Aliases for SHCBP1 Gene

Aliases for SHCBP1 Gene

  • SHC Binding And Spindle Associated 1 2 3 5
  • Protein Expressed In Activated Lymphocytes 2 3
  • SHC SH2 Domain-Binding Protein 1 3 4
  • PAL 2 3
  • SHC SH2-Domain Binding Protein 1 2
  • FLJ22009 2
  • SHCBP1 5

External Ids for SHCBP1 Gene

Previous GeneCards Identifiers for SHCBP1 Gene

  • GC16M037025
  • GC16M046555
  • GC16M046354
  • GC16M046395
  • GC16M045171
  • GC16M046614
  • GC16M032503

Summaries for SHCBP1 Gene

GeneCards Summary for SHCBP1 Gene

SHCBP1 (SHC Binding And Spindle Associated 1) is a Protein Coding gene. Diseases associated with SHCBP1 include Hermansky-Pudlak Syndrome 3. Among its related pathways are Commom Cytokine Receptor G Chain Siganaling Pathway. Gene Ontology (GO) annotations related to this gene include SH2 domain binding. An important paralog of this gene is SHCBP1L.

UniProtKB/Swiss-Prot Summary for SHCBP1 Gene

  • May play a role in signaling pathways governing cellular proliferation, cell growth and differentiation. May be a component of a novel signaling pathway downstream of Shc. Acts as a positive regulator of FGF signaling in neural progenitor cells.

Gene Wiki entry for SHCBP1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SHCBP1 Gene

Genomics for SHCBP1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SHCBP1 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
GH16J046620 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 250.7 +0.4 370 2 SP1 ZMYM3 POLR2A NFIC CHD4 YY1 MXD4 SMAD5 SIN3A CHD2 RF00017-1843 SHCBP1 lnc-VPS35-1
GH16J046623 Enhancer 0.5 ENCODE 250.7 -1.0 -965 0.2 ZMYM3 CHD4 SAP130 FOXP1 SOX5 ELF3 NR2F6 SOX13 SHCBP1 lnc-VPS35-1 ENSG00000261512 VPS35
GH16J046622 Promoter 0.3 Ensembl 250.7 -1.9 -1922 0.6 ENSG00000261512 SHCBP1 piR-51402-001 lnc-VPS35-1 RAB43P1 VPS35
GH16J046882 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 12.2 -263.8 -263784 6.2 BCLAF1 MYC ZNF600 SIX5 SSRP1 ZNF580 ZNF592 ZMYM3 ATF2 KLF9 GPT2 HSALNG0111175-001 SNORD148 lnc-C16orf87-2 SHCBP1 ENSG00000261131 ANKRD26P1 DNAJA2
GH16J046828 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 14.4 -209.1 -209106 3.4 SP1 ZNF207 NCOR1 IKZF1 ZNF580 ZNF592 POLR2A CEBPA NFIC YY1 C16orf87 lnc-MYLK3-6 SHCBP1 RF00017-1844 MYLK3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SHCBP1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SHCBP1

Top Transcription factor binding sites by QIAGEN in the SHCBP1 gene promoter:
  • AML1a
  • FOXL1
  • FOXO1
  • FOXO1a
  • NF-kappaB
  • NF-kappaB1
  • Nkx5-1
  • Pax-5
  • POU2F1
  • POU2F1a

Genomic Locations for SHCBP1 Gene

Latest Assembly
chr16:46,578,591-46,621,379
(GRCh38/hg38)
Size:
42,789 bases
Orientation:
Minus strand

Previous Assembly
chr16:46,612,503-46,655,291
(GRCh37/hg19 by Entrez Gene)
Size:
42,789 bases
Orientation:
Minus strand

chr16:46,614,466-46,655,538
(GRCh37/hg19 by Ensembl)
Size:
41,073 bases
Orientation:
Minus strand

Genomic View for SHCBP1 Gene

Genes around SHCBP1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SHCBP1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SHCBP1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SHCBP1 Gene

Proteins for SHCBP1 Gene

  • Protein details for SHCBP1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8NEM2-SHCBP_HUMAN
    Recommended name:
    SHC SH2 domain-binding protein 1
    Protein Accession:
    Q8NEM2
    Secondary Accessions:
    • Q96N60
    • Q9BVS0
    • Q9H6P6

    Protein attributes for SHCBP1 Gene

    Size:
    672 amino acids
    Molecular mass:
    75690 Da
    Quaternary structure:
    • Interacts directly with isoform p52shc of SHC1 via its SH2 domain (By similarity). Interacts with TRIM71; leading to enhanced SHCBP1 protein stability (By similarity). Interacts with both members of the centralspindlin complex, KIF23 and RACGAP1 (PubMed:21187330).
    SequenceCaution:
    • Sequence=BAB15208.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

neXtProt entry for SHCBP1 Gene

Post-translational modifications for SHCBP1 Gene

  • Ubiquitination at Lys296, Lys300, Lys315, and Lys517
  • Modification sites at PhosphoSitePlus

Other Protein References for SHCBP1 Gene

No data available for DME Specific Peptides for SHCBP1 Gene

Domains & Families for SHCBP1 Gene

Gene Families for SHCBP1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SHCBP1 Gene

InterPro:
Blocks:
  • Parallel beta-helix repeat

Suggested Antigen Peptide Sequences for SHCBP1 Gene

GenScript: Design optimal peptide antigens:
  • SHC SH2 domain-binding protein 1 (SHCBP_HUMAN)
genes like me logo Genes that share domains with SHCBP1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for SHCBP1 Gene

Function for SHCBP1 Gene

Molecular function for SHCBP1 Gene

UniProtKB/Swiss-Prot Function:
May play a role in signaling pathways governing cellular proliferation, cell growth and differentiation. May be a component of a novel signaling pathway downstream of Shc. Acts as a positive regulator of FGF signaling in neural progenitor cells.

Phenotypes From GWAS Catalog for SHCBP1 Gene

Gene Ontology (GO) - Molecular Function for SHCBP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25852190
genes like me logo Genes that share ontologies with SHCBP1: view
genes like me logo Genes that share phenotypes with SHCBP1: view

Animal Models for SHCBP1 Gene

MGI Knock Outs for SHCBP1:
  • Shcbp1 Shcbp1<tm1d(EUCOMM)Wtsi>

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SHCBP1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SHCBP1 Gene

Localization for SHCBP1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SHCBP1 Gene

Midbody. Cytoplasm, cytoskeleton, spindle. Note=Displays weak localization to the spindle midzone in some early telophase cells and is concentrated at the midbody in late cytokinesis. {ECO:0000269 PubMed:21187330}.

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 SHCBP1 gene
Compartment Confidence
cytoskeleton 4
nucleus 2
cytosol 2
plasma membrane 1
extracellular 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Midbody (3)
  • Mitotic spindle (3)
  • Microtubules (2)
  • Nuclear bodies (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SHCBP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005819 spindle IEA --
GO:0005856 cytoskeleton IEA --
GO:0030496 midbody IEA --
genes like me logo Genes that share ontologies with SHCBP1: view

Pathways & Interactions for SHCBP1 Gene

genes like me logo Genes that share pathways with SHCBP1: view

Pathways by source for SHCBP1 Gene

1 Sino Biological pathway for SHCBP1 Gene

Gene Ontology (GO) - Biological Process for SHCBP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008543 fibroblast growth factor receptor signaling pathway ISS --
GO:2000177 regulation of neural precursor cell proliferation ISS --
genes like me logo Genes that share ontologies with SHCBP1: view

No data available for SIGNOR curated interactions for SHCBP1 Gene

Drugs & Compounds for SHCBP1 Gene

No Compound Related Data Available

Transcripts for SHCBP1 Gene

mRNA/cDNA for SHCBP1 Gene

3 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
7 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 SHCBP1

Alternative Splicing Database (ASD) splice patterns (SP) for SHCBP1 Gene

No ASD Table

Relevant External Links for SHCBP1 Gene

GeneLoc Exon Structure for
SHCBP1

Expression for SHCBP1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SHCBP1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SHCBP1 Gene

This gene is overexpressed in Testis (55.9) and Fetal ovary (8.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SHCBP1 Gene



Protein tissue co-expression partners for SHCBP1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SHCBP1

SOURCE GeneReport for Unigene cluster for SHCBP1 Gene:

Hs.123253
genes like me logo Genes that share expression patterns with SHCBP1: view

Primer products for research

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for SHCBP1 Gene

Orthologs for SHCBP1 Gene

This gene was present in the common ancestor of animals.

Orthologs for SHCBP1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SHCBP1 29 30
  • 99.7 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SHCBP1 29 30
  • 90.17 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SHCBP1 29 30
  • 89.64 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Shcbp1 29 16 30
  • 82.88 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Shcbp1 29
  • 82.78 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 30
  • 77 (a)
OneToMany
-- 30
  • 76 (a)
OneToMany
Oppossum
(Monodelphis domestica)
Mammalia SHCBP1 30
  • 76 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SHCBP1 29 30
  • 73.76 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SHCBP1 30
  • 63 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia shcbp1 29
  • 67.24 (n)
Str.10946 29
African clawed frog
(Xenopus laevis)
Amphibia Xl.13015 29
Zebrafish
(Danio rerio)
Actinopterygii shcbp1 29 30
  • 60.95 (n)
OneToOne
wufi22a03 29
Fruit Fly
(Drosophila melanogaster)
Insecta nesd 30
  • 18 (a)
OneToMany
Species where no ortholog for SHCBP1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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 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 SHCBP1 Gene

ENSEMBL:
Gene Tree for SHCBP1 (if available)
TreeFam:
Gene Tree for SHCBP1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SHCBP1: view image
Alliance of Genome Resources:
Additional Orthologs for SHCBP1

Paralogs for SHCBP1 Gene

Paralogs for SHCBP1 Gene

Pseudogenes.org Pseudogenes for SHCBP1 Gene

genes like me logo Genes that share paralogs with SHCBP1: view

Variants for SHCBP1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SHCBP1 Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
rs76534624 Benign: not provided 46,618,315(-) G/C
NM_024745.5(SHCBP1):c.161C>G (p.Ser54Cys)
MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,INTRON
rs11545690 -- p.Met60Arg
rs6598679 -- p.Met21Thr

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SHCBP1 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 SHCBP1 Gene

Variant ID Type Subtype PubMed ID
dgv2975n100 CNV gain 25217958
esv3571142 CNV gain 25503493
esv3571153 CNV gain 25503493
esv3638533 CNV gain 21293372
esv3638534 CNV gain 21293372
nsv1056162 CNV gain 25217958
nsv1066115 CNV gain 25217958
nsv428327 CNV gain 18775914
nsv526656 CNV gain 19592680
nsv833216 CNV loss 17160897

Variation tolerance for SHCBP1 Gene

Residual Variation Intolerance Score: 68.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.39; 27.47% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SHCBP1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SHCBP1
Leiden Open Variation Database (LOVD)
SHCBP1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SHCBP1 Gene

Disorders for SHCBP1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SHCBP1 Gene - From: COP

Disorder Aliases PubMed IDs
hermansky-pudlak syndrome 3
  • hps3
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SHCBP1

genes like me logo Genes that share disorders with SHCBP1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SHCBP1 Gene

Publications for SHCBP1 Gene

  1. SHCBP1 is required for midbody organization and cytokinesis completion. (PMID: 25486361) Asano E … Senga T (Cell cycle (Georgetown, Tex.) 2014) 2 3
  2. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (PMID: 16964243) Beausoleil SA … Gygi SP (Nature biotechnology 2006) 3 4
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. Cloning and characterization of mPAL, a novel Shc SH2 domain-binding protein expressed in proliferating cells. (PMID: 10086341) Schmandt R … McGlade CJ (Oncogene 1999) 2 3

Products for SHCBP1 Gene

Sources for SHCBP1 Gene