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DIP2B disco interacting protein 2 homolog B [ Homo sapiens (human) ]

Gene ID: 57609, updated on 14-Nov-2024

Summary

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Official Symbol
DIP2Bprovided by HGNC
Official Full Name
disco interacting protein 2 homolog Bprovided by HGNC
Primary source
HGNC:HGNC:29284
See related
Ensembl:ENSG00000066084 MIM:611379; AllianceGenome:HGNC:29284
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
Summary
This gene encodes a member of the disco-interacting protein homolog 2 protein family. The encoded protein contains a binding site for the transcriptional regulator DNA methyltransferase 1 associated protein 1 as well as AMP-binding sites. The presence of these sites suggests that the encoded protein may participate in DNA methylation. This gene is located near a folate-sensitive fragile site, and CGG-repeat expansion in the promoter of this gene which affects transcription has been detected in individuals containing this fragile site on chromosome 12. [provided by RefSeq, Aug 2011]
Expression
Ubiquitous expression in brain (RPKM 13.6), skin (RPKM 9.4) and 25 other tissues See more
Orthologs
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Genomic context

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See DIP2B in Genome Data Viewer
Location:
12q13.12
Exon count:
38
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (50504985..50748657)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (50468079..50711842)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (50898768..51142440)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene La ribonucleoprotein 4 Neighboring gene small nucleolar RNA, C/D box 133 Neighboring gene uncharacterized LOC124903127 Neighboring gene MPRA-validated peak1730 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4452 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6353 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4453 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6355 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6354 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:50923514-50924014 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:50924015-50924515 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6357 Neighboring gene fragile site, folic acid type, rare, fra(12)(q13.1) Neighboring gene Sharpr-MPRA regulatory region 12282 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6359 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6360 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51005279-51005780 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51005781-51006280 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6361 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6362 Neighboring gene RNA, U6 small nuclear 769, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6363 Neighboring gene RNA, U6 small nuclear 238, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr12:51111745-51111935 Neighboring gene uncharacterized LOC124902932 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:51142690-51143323 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:51142055-51142689 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51155479-51156347 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4454 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4455 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6364 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:51162690-51163190 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:51163191-51163691 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:51180913-51181842 Neighboring gene activating transcription factor 1 Neighboring gene RNA, 7SL, cytoplasmic 519, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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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Related articles in PubMed

  1. Identification and characterization of a novel luciferase-like protein in the human female reproductive tract. Khorram O, et al. J Clin Endocrinol Metab, 2004 Nov. PMID 15531550
  2. Multi-omics analysis to identify susceptibility genes for colorectal cancer. Yuan Y, et al. Hum Mol Genet, 2021 Apr 27. PMID 33481017, Free PMC Article
  3. Meta-analysis of three genome-wide association studies identifies susceptibility loci for colorectal cancer at 1q41, 3q26.2, 12q13.13 and 20q13.33. Houlston RS, et al. Nat Genet, 2010 Nov. PMID 20972440, Free PMC Article
  4. CGG-repeat expansion in the DIP2B gene is associated with the fragile site FRA12A on chromosome 12q13.1. Winnepenninckx B, et al. Am J Hum Genet, 2007 Feb. PMID 17236128, Free PMC Article
  5. Bridging expressed sequence alignments through targeted cDNA sequencing. Xie H, et al. Genomics, 2004 Apr. PMID 15028280

See all (50) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Multi-omics analysis to identify susceptibility genes for colorectal cancer.
    Title: Multi-omics analysis to identify susceptibility genes for colorectal cancer.
  2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  3. Deficiency of DIP2B, a brain-expressed gene, may mediate the neurocognitive problems associated with FRA12A.
    Title: CGG-repeat expansion in the DIP2B gene is associated with the fragile site FRA12A on chromosome 12q13.1.
Submit: New GeneRIF Correction

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
Intellectual disability, FRA12A type
MedGen: C1969893 OMIM: 136630 GeneReviews: Not available
not available

EBI GWAS Catalog

Description
Identification of susceptibility loci for colorectal cancer in a genome-wide meta-analysis.
EBI GWAS Catalog
Meta-analysis of three genome-wide association studies identifies susceptibility loci for colorectal cancer at 1q41, 3q26.2, 12q13.13 and 20q13.33.
EBI GWAS Catalog
Multiethnic meta-analysis of genome-wide association studies in >100 000 subjects identifies 23 fibrinogen-associated Loci but no strong evidence of a causal association between circulating fibrinogen and cardiovascular disease.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1463, MGC104005

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables alpha-tubulin binding ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in negative regulation of axon extension ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in nervous system development IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of peptidyl-lysine acetylation ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in axon ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in dendrite ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in extracellular exosome HDA PubMed 
located_in membrane HDA PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in perikaryon ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
disco-interacting protein 2 homolog B
Names
DIP2 disco-interacting protein 2 homolog B

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

  1. NG_021196.1 RefSeqGene

    Range
    5001..248673
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_173602.3 → NP_775873.2  disco-interacting protein 2 homolog B

    See identical proteins and their annotated locations for NP_775873.2

    Status: REVIEWED

    Source sequence(s)
    AB040896, AC078818, AK091597, AK097369, BC030156, BU101773, BU102128, BU429622, BX537905
    Consensus CDS
    CCDS31799.1
    UniProtKB/Swiss-Prot
    Q6B011, Q8N1L5, Q8NB38, Q9P265
    Related
    ENSP00000301180.5, ENST00000301180.10
    Conserved Domains (4) summary
    COG0318
    Location:336 → 912
    CaiC; Acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II [Lipid transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism]
    pfam00501
    Location:995 → 1470
    AMP-binding; AMP-binding enzyme
    pfam06464
    Location:14 → 131
    DMAP_binding; DMAP1-binding Domain
    cl17068
    Location:360 → 924
    AFD_class_I; Adenylate forming domain, Class I superfamily

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

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    50504985..50748657
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    50468079..50711842
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_020849.2: Suppressed sequence

    Description
    NM_020849.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9P265.3 GenPept UniProtKB/Swiss-Prot:Q9P265

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
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