Human Gene ARID5B (uc001jlt.2) Description and Page Index
  Description: Homo sapiens AT rich interactive domain 5B (MRF1-like) (ARID5B), transcript variant 1, mRNA.
RefSeq Summary (NM_032199): This gene encodes a member of the AT-rich interaction domain (ARID) family of DNA binding proteins. The encoded protein forms a histone H3K9Me2 demethylase complex with PHD finger protein 2 and regulates the transcription of target genes involved in adipogenesis and liver development. This gene also plays a role in cell growth and differentiation of B-lymphocyte progenitors, and single nucleotide polymorphisms in this gene are associated with acute lymphoblastic leukemia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Sep 2011].
Transcript (Including UTRs)
   Position: hg19 chr10:63,661,013-63,856,707 Size: 195,695 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr10:63,661,469-63,852,789 Size: 191,321 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:63,661,013-63,856,707)mRNA (may differ from genome)Protein (1188 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: ARI5B_HUMAN
DESCRIPTION: RecName: Full=AT-rich interactive domain-containing protein 5B; Short=ARID domain-containing protein 5B; AltName: Full=MRF1-like protein; AltName: Full=Modulator recognition factor 2; Short=MRF-2;
FUNCTION: Transcription coactivator that binds to the 5'-AATA[CT]- 3' core sequence and plays a key role in adipogenesis and liver development. Acts by forming a complex with phosphorylated PHF2, which mediates demethylation at Lys-336, leading to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2- ARID5B complex acts as a coactivator of HNF4A in liver. Required for adipogenesis: regulates triglyceride metabolism in adipocytes by regulating expression of adipogenic genes. Overexpression leads to induction of smooth muscle marker genes, suggesting that it may also act as a regulator of smooth muscle cell differentiation and proliferation. Represses the cytomegalovirus enhancer.
SUBCELLULAR LOCATION: Nucleus (By similarity).
TISSUE SPECIFICITY: Widely expressed, including in liver (at protein level).
DOMAIN: The ARID domain mediates the interaction with DNA.
PTM: Methylation at Lys-336 prevents DNA-binding. Demethylation by PHF2 promotes recruitment of the PHF2-ARID5B complex to promoters.
DISEASE: Note=Defects in ARID5B may be a cause of susceptibility to coronary atherosclerosis in the Japanese population.
DISEASE: Defects in ARID5B may be a cause of susceptibility to acute lymphoblastic leukemia (ALL) [MIM:613065]. Note=ALL is a subtype of acute leukemia, a cancer of the white blood cells. ALL is a malignant disease of bone marrow and the most common malignancy diagnosed in children. The malignant cells are lymphoid precursor cells (lymphoblasts) that are arrested in an early stage of development. The lymphoblasts replace the normal marrow elements, resulting in a marked decrease in the production of normal blood cells. Consequently, anemia, thrombocytopenia, and neutropenia occur to varying degrees. The lymphoblasts also proliferate in organs other than the marrow, particularly the liver, spleen, and lymphonodes.
SIMILARITY: Belongs to the ARID5B family.
SIMILARITY: Contains 1 ARID domain.
SEQUENCE CAUTION: Sequence=AAH15120.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=AAH36831.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=AAH66345.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=AAI07801.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=BAB15012.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ARID5B
CDC HuGE Published Literature: ARID5B
Positive Disease Associations: Acute lymphoblastic leukemia (childhood) , Arthritis, Rheumatoid , Cholesterol, HDL , Diastolic blood pressure , Leukemia, Lymphoid , Receptors, Tumor Necrosis Factor, Type II
Related Studies:
  1. Acute lymphoblastic leukemia (childhood)
    Papaemmanuil ,et al. 2009, Loci on 7p12.2, 10q21.2 and 14q11.2 are associated with risk of childhood acute lymphoblastic leukemia, Nature genetics 2009 41- 9 : 1006-10. [PubMed 19684604]
  2. Acute lymphoblastic leukemia (childhood)
    Trevino ,et al. 2009, Germline genomic variants associated with childhood acute lymphoblastic leukemia, Nature genetics 2009 41- 9 : 1001-5. [PubMed 19684603]
    germline variants affect susceptibility to, and characteristics of, specific ALL subtypes.
  3. Arthritis, Rheumatoid
    Yukinori Okada et al. Nature genetics 2012, Meta-analysis identifies nine new loci associated with rheumatoid arthritis in the Japanese population., Nature genetics. [PubMed 22446963]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: ARID5B
Diseases sorted by gene-association score: childhood leukemia (9), lymphoblastic leukemia (5)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D013629 Tamoxifen
  • C006253 pirinixic acid
  • C028474 1,4-bis(2-(3,5-dichloropyridyloxy))benzene
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • D015124 8-Bromo Cyclic Adenosine Monophosphate
  • D000393 Air Pollutants
  • D017638 Asbestos, Crocidolite
  • D001564 Benzo(a)pyrene
  • D002737 Chloroprene
  • D002945 Cisplatin
          more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 26.17 RPKM in Muscle - Skeletal
Total median expression: 503.48 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -121.23456-0.266 Picture PostScript Text
3' UTR -1126.973918-0.288 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001606 - ARID/BRIGHT_DNA-bd

Pfam Domains:
PF01388 - ARID/BRIGHT DNA binding domain

SCOP Domains:
46774 - ARID-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1IG6
- NMR MuPIT

2OEH
- NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q14865
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001227 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0003677 DNA binding
GO:0003713 transcription coactivator activity
GO:0005515 protein binding
GO:0032452 histone demethylase activity
GO:0044212 transcription regulatory region DNA binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001822 kidney development
GO:0001889 liver development
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006807 nitrogen compound metabolic process
GO:0008584 male gonad development
GO:0008585 female gonad development
GO:0009791 post-embryonic development
GO:0010761 fibroblast migration
GO:0016577 histone demethylation
GO:0030325 adrenal gland development
GO:0035264 multicellular organism growth
GO:0045444 fat cell differentiation
GO:0045892 negative regulation of transcription, DNA-templated
GO:0048008 platelet-derived growth factor receptor signaling pathway
GO:0048468 cell development
GO:0048644 muscle organ morphogenesis
GO:0048705 skeletal system morphogenesis
GO:0051091 positive regulation of sequence-specific DNA binding transcription factor activity
GO:0060021 palate development
GO:0060325 face morphogenesis
GO:0060612 adipose tissue development
GO:0060613 fat pad development
GO:1990830 cellular response to leukemia inhibitory factor

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm


-  Descriptions from all associated GenBank mRNAs
  AK296921 - Homo sapiens cDNA FLJ60664 complete cds, highly similar to AT-rich interactive domain-containing protein5B.
BC107800 - Homo sapiens AT rich interactive domain 5B (MRF1-like), mRNA (cDNA clone IMAGE:4105813), partial cds.
BC056680 - Homo sapiens AT rich interactive domain 5B (MRF1-like), mRNA (cDNA clone IMAGE:4248986), partial cds.
AB527389 - Synthetic construct DNA, clone: pF1KE0395, Homo sapiens ARID5B gene for AT rich interactive domain 5B, without stop codon, in Flexi system.
BC156570 - Synthetic construct Homo sapiens clone IMAGE:100062041, MGC:190148 AT rich interactive domain 5B (MRF1-like) (ARID5B) mRNA, encodes complete protein.
BC152736 - Synthetic construct Homo sapiens clone IMAGE:100016022, MGC:184119 AT rich interactive domain 5B (MRF1-like) (ARID5B) mRNA, encodes complete protein.
LN607831 - Homo sapiens partial mRNA for AT-rich interactive domain 5B (MRF1-like) (ARID5B gene).
BC015120 - Homo sapiens AT rich interactive domain 5B (MRF1-like), mRNA (cDNA clone IMAGE:3681098), partial cds.
BC066345 - Homo sapiens AT rich interactive domain 5B (MRF1-like), mRNA (cDNA clone IMAGE:30345306), partial cds.
AK024803 - Homo sapiens cDNA: FLJ21150 fis, clone CAS09561.
M73837 - Homo sapiens modulator recognition factor 2 (MRF-2) mRNA, partial cds.
JD057461 - Sequence 38485 from Patent EP1572962.
BC036831 - Homo sapiens AT rich interactive domain 5B (MRF1-like), mRNA (cDNA clone IMAGE:5529276), partial cds.
BX641020 - Homo sapiens mRNA; cDNA DKFZp686G23148 (from clone DKFZp686G23148).
BX537690 - Homo sapiens mRNA; cDNA DKFZp686E18111 (from clone DKFZp686E18111).
BX648835 - Homo sapiens mRNA; cDNA DKFZp686H19148 (from clone DKFZp686H19148).
AK123882 - Homo sapiens cDNA FLJ41888 fis, clone OCBBF2024463.
JD465437 - Sequence 446461 from Patent EP1572962.
JD256301 - Sequence 237325 from Patent EP1572962.
JD499210 - Sequence 480234 from Patent EP1572962.
JD160515 - Sequence 141539 from Patent EP1572962.
JD221638 - Sequence 202662 from Patent EP1572962.
JD393946 - Sequence 374970 from Patent EP1572962.
JD163240 - Sequence 144264 from Patent EP1572962.
JD098140 - Sequence 79164 from Patent EP1572962.
JD469188 - Sequence 450212 from Patent EP1572962.
JD510121 - Sequence 491145 from Patent EP1572962.
JD087348 - Sequence 68372 from Patent EP1572962.
JD521953 - Sequence 502977 from Patent EP1572962.
JD110208 - Sequence 91232 from Patent EP1572962.
AL049471 - Homo sapiens mRNA; cDNA DKFZp586N012 (from clone DKFZp586N012).
JD041695 - Sequence 22719 from Patent EP1572962.
JD453887 - Sequence 434911 from Patent EP1572962.
JD281573 - Sequence 262597 from Patent EP1572962.
JD181672 - Sequence 162696 from Patent EP1572962.
JD233316 - Sequence 214340 from Patent EP1572962.
JD565786 - Sequence 546810 from Patent EP1572962.
JD083544 - Sequence 64568 from Patent EP1572962.
JD206568 - Sequence 187592 from Patent EP1572962.
JD083494 - Sequence 64518 from Patent EP1572962.
JD313226 - Sequence 294250 from Patent EP1572962.
JD245599 - Sequence 226623 from Patent EP1572962.
JD455205 - Sequence 436229 from Patent EP1572962.
BC017404 - Homo sapiens, clone IMAGE:4292351, mRNA.
JD101263 - Sequence 82287 from Patent EP1572962.
JD103149 - Sequence 84173 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q14865 (Reactome details) participates in the following event(s):

R-HSA-4724284 KDM3A, KDM3B, KDM7A, PHF2:ARID5B, PHF8 demethylate MeK10-histone H3
R-HSA-5661115 KDM3A, KDM3B, KDM7A, PHF2:ARID5B, PHF8 demethylate Me2K10-histone H3
R-HSA-3214842 HDMs demethylate histones
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-4839726 Chromatin organization

-  Other Names for This Gene
  Alternate Gene Symbols: ARI5B_HUMAN, B4DLB3, DESRT, MRF2, NM_032199, NP_115575, Q05DG6, Q14865, Q32Q59, Q5VST4, Q6NZ42, Q7Z3M4, Q8N421, Q9H786
UCSC ID: uc001jlt.2
RefSeq Accession: NM_032199
Protein: Q14865 (aka ARI5B_HUMAN or AR5B_HUMAN)
CCDS: CCDS31208.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_032199.2
exon count: 10CDS single in 3' UTR: no RNA size: 7948
ORF size: 3567CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 7145.00frame shift in genome: no % Coverage: 99.91
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.