely expressed
Localisation	Nuclear
Function	Probably in regulating transcription through changes in chromatin structure
Homology	RBP2 homologue 1 (RBP2-H1)

Implicated in

Entity	t(11;12)(p15;p13) in Acute megakaryoblastic leukemia (AML -M7) --> NUP98/JARID1A
Note	Only one case to date, a 1- year-old boy
Prognosis	Patient reached complete remission and remains in complete remission (CR) for at least 5 years
Cytogenetics	complex/variant t(11;12)(p15;p13); i.e. t(11;21;12)(p15;p13;p13), but misdiagnosed as add(11)(p15) and der(21)t(11;21)(p15;p13). Chromosome 12 was cytogenetically normal by conventional banding techniques and only identified as a partner in this translocation after FISH.
Hybrid/Mutated Gene	5' NUP98 - 3' JARID1A, including the first 13 exons of NUP98 and exons 28-31 of JARID1A
Abnormal Protein	The NUP98-JARID1A fusion protein contains the Phe-Gly (FG) repeats of the N-terminal part of NUP98. The JARID1A sequence starting with exon 28 still contains the sequence encoding the C-terminal PHD domain.

External links

	Nomenclature
HGNC	JARID1A   9886
Entrez_Gene	JARID1A  5927  jumonji, AT rich interactive domain 1A
	Cards
Atlas	JARID1AID41033ch12p13
GeneCards	JARID1A
Ensembl	ENSG00000073614 [Gene_View]  JARID1A [Vega]
Genatlas	JARID1A
	Genomic and cartography
GoldenPath	JARID1A  -  12p13   chr12:259484-368881 -  12p11   [Description]    (hg18-Mar_2006)
Ensembl	JARID1A - 12p11 [CytoView]
NCBI	Mapview
OMIM	180202 Disease map [OMIM]
HomoloGene	JARID1A
	Gene and transcription
Genbank	AA101935 [ ENTREZ ]
Genbank	AB209999 [ ENTREZ ]
Genbank	AF007135 [ ENTREZ ]
Genbank	AK057703 [ ENTREZ ]
Genbank	AK225060 [ ENTREZ ]
RefSeq	NM_001042603 [ SRS ]    NM_001042603 [ ENTREZ ]
RefSeq	NM_005056 [ SRS ]    NM_005056 [ ENTREZ ]
RefSeq	AC_000055 [ SRS ]    AC_000055 [ ENTREZ ]
RefSeq	AC_000144 [ SRS ]    AC_000144 [ ENTREZ ]
RefSeq	NC_000012 [ SRS ]    NC_000012 [ ENTREZ ]
RefSeq	NT_009759 [ SRS ]    NT_009759 [ ENTREZ ]
RefSeq	NW_001838049 [ SRS ]    NW_001838049 [ ENTREZ ]
RefSeq	NW_925295 [ SRS ]    NW_925295 [ ENTREZ ]
CCDS	JARID1A CCDS - NCBI
AceView	JARID1A AceView - NCBI
Unigene	Hs.76272 [ SRS ]    Hs.76272 [ NCBI ]
Fast-db	258 (alternative variants)
	Protein : pattern, domain, 3D structure
SwissProt	P29375 [ SRS]    P29375 [ EXPASY ]     P29375 [ INTERPRO ]     P29375 [ UNIPROT ] P29375 [ VarSplice FASTA ]
Prosite	PS51011 ARID [ SRS ]    PS51011 ARID [ Expasy ]
Prosite	PS51184 JMJC [ SRS ]    PS51184 JMJC [ Expasy ]
Prosite	PS51183 JMJN [ SRS ]    PS51183 JMJN [ Expasy ]
Prosite	PS01359 ZF_PHD_1 [ SRS ]    PS01359 ZF_PHD_1 [ Expasy ]
Prosite	PS50016 ZF_PHD_2 [ SRS ]    PS50016 ZF_PHD_2 [ Expasy ]
Interpro	IPR001606 ARID [ SRS ]    IPR001606 ARID [ EBI ]
Interpro	IPR013637 PLU-1 [ SRS ]    IPR013637 PLU-1 [ EBI ]
Interpro	IPR013129 TF_JmjC [ SRS ]    IPR013129 TF_JmjC [ EBI ]
Interpro	IPR003347 TF_JmjC_AAH [ SRS ]    IPR003347 TF_JmjC_AAH [ EBI ]
Interpro	IPR003349 TF_JmjN [ SRS ]    IPR003349 TF_JmjN [ EBI ]
Interpro	IPR004198 Znf_C5HC2 [ SRS ]    IPR004198 Znf_C5HC2 [ EBI ]
Interpro	IPR001965 Znf_PHD [ SRS ]    IPR001965 Znf_PHD [ EBI ]
Interpro	IPR013083 Znf_RING/FYVE/PHD [ SRS ]    IPR013083 Znf_RING/FYVE/PHD [ EBI ]
CluSTr	P29375
Pfam	PF01388 ARID [ SRS ]    PF01388 ARID [ Sanger ]    pfam01388 [ NCBI-CDD ]
Pfam	PF02373 JmjC [ SRS ]    PF02373 JmjC [ Sanger ]    pfam02373 [ NCBI-CDD ]
Pfam	PF02375 JmjN [ SRS ]    PF02375 JmjN [ Sanger ]    pfam02375 [ NCBI-CDD ]
Pfam	PF00628 PHD [ SRS ]    PF00628 PHD [ Sanger ]    pfam00628 [ NCBI-CDD ]
Pfam	PF08429 PLU-1 [ SRS ]    PF08429 PLU-1 [ Sanger ]    pfam08429 [ NCBI-CDD ]
Pfam	PF02928 zf-C5HC2 [ SRS ]    PF02928 zf-C5HC2 [ Sanger ]    pfam02928 [ NCBI-CDD ]
Smart	SM00501 BRIGHT [EMBL]
Smart	SM00558 JmjC [EMBL]
Smart	SM00545 JmjN [EMBL]
Smart	SM00249 PHD [EMBL]
Blocks	P29375
HPRD	08915
	Protein Interaction databases
DIP	P29375
IntAct	P29375
	Polymorphism : SNP, mutations, diseases
OMIM	180202    [ map ]
GENETests	180202
SNP	JARID1A [dbSNP-NCBI]
SNP	NM_001042603 [SNP-NCI]
SNP	NM_005056 [SNP-NCI]
SNP	JARID1A [GeneSNPs - Utah]  JARID1A] [HGBASE - SRS]
HAPMAP	JARID1A [HAPMAP]
COSMIC	JARID1A [Somatic mutation (COSMIC-CGP-Sanger)]
TICdb	JARID1A [Translocation breakpoints In Cancer]
HGMD	JARID1A
Genetic Association	JARID1A
CDC HuGE	JARID1A
	General knowledge
Family Browser	JARID1A [UCSC Family Browser]
SOURCE	NM_001042603
SOURCE	NM_005056
SMD	Hs.76272
SAGE	Hs.76272
Enzyme	1.14.11.- [ Enzyme-Expasy ]   1.14.11.- [ Enzyme-SRS ]   1.14.11.- [ IntEnz-EBI ]   1.14.11.- [ BRENDA ]   1.14.11.- [ KEGG ]
GO	DNA binding [Amigo]  DNA binding
GO	transcription factor activity [Amigo]  transcription factor activity
GO	iron ion binding [Amigo]  iron ion binding
GO	protein binding [Amigo]  protein binding
GO	protein binding [Amigo]  protein binding
GO	intracellular [Amigo]  intracellular
GO	nucleus [Amigo]  nucleus
GO	nucleus [Amigo]  nucleus
GO	transcription [Amigo]  transcription
GO	regulation of transcription, DNA-dependent [Amigo]  regulation of transcription, DNA-dependent
GO	transcription from RNA polymerase II promoter [Amigo]  transcription from RNA polymerase II promoter
GO	multicellular organismal development [Amigo]  multicellular organismal development
GO	zinc ion binding [Amigo]  zinc ion binding
GO	oxidoreductase activity [Amigo]  oxidoreductase activity
GO	chromatin modification [Amigo]  chromatin modification
GO	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen [Amigo]  oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
GO	cyclin-dependent protein kinase activating kinase holoenzyme complex [Amigo]  cyclin-dependent protein kinase activating kinase holoenzyme complex
GO	metal ion binding [Amigo]  metal ion binding
GO	oxidation reduction [Amigo]  oxidation reduction
PubGene	JARID1A
TreeFam	JARID1A
CTD	5927 [Comparative ToxicoGenomics Database]
	Other databases
	Probes
Probe	JARID1A Related clones (RZPD - Berlin)
	PubMed
PubMed	22 Pubmed reference(s) in Entrez

Bibliography

Differential specificity for binding of retinoblastoma binding protein 2 to RB, p107, and TATA-binding protein.

Kim YW, Otterson GA, Kratzke RA, Coxon AB, Kaye FJ

Molecular and cellular biology. 1994 ; 14 (11) : 7256-7264.

PMID 7935440

Binding of pRB to the PHD protein RBP2 promotes cellular differentiation.

Benevolenskaya EV, Murray HL, Branton P, Young RA, Kaelin WG Jr

Molecular cell. 2005 ; 18 (6) : 623-635.

PMID 15949438

Identification of NUP98 abnormalities in acute leukemia: JARID1A (12p13) as a new partner gene.

van Zutven LJ, Onen E, Velthuizen SC, van Drunen E, von Bergh AR, van den Heuvel-Eibrink MM, Veronese A, Mecucci C, Negrini M, de Greef GE, Beverloo HB

Genes, chromosomes & cancer. 2006 ; 45 (5) : 437-446.

PMID 16419055

REVIEW articles	automatic search in PubMed
Last year publications	automatic search in PubMed

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Contributor(s)

Written	04-2006	Laura J.C.M. van Zutven, Anne R.M. von Bergh
		Afdeling Klinische Genetica, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands

Citation

This paper should be referenced as such :

van Zutven LJCM, von Bergh ARM . JARID1A (Jumonji, AT rich interactive domain 1A (RBBP2-like)). Atlas Genet Cytogenet Oncol Haematol. April 2006 . URL : http://AtlasGeneticsOncology.org/Genes/JARID1AID41033ch12p13.html

© Atlas of Genetics and Cytogenetics in Oncology and Haematology

indexed on : Sat Dec 6 17:56:37 2008