SH2D1B Gene (Protein Coding)

SH2 Domain Containing 1B

GC01M162395
GIFtS:
40
By binding phosphotyrosines through its free SRC (MIM 190090) homology-2 (SH2) domain, EAT2 regulates signal transduction through receptors expressed on the surface of antigen-presenting cells (Morra et al., 2001 [PubMed 11689425]).[supplied by OMIM, Mar 2008] See more...

Aliases for SH2D1B Gene

Aliases for SH2D1B Gene

  • SH2 Domain Containing 1B 2 3 5
  • EAT2 2 3 4
  • SH2 Domain-Containing Protein 1B 3 4
  • EWS/FLI1-Activated Transcript 2 3 4
  • EAT-2 3 4
  • SH2 Domain-Containing Molecule EAT2 3
  • SH2D1B 5

External Ids for SH2D1B Gene

Previous GeneCards Identifiers for SH2D1B Gene

  • GC01M159097
  • GC01M160631
  • GC01M162366
  • GC01M133609

Summaries for SH2D1B Gene

Entrez Gene Summary for SH2D1B Gene

  • By binding phosphotyrosines through its free SRC (MIM 190090) homology-2 (SH2) domain, EAT2 regulates signal transduction through receptors expressed on the surface of antigen-presenting cells (Morra et al., 2001 [PubMed 11689425]).[supplied by OMIM, Mar 2008]

GeneCards Summary for SH2D1B Gene

SH2D1B (SH2 Domain Containing 1B) is a Protein Coding gene. Diseases associated with SH2D1B include Benign Paroxysmal Positional Nystagmus and Dendritic Cell Deficiency. Among its related pathways are Class I MHC mediated antigen processing and presentation and Immune response Role of DAP12 receptors in NK cells. Gene Ontology (GO) annotations related to this gene include protein binding, bridging. An important paralog of this gene is SH2D1A.

UniProtKB/Swiss-Prot Summary for SH2D1B Gene

  • Cytoplasmic adapter regulating receptors of the signaling lymphocytic activation molecule (SLAM) family such as CD84, SLAMF1, LY9 and CD244 (PubMed:11689425). In SLAM signaling seems to cooperate with SH2D1A/SAP. Plays a role in regulation of effector functions of natural killer (NK) cells by controlling signal transduction through CD244/2B4 without effecting its tyrosine phosphorylation; downstream signaling involves PLCG1 and ERK activation (PubMed:24687958). Activation of SLAMF7-mediated NK cell function does not effect receptor tyrosine phosphorylation but distal signaling (By similarity). In the context of NK cell-mediated cytotoxicity does not enhance conjugate formation with target cells but stimulates polarization of the microtubule-organizing center and cytotoxic granules toward the NK cell synapse (PubMed:24687958). Negatively regulates CD40-induced cytokine production in dendritic cells downstream of SLAM family receptors probably by inducing activation of the PI3K pathway to inhibit p38 MAPK and JNK activation (By similarity).

Gene Wiki entry for SH2D1B Gene

Additional gene information for SH2D1B Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SH2D1B Gene

Genomics for SH2D1B Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for SH2D1B 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
GH01J162411 Promoter/Enhancer 0.9 EPDnew Ensembl ENCODE 250.7 -0.8 -763 2.6 ZNF592 LARP7 ZNF24 SH2D1B lnc-SH2D1B-2 C1orf226 SPATA46 ENSG00000227094 SLAMF6P1 HSALNG0008001 UHMK1
GH01J162380 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 11 +30.0 30024 4.1 NCOR1 IKZF1 ZNF592 ATF3 BRCA1 NFIC CEBPB DEK MAX EP300 C1orf226 SH2D1B UHMK1 RGS4 ENSG00000254706 lnc-SH2D1B-2
GH01J162628 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 6.1 -220.5 -220461 7.2 BCLAF1 SP1 ZNF207 JUND POLR2A ATF3 NFIC BCL11A REST TARDBP DDR2 DUSP12 UHMK1 SH2D1B RF00017-325 HSD17B7
GH01J162246 Enhancer 1.3 FANTOM5 Ensembl ENCODE 9.8 +162.6 162622 6.2 CEBPA CHD4 YY1 KLF11 HOMEZ SIN3A KMT2B THAP11 FOXA2 KDM6A DUSP12 C1orf226 ENSG00000227094 SPATA46 SH2D1B NOS1AP lnc-SPATA46-3 piR-36756-007 ENSG00000254706
GH01J162065 Enhancer 0.7 Ensembl ENCODE 10.3 +346.7 346719 0.8 CTCF RAD21 ZNF362 SNIP1 PRDM4 ZFP69B ZNF384 NFIL3 SMC3 ZNF692 RF00017-323 C1orf226 DEDD USP21 ENSG00000215840 B4GALT3 SH2D1B DUSP12 MIR556 SPATA46
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SH2D1B on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SH2D1B

Top Transcription factor binding sites by QIAGEN in the SH2D1B gene promoter:
  • AhR
  • Arnt
  • Evi-1
  • HSF2
  • ISGF-3
  • NF-1

Genomic Locations for SH2D1B Gene

Latest Assembly
chr1:162,395,268-162,412,138
(GRCh38/hg38)
Size:
16,871 bases
Orientation:
Minus strand

Previous Assembly
chr1:162,365,058-162,381,926
(GRCh37/hg19 by Entrez Gene)
Size:
16,869 bases
Orientation:
Minus strand

chr1:162,365,056-162,381,928
(GRCh37/hg19 by Ensembl)
Size:
16,873 bases
Orientation:
Minus strand

Genomic View for SH2D1B Gene

Genes around SH2D1B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SH2D1B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SH2D1B Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for SH2D1B Gene

Proteins for SH2D1B Gene

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  • Protein details for SH2D1B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O14796-SH21B_HUMAN
    Recommended name:
    SH2 domain-containing protein 1B
    Protein Accession:
    O14796
    Secondary Accessions:
    • B2RBN6
    • Q5T0L1
    • Q8NI18
    • Q969K9

    Protein attributes for SH2D1B Gene

    Size:
    132 amino acids
    Molecular mass:
    15297 Da
    Quaternary structure:
    • Binds to the phosphorylated receptors CD84, SLAMF1, LY9 and CD244. Does not bind to non-phosphorylated SLAMF1 (PubMed:11689425). Interacts with SLAMF7 (via ITSM phosphorylated on 'Tyr-304'). Interacts with Src kinases HCK, LYN, FYN, FGR and LCK (via kinase domains) (By similarity). Interacts (phosphorylated at Tyr-127) with PLCG1.

    Three dimensional structures from OCA and Proteopedia for SH2D1B Gene

    Alternative splice isoforms for SH2D1B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SH2D1B Gene

Protein Expression for SH2D1B Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for SH2D1B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SH2D1B Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SH2D1B Gene

Domains & Families for SH2D1B Gene

Gene Families for SH2D1B Gene

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

Protein Domains for SH2D1B Gene

InterPro:
Blocks:
  • SH2 domain signature

Suggested Antigen Peptide Sequences for SH2D1B Gene

GenScript: Design optimal peptide antigens:
  • EWS/FLI1-activated transcript 2 (SH21B_HUMAN)
genes like me logo Genes that share domains with SH2D1B: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for SH2D1B Gene

Function for SH2D1B Gene

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Molecular function for SH2D1B Gene

UniProtKB/Swiss-Prot Function:
Cytoplasmic adapter regulating receptors of the signaling lymphocytic activation molecule (SLAM) family such as CD84, SLAMF1, LY9 and CD244 (PubMed:11689425). In SLAM signaling seems to cooperate with SH2D1A/SAP. Plays a role in regulation of effector functions of natural killer (NK) cells by controlling signal transduction through CD244/2B4 without effecting its tyrosine phosphorylation; downstream signaling involves PLCG1 and ERK activation (PubMed:24687958). Activation of SLAMF7-mediated NK cell function does not effect receptor tyrosine phosphorylation but distal signaling (By similarity). In the context of NK cell-mediated cytotoxicity does not enhance conjugate formation with target cells but stimulates polarization of the microtubule-organizing center and cytotoxic granules toward the NK cell synapse (PubMed:24687958). Negatively regulates CD40-induced cytokine production in dendritic cells downstream of SLAM family receptors probably by inducing activation of the PI3K pathway to inhibit p38 MAPK and JNK activation (By similarity).

Phenotypes From GWAS Catalog for SH2D1B Gene

Gene Ontology (GO) - Molecular Function for SH2D1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 12928397
GO:0030674 protein binding, bridging TAS 16425036
genes like me logo Genes that share ontologies with SH2D1B: view
genes like me logo Genes that share phenotypes with SH2D1B: view

Animal Models for SH2D1B Gene

MGI Knock Outs for SH2D1B:

Animal Models for research

miRNA for SH2D1B Gene

miRTarBase miRNAs that target SH2D1B

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SH2D1B

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SH2D1B Gene

Localization for SH2D1B Gene

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 SH2D1B gene
Compartment Confidence
cytosol 5
plasma membrane 2
extracellular 2
mitochondrion 2
nucleus 2
cytoskeleton 1
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1

Gene Ontology (GO) - Cellular Components for SH2D1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with SH2D1B: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for SH2D1B Gene

Pathways & Interactions for SH2D1B Gene

genes like me logo Genes that share pathways with SH2D1B: view

Pathways by source for SH2D1B Gene

1 KEGG pathway for SH2D1B Gene

Gene Ontology (GO) - Biological Process for SH2D1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002250 adaptive immune response IEA --
GO:0002366 leukocyte activation involved in immune response ISS --
GO:0002376 immune system process IEA --
GO:0002717 positive regulation of natural killer cell mediated immunity ISS --
GO:0045087 innate immune response IEA --
genes like me logo Genes that share ontologies with SH2D1B: view

No data available for SIGNOR curated interactions for SH2D1B Gene

Drugs & Compounds for SH2D1B Gene

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(1) Drugs for SH2D1B Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with SH2D1B: view

Transcripts for SH2D1B Gene

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mRNA/cDNA for SH2D1B Gene

1 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SH2D1B

Alternative Splicing Database (ASD) splice patterns (SP) for SH2D1B Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b
SP1: - -
SP2: -
SP3: - - -
SP4: -

Relevant External Links for SH2D1B Gene

GeneLoc Exon Structure for
SH2D1B

Expression for SH2D1B Gene

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  1. Primer products for research
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SH2D1B Gene

mRNA expression in normal human tissues for SH2D1B Gene
mRNA expression by BioGPS for SH2D1B GenemRNA expression by GTEx for SH2D1B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SH2D1B Gene

This gene is overexpressed in Whole Blood (x20.1), Muscle - Skeletal (x15.4), and Spleen (x4.4).

Protein differential expression in normal tissues from HIPED for SH2D1B Gene

This gene is overexpressed in NK cells (63.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SH2D1B Gene



Protein tissue co-expression partners for SH2D1B Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SH2D1B

SOURCE GeneReport for Unigene cluster for SH2D1B Gene:

Hs.350581

Evidence on tissue expression from TISSUES for SH2D1B Gene

  • Blood(4.5)
  • Spleen(4.4)
  • Lung(4.3)
  • Intestine(2)
genes like me logo Genes that share expression patterns with SH2D1B: view

Primer products for research

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SH2D1B Gene

Orthologs for SH2D1B Gene

This gene was present in the common ancestor of chordates.

Orthologs for SH2D1B Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia SH2D1B 29 30
  • 99.24 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia SH2D1B 29 30
  • 84.6 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Sh2d1b1 29 16 30
  • 80.05 (n)
 OneToMany
Sh2d1b2 30
  • 65 (a)
 OneToMany
Dog
(Canis familiaris)
 Mammalia SH2D1B 29 30
  • 79.39 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Sh2d1b 29
  • 77.27 (n)
Oppossum
(Monodelphis domestica)
 Mammalia SH2D1B 30
  • 64 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves SH2D1B 29 30
  • 60.31 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia SH2D1B 30
  • 36 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia LOC100486929 29
  • 59.26 (n)
Zebrafish
(Danio rerio)
 Actinopterygii si:dkey-11p10.10 29
  • 51.77 (n)
SH2D1B 30
  • 38 (a)
 OneToOne
Species where no ortholog for SH2D1B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • 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)
  • Worm (Caenorhabditis elegans)

Evolution for SH2D1B Gene

ENSEMBL:
Gene Tree for SH2D1B (if available)
TreeFam:
Gene Tree for SH2D1B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SH2D1B: view image
Alliance of Genome Resources:
Additional Orthologs for SH2D1B

Paralogs for SH2D1B Gene

Paralogs for SH2D1B Gene

(4) SIMAP similar genes for SH2D1B Gene using alignment to 1 proteins:

  • SH21B_HUMAN

Pseudogenes.org Pseudogenes for SH2D1B Gene

genes like me logo Genes that share paralogs with SH2D1B: view

Variants for SH2D1B Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SH2D1B Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs34001279 -- p.Asn122Lys
rs35688243 -- p.Ile36Thr

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SH2D1B Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SH2D1B Gene

Variant ID Type Subtype PubMed ID
esv2758973 CNV gain 17122850
esv34209 CNV gain 17911159
nsv516482 CNV gain+loss 19592680

Variation tolerance for SH2D1B Gene

Residual Variation Intolerance Score: 75.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.14; 69.40% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SH2D1B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SH2D1B
Leiden Open Variation Database (LOVD)
SH2D1B

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SH2D1B Gene

Disorders for SH2D1B Gene

MalaCards: The human disease database

(7) MalaCards diseases for SH2D1B Gene - From: COP

Disorder Aliases PubMed IDs
benign paroxysmal positional nystagmus
  • benign paroxysmal positional vertigo
dendritic cell deficiency
episodic ataxia, type 2
  • ea2
submandibular gland disease
  • submandibular gland diseases
selective immunoglobulin deficiency disease
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SH2D1B

Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with SH2D1B: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SH2D1B Gene

Publications for SH2D1B Gene

  1. Structural basis for the interaction of the free SH2 domain EAT-2 with SLAM receptors in hematopoietic cells. (PMID: 11689425) Morra M … Terhorst C (The EMBO journal 2001) 2 3 4 22
  2. EAT-2 is a novel SH2 domain containing protein that is up regulated by Ewing's sarcoma EWS/FLI1 fusion gene. (PMID: 9000139) Thompson AD … Denny C (Oncogene 1996) 2 3 4
  3. EAT-2, a SAP-like adaptor, controls NK cell activation through phospholipase Cγ, Ca++, and Erk, leading to granule polarization. (PMID: 24687958) Pérez-Quintero LA … Veillette A (The Journal of experimental medicine 2014) 3 4
  4. Identification and characterization of two related murine genes, Eat2a and Eat2b, encoding single SH2-domain adapters. (PMID: 16425036) Calpe S … Lanyi A (Immunogenetics 2006) 3 22
  5. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4

ExternalLinks

View latest publications for SH2D1B gene in Mastermind

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Sources for SH2D1B Gene