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Aliases for ARID4B Gene

Aliases for ARID4B Gene

  • AT-Rich Interaction Domain 4B 2 3 5
  • Histone Deacetylase Complex Subunit SAP180 3 4
  • AT Rich Interactive Domain 4B (RBP1-Like) 2 3
  • Breast Cancer-Associated Antigen BRCAA1 3 4
  • Retinoblastoma-Binding Protein 1-Like 1 3 4
  • 180 KDa Sin3-Associated Polypeptide 3 4
  • ARID Domain-Containing Protein 4B 3 4
  • Sin3-Associated Polypeptide P180 3 4
  • RBBP1L1 3 4
  • RBP1L1 3 4
  • BRCAA1 3 4
  • SAP180 3 4
  • AT-Rich Interactive Domain-Containing Protein 4B 3
  • AT Rich Interactive Domain 4B (RBP1- Like) 2
  • Retinoblastoma Binding Protein 1-Like 1 2
  • Breast Carcinoma-Associated Antigen 3
  • Breast Cancer-Associated Antigen 1 3
  • SIN3A-Associated Protein 180 3
  • Rb-Binding Protein Homolog 3
  • BCAA 3

External Ids for ARID4B Gene

Previous HGNC Symbols for ARID4B Gene

  • RBP1L1

Previous GeneCards Identifiers for ARID4B Gene

  • GC01M232336
  • GC01M232371
  • GC01M231621
  • GC01M233396
  • GC01M235295
  • GC01M205778
  • GC01M235296
  • GC01M235298

Summaries for ARID4B Gene

Entrez Gene Summary for ARID4B Gene

  • This gene encodes a protein with sequence similarity to retinoblastoma-binding protein-1. The encoded protein is a subunit of the histone deacetylase-dependant SIN3A transcriptional corepressor complex, which functions in diverse cellular processes including proliferation, differentiation, apoptosis, oncogenesis, and cell fate determination. The gene product is recognized by IgG antibody isolated from a breast cancer patient and appears to be a molecular marker associated with a broad range of human malignancies. Alternate transcriptional splice variants encoding different isoforms have been characterized. [provided by RefSeq, Jul 2008]

GeneCards Summary for ARID4B Gene

ARID4B (AT-Rich Interaction Domain 4B) is a Protein Coding gene. Diseases associated with ARID4B include Breast Cancer. Among its related pathways are Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and Chromatin organization. Gene Ontology (GO) annotations related to this gene include transcription regulatory region DNA binding. An important paralog of this gene is ARID4A.

UniProtKB/Swiss-Prot for ARID4B Gene

  • Acts as a transcriptional repressor. May function in the assembly and/or enzymatic activity of the Sin3A corepressor complex or in mediating interactions between the complex and other regulatory complexes.

Gene Wiki entry for ARID4B Gene

Additional gene information for ARID4B Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ARID4B Gene

Genomics for ARID4B Gene

GeneHancer (GH) Regulatory Elements for ARID4B Gene

Promoters and enhancers for ARID4B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J235324 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 749.7 0.0 -36 7.5 FEZF1 YY1 ZNF213 E2F8 ZNF416 ZNF143 ZNF263 SP3 NFYC ZNF610 ARID4B GGPS1 PIR53063 RPS21P1 LYST LDHAP2 B3GALNT2 TARBP1 IRF2BP2
GH01J234598 Promoter/Enhancer 2.9 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 149.3 +716.5 716451 26.9 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 IRF2BP2 ARID4B RPS21P1 LOC102724100 LOC105373206 GGPS1 TARBP1 LINC01354 ENSG00000230404 B3GALNT2
GH01J234714 Enhancer 1.9 FANTOM5 Ensembl ENCODE dbSUPER 208.1 +606.7 606682 14.8 CLOCK MLX FEZF1 DMAP1 YBX1 IRF4 YY1 SLC30A9 ZNF213 E2F8 PIR33120 ARID4B RPS21P1 IRF2BP2 LOC102724100 GGPS1 LOC105373206 ENSG00000230404 ENSG00000228830 B3GALNT2
GH01J234968 Promoter/Enhancer 2.2 FANTOM5 Ensembl ENCODE dbSUPER 139 +349.3 349281 21.3 MLX FEZF1 DMAP1 YBX1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 ENSG00000258082 ARID4B GGPS1 RPS21P1 IRF2BP2 LOC102724100 LOC105373206 LDHAP2 LOC101927851 ENSG00000230404
GH01J236062 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 66.4 -737.6 -737633 6.3 HDGF PKNOX1 FOXA2 MLX ARID4B DMAP1 ZNF2 IRF4 YY1 SLC30A9 NID1 GC01P236064 ARID4B ENSG00000273058 GGPS1 ENSG00000230325 HEATR1 RPS21P1 MTR LYST
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ARID4B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ARID4B gene promoter:
  • Sox9
  • LCR-F1
  • IRF-7A
  • HOXA9
  • YY1
  • CUTL1
  • HOXA9B
  • Meis-1
  • Meis-1a
  • FOXO4

Genomic Locations for ARID4B Gene

Genomic Locations for ARID4B Gene
chr1:235,131,634-235,328,298
(GRCh38/hg38)
Size:
196,665 bases
Orientation:
Minus strand
chr1:235,294,949-235,491,534
(GRCh37/hg19)
Size:
196,586 bases
Orientation:
Minus strand

Genomic View for ARID4B Gene

Genes around ARID4B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ARID4B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ARID4B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ARID4B Gene

Proteins for ARID4B Gene

  • Protein details for ARID4B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q4LE39-ARI4B_HUMAN
    Recommended name:
    AT-rich interactive domain-containing protein 4B
    Protein Accession:
    Q4LE39
    Secondary Accessions:
    • A1L465
    • Q3MHV4
    • Q5HY99
    • Q5T2C2
    • Q5T2C3
    • Q5T2C4
    • Q5T2C5
    • Q5T2C6
    • Q6P600
    • Q86UX1
    • Q86WR4
    • Q9H915
    • Q9NYU3
    • Q9NZB6
    • Q9NZG4
    • Q9P2W4
    • Q9UF62
    • Q9Y6E1

    Protein attributes for ARID4B Gene

    Size:
    1312 amino acids
    Molecular mass:
    147809 Da
    Quaternary structure:
    • Component of a Sin3A corepressor complex consisting of SIN3A, SAP130, SUDS3/SAP45, SAP180, HDAC1 and HDAC2.
    SequenceCaution:
    • Sequence=AAD41239.1; Type=Frameshift; Positions=859, 869, 1287, 1311; Evidence={ECO:0000305}; Sequence=AAF23433.3; Type=Frameshift; Positions=1287, 1311; Evidence={ECO:0000305}; Sequence=BAB14428.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAE06114.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAI13751.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for ARID4B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ARID4B Gene

Post-translational modifications for ARID4B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for ARID4B Gene

Domains & Families for ARID4B Gene

Gene Families for ARID4B Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Suggested Antigen Peptide Sequences for ARID4B Gene

Graphical View of Domain Structure for InterPro Entry

Q4LE39

UniProtKB/Swiss-Prot:

ARI4B_HUMAN :
  • The C-terminus mediates interaction with mSin3A corepressor complex.
Domain:
  • The C-terminus mediates interaction with mSin3A corepressor complex.
  • The N-terminus is involved in transcriptional repression by HDAC-independent mechanisms.
  • The ARID domain is involved in stabilizing the mSin3A corepressor complex on DNA.
genes like me logo Genes that share domains with ARID4B: view

Function for ARID4B Gene

Molecular function for ARID4B Gene

UniProtKB/Swiss-Prot Function:
Acts as a transcriptional repressor. May function in the assembly and/or enzymatic activity of the Sin3A corepressor complex or in mediating interactions between the complex and other regulatory complexes.

Phenotypes From GWAS Catalog for ARID4B Gene

Gene Ontology (GO) - Molecular Function for ARID4B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding ISA --
GO:0003674 molecular_function ND --
GO:0003677 DNA binding IEA --
GO:0004407 histone deacetylase activity TAS --
GO:0005515 protein binding IPI 20195357
genes like me logo Genes that share ontologies with ARID4B: view
genes like me logo Genes that share phenotypes with ARID4B: view

Animal Models for ARID4B Gene

MGI Knock Outs for ARID4B:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for ARID4B Gene

Localization for ARID4B Gene

Subcellular locations from UniProtKB/Swiss-Prot for ARID4B Gene

Nucleus. Cytoplasm. Note=Cytoplasmic in breast cancer cells.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ARID4B gene
Compartment Confidence
nucleus 4

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ARID4B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005634 nucleus IEA,IBA --
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with ARID4B: view

Pathways & Interactions for ARID4B Gene

genes like me logo Genes that share pathways with ARID4B: view

Pathways by source for ARID4B Gene

Gene Ontology (GO) - Biological Process for ARID4B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006349 regulation of gene expression by genetic imprinting IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA --
GO:0007283 spermatogenesis IEA --
genes like me logo Genes that share ontologies with ARID4B: view

No data available for SIGNOR curated interactions for ARID4B Gene

Drugs & Compounds for ARID4B Gene

No Compound Related Data Available

Transcripts for ARID4B Gene

Unigene Clusters for ARID4B Gene

AT rich interactive domain 4B (RBP1-like):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ARID4B Gene

No ASD Table

Relevant External Links for ARID4B Gene

GeneLoc Exon Structure for
ARID4B
ECgene alternative splicing isoforms for
ARID4B

Expression for ARID4B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ARID4B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for ARID4B Gene

This gene is overexpressed in Peripheral blood mononuclear cells (13.0), Gallbladder (11.1), CD8 Tcells (10.3), and Cerebrospinal fluid (8.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ARID4B Gene



Protein tissue co-expression partners for ARID4B Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ARID4B Gene:

ARID4B

SOURCE GeneReport for Unigene cluster for ARID4B Gene:

Hs.575782

mRNA Expression by UniProt/SwissProt for ARID4B Gene:

Q4LE39-ARI4B_HUMAN
Tissue specificity: Highly expressed in the testis and in breast, lung, colon, pancreatic and ovarian cancers. Expressed at low levels in the thymus, prostate and ovary.

Evidence on tissue expression from TISSUES for ARID4B Gene

  • Nervous system(4.7)
  • Kidney(4.3)
  • Lung(4.3)
genes like me logo Genes that share expression patterns with ARID4B: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for ARID4B Gene

Orthologs for ARID4B Gene

This gene was present in the common ancestor of animals.

Orthologs for ARID4B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ARID4B 34 33
  • 99.67 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 96 (a)
OneToMany
-- 34
  • 70 (a)
OneToMany
dog
(Canis familiaris)
Mammalia ARID4B 34 33
  • 93.69 (n)
OneToOne
cow
(Bos Taurus)
Mammalia ARID4B 34 33
  • 90.54 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Arid4b 16 34 33
  • 88.27 (n)
oppossum
(Monodelphis domestica)
Mammalia ARID4B 34
  • 87 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia LOC100912163 33
  • 86.15 (n)
chicken
(Gallus gallus)
Aves ARID4B 34 33
  • 79.16 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia ARID4B 34
  • 77 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia arid4b 33
  • 68.25 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC100537923 33
  • 59.47 (n)
tomm20a 34
  • 54 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea arid-1 34
  • 16 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 45 (a)
OneToMany
Species where no ortholog for ARID4B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for ARID4B Gene

ENSEMBL:
Gene Tree for ARID4B (if available)
TreeFam:
Gene Tree for ARID4B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ARID4B: view image

Paralogs for ARID4B Gene

Paralogs for ARID4B Gene

(1) SIMAP similar genes for ARID4B Gene using alignment to 4 proteins:

  • ARI4B_HUMAN
  • A0PJ81_HUMAN
  • H0Y7Y8_HUMAN
  • H7C5R6_HUMAN
genes like me logo Genes that share paralogs with ARID4B: view

Variants for ARID4B Gene

Sequence variations from dbSNP and Humsavar for ARID4B Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000029341 -- 235,327,792(-) C/A 5_prime_UTR_variant, genic_upstream_transcript_variant, intron_variant, non_coding_transcript_variant, upstream_transcript_variant
rs1000031927 -- 235,272,747(-) A/G genic_upstream_transcript_variant, intron_variant
rs1000061820 -- 235,228,377(-) C/A genic_upstream_transcript_variant, intron_variant
rs1000090252 -- 235,223,525(-) C/T intron_variant
rs1000107730 -- 235,258,507(-) T/G genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for ARID4B Gene

Variant ID Type Subtype PubMed ID
dgv30n21 CNV gain 19592680
esv1108970 CNV deletion 17803354
esv1314619 CNV insertion 17803354
esv1721702 CNV insertion 17803354
esv2725307 CNV deletion 23290073
esv2725318 CNV deletion 23290073
nsv1013571 CNV gain 25217958
nsv1068631 CNV deletion 25765185
nsv1130637 CNV deletion 24896259
nsv1148731 CNV insertion 26484159
nsv549391 CNV loss 21841781
nsv827453 CNV loss 20364138
nsv947473 CNV duplication 23825009
nsv956652 CNV deletion 24416366

Variation tolerance for ARID4B Gene

Residual Variation Intolerance Score: 3.24% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.32; 63.05% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ARID4B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ARID4B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ARID4B Gene

Disorders for ARID4B Gene

MalaCards: The human disease database

(1) MalaCards diseases for ARID4B Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
breast cancer
  • breast cancer, familial
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for ARID4B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with ARID4B: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ARID4B Gene

Publications for ARID4B Gene

  1. Characterization of BRCAA1 and its novel antigen epitope identification. (PMID: 15247124) Cui D … Sarai A (Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 2004) 3 4 22 58
  2. Identification and characterization of three new components of the mSin3A corepressor complex. (PMID: 12724404) Fleischer TC … Ayer DE (Molecular and cellular biology 2003) 3 4 22 58
  3. RBP1L1, a retinoblastoma-binding protein-related gene encoding an antigenic epitope abundantly expressed in human carcinomas and normal testis. (PMID: 11481388) Cao J … Irie R (Journal of the National Cancer Institute 2001) 2 3 4 58
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  5. MicroRNAs and target site screening reveals a pre-microRNA-30e variant associated with schizophrenia. (PMID: 20347265) Xu Y … Liu P (Schizophrenia research 2010) 3 44 58

Products for ARID4B Gene