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SH2D4B SH2 domain containing 4B [ Homo sapiens (human) ]

Gene ID: 387694, updated on 5-Mar-2024

Summary

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Official Symbol
SH2D4Bprovided by HGNC
Official Full Name
SH2 domain containing 4Bprovided by HGNC
Primary source
HGNC:HGNC:31440
See related
Ensembl:ENSG00000178217 AllianceGenome:HGNC:31440
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

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See SH2D4B in Genome Data Viewer
Location:
10q23.1
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (80537902..80646560)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (81405201..81518620)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (82297658..82406316)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:82214375-82214892 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3657 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3658 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3659 Neighboring gene Sharpr-MPRA regulatory region 907 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:82224527-82225098 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:82225099-82225670 Neighboring gene Sharpr-MPRA regulatory region 4556 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3660 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3661 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3663 Neighboring gene tetraspanin 14 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2547 Neighboring gene Sharpr-MPRA regulatory region 2609 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:82257110-82258073 Neighboring gene Sharpr-MPRA regulatory region 10623 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3664 Neighboring gene uncharacterized LOC124902471 Neighboring gene TSPAN14 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3665 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2548 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3667 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3668 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3669 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3670 Neighboring gene MPRA-validated peak1027 silencer Neighboring gene uncharacterized LOC105378387 Neighboring gene long intergenic non-protein coding RNA 2655 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:82459171-82459696 Neighboring gene ribosomal protein S7 pseudogene 9

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
  • 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 of novel germline polymorphisms governing capecitabine sensitivity. O'Donnell PH, et al. Cancer, 2012 Aug 15. PMID 22864933, Free PMC Article
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. Rose JE, et al. Mol Med, 2010 Jul-Aug. PMID 20379614, Free PMC Article
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039
  4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
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

EBI GWAS Catalog

Description
Identification of novel germline polymorphisms governing capecitabine sensitivity.
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)

Genotypes

General gene information

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Markers

Homology

Clone Names

  • FLJ41984

Gene Ontology Provided by GOA

Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
SH2 domain-containing protein 4B
Names
novel SH2 domain-containing protein

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.

mRNA and Protein(s)

  1. NM_001145719.1 → NP_001139191.1  SH2 domain-containing protein 4B isoform 2

    See identical proteins and their annotated locations for NP_001139191.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) represents transcription from an alternate promoter site. The transcript has a distinct first exon, which includes the inferred translation initiation site, resulting in a protein (isoform 2) with a distinct N-terminus.
    Source sequence(s)
    AK123885, AK123978
    Consensus CDS
    CCDS44449.1
    UniProtKB/Swiss-Prot
    Q5SQS7
    Related
    ENSP00000314242.4, ENST00000313455.5
    Conserved Domains (1) summary
    PTZ00121
    Location:52 → 273
    PTZ00121; MAEBL; Provisional

  2. NM_001388272.1 → NP_001375201.1  SH2 domain-containing protein 4B isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC021028, AL731544
    Consensus CDS
    CCDS91286.1
    UniProtKB/Swiss-Prot
    Q5SQS5, Q5SQS7, Q6ZVW9, Q6ZVZ3
    UniProtKB/TrEMBL
    A0A2R8Y5Q0
    Related
    ENSP00000494732.1, ENST00000646907.2
    Conserved Domains (2) summary
    PTZ00121
    Location:30 → 355
    PTZ00121; MAEBL; Provisional
    cd10351
    Location:319 → 421
    SH2_SH2D4B; Src homology 2 domain found in the SH2 domain containing protein 4B (SH2D4B)

  3. NM_207372.2 → NP_997255.2  SH2 domain-containing protein 4B isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents transcription from an alternate promoter site. The transcript has a distinct first exon, which includes the inferred translation initiation site, resulting in a protein (isoform 1) with a distinct N-terminus.
    Source sequence(s)
    AK123885, AK123978
    Consensus CDS
    CCDS7370.1
    UniProtKB/Swiss-Prot
    Q5SQS7
    Related
    ENSP00000345295.2, ENST00000339284.6
    Conserved Domains (1) summary
    PTZ00121
    Location:30 → 321
    PTZ00121; MAEBL; Provisional

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    80537902..80646560
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    81405201..81518620
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054365880.1 → XP_054221855.1  SH2 domain-containing protein 4B isoform X1

  2. XM_054365881.1 → XP_054221856.1  SH2 domain-containing protein 4B isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5SQS7.1 GenPept UniProtKB/Swiss-Prot:Q5SQS7

Gene LinkOut

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

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