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Aliases for ITSN1 Gene

Aliases for ITSN1 Gene

  • Intersectin 1 2 3 5
  • Human Intersectin-SH3 Domain-Containing Protein SH3P17 2 3
  • Src Homology 3 Domain-Containing Protein 2 3
  • Intersectin 1 Short Form Variant, 11 2 3
  • Intersectin 1 Short Form Variant 3 2 3
  • Intersectin 1 (SH3 Domain Protein) 2 3
  • SH3 Domain-Containing Protein 1A 3 4
  • Intersectin Short Variant 12 2 3
  • SH3D1A 3 4
  • SH3P17 3 4
  • ITSN 3 4
  • SH3 Domain Protein-1A 2
  • Intersectin-1 3

External Ids for ITSN1 Gene

Previous HGNC Symbols for ITSN1 Gene

  • SH3D1A
  • ITSN

Previous GeneCards Identifiers for ITSN1 Gene

  • GC21P031592
  • GC21P033935
  • GC21P033936
  • GC21P035014
  • GC21P020493

Summaries for ITSN1 Gene

Entrez Gene Summary for ITSN1 Gene

  • The protein encoded by this gene is a cytoplasmic membrane-associated protein that indirectly coordinates endocytic membrane traffic with the actin assembly machinery. In addition, the encoded protein may regulate the formation of clathrin-coated vesicles and could be involved in synaptic vesicle recycling. This protein has been shown to interact with dynamin, CDC42, SNAP23, SNAP25, SPIN90, EPS15, EPN1, EPN2, and STN2. Multiple transcript variants encoding different isoforms have been found for this gene, but the full-length nature of only two of them have been characterized so far. [provided by RefSeq, Jul 2008]

GeneCards Summary for ITSN1 Gene

ITSN1 (Intersectin 1) is a Protein Coding gene. Diseases associated with ITSN1 include Tracheomalacia. Among its related pathways are Signaling by GPCR and Internalization of ErbB1. GO annotations related to this gene include calcium ion binding and Rho guanyl-nucleotide exchange factor activity. An important paralog of this gene is ITSN2.

UniProtKB/Swiss-Prot for ITSN1 Gene

  • Acts as guanine nucleotide exchange factor (GEF) specific for the CDC42 GTPase (By similarity). Adapter protein that may provide indirect link between the endocytic membrane traffic and the actin assembly machinery. May regulate the formation of clathrin-coated vesicles. Involved in endocytosis of integrin beta-1 (ITGB1) and transferrin receptor (TFR); internalization of ITGB1 as DAB2-dependent cargo but not TFR may involve association with DAB2. Isoform 1 could be involved in brain-specific synaptic vesicle recycling. Inhibits ARHGAP31 activity toward RAC1.

Gene Wiki entry for ITSN1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ITSN1 Gene

Genomics for ITSN1 Gene

Regulatory Elements for ITSN1 Gene

Enhancers for ITSN1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH21F033682 1.5 FANTOM5 Ensembl ENCODE 21.5 +42.4 42407 4.8 PKNOX1 ARID4B SIN3A BRCA1 FOS REST SMARCA4 PBX2 GLIS1 RCOR2 ITSN1 TMEM50B CRYZL1 GC21P033897
GH21F033654 1.4 Ensembl ENCODE 14.5 +13.8 13820 3.6 PKNOX1 ARNT SIN3A ZNF766 CBX5 FOS KLF13 SP3 REST SMARCA4 ITSN1 TMEM50B ATP5O ENSG00000249209 GART LOC388820 CRYZL1 GC21P033897
GH21F033759 1.3 Ensembl ENCODE 10.5 +119.6 119631 4.3 PKNOX1 ATF1 FEZF1 CBX5 FOS NCOA1 REST TSHZ1 ZNF292 MAFF C21orf140 ITSN1 TMEM50B CRYZL1 GC21P033897
GH21F033703 0.9 Ensembl ENCODE 10.9 +61.7 61693 1.2 JUND ATF3 ZNF133 JUNB KDM1A ATF2 GABPA NR2C2 CRYZL1 ITSN1 GC21P033897
GH21F033706 0.4 ENCODE 10.8 +64.8 64779 0.9 CEBPB CRYZL1 ITSN1 GC21P033897
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around ITSN1 on UCSC Golden Path with GeneCards custom track

Promoters for ITSN1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000612970 200 4401 HDGF PKNOX1 ARNT CREB3L1 ARID4B SIN3A ZNF2 YY1 ZNF766 ZNF143

Genomic Location for ITSN1 Gene

Chromosome:
21
Start:
33,642,400 bp from pter
End:
33,899,861 bp from pter
Size:
257,462 bases
Orientation:
Plus strand

Genomic View for ITSN1 Gene

Genes around ITSN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ITSN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ITSN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ITSN1 Gene

Proteins for ITSN1 Gene

  • Protein details for ITSN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q15811-ITSN1_HUMAN
    Recommended name:
    Intersectin-1
    Protein Accession:
    Q15811
    Secondary Accessions:
    • A7Y322
    • A8CTX8
    • A8CTY3
    • A8CTY7
    • A8D7D0
    • A8DCP3
    • B4DTM2
    • E7ERJ1
    • E9PE44
    • E9PG01
    • E9PHV2
    • O95216
    • Q0PW94
    • Q0PW95
    • Q0PW97
    • Q14BD3
    • Q1ED40
    • Q20BK3
    • Q9UET5
    • Q9UK60
    • Q9UNK1
    • Q9UNK2
    • Q9UQ92

    Protein attributes for ITSN1 Gene

    Size:
    1721 amino acids
    Molecular mass:
    195422 Da
    Quaternary structure:
    • Interacts with dynamin, CDC42, SNAP25 and SNAP23. Clusters several dynamin in a manner that is regulated by alternative splicing. Interacts with clathrin-associated proteins and other components of the endocytic machinery, such as SPIN90, EPS15, EPN1, EPN2, STON2, FCHO1, FCHO2 and DAB2. Interacts (via SH3 domains) with REPS1 and SGIP1. Interacts with ARHGAP31. Interacts with ADAM15.
    SequenceCaution:
    • Sequence=AAC50592.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for ITSN1 Gene

    Alternative splice isoforms for ITSN1 Gene

neXtProt entry for ITSN1 Gene

Post-translational modifications for ITSN1 Gene

  • Ubiquitination at Lys 658
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for ITSN1 Gene

Domains & Families for ITSN1 Gene

Graphical View of Domain Structure for InterPro Entry

Q15811

UniProtKB/Swiss-Prot:

ITSN1_HUMAN :
  • SH3-3, SH3-4 and SH3-5, but not SH3-1 and SH3-2 domains, bind to dynamin (By similarity). SH3-1 and SH3-4 bind to ARHGAP31.
Domain:
  • SH3-3, SH3-4 and SH3-5, but not SH3-1 and SH3-2 domains, bind to dynamin (By similarity). SH3-1 and SH3-4 bind to ARHGAP31.
  • The KLERQ domain binds to SNAP-25 and SNAP-23.
  • In an autoinhibited form the SH3 domain 5 may bind intramolecularly to the DH domain, thus blocking the CDC42-binding site.
  • Contains 1 C2 domain.
  • Contains 1 DH (DBL-homology) domain.
  • Contains 2 EF-hand domains.
  • Contains 2 EH domains.
  • Contains 1 PH domain.
  • Contains 5 SH3 domains.
genes like me logo Genes that share domains with ITSN1: view

Function for ITSN1 Gene

Molecular function for ITSN1 Gene

UniProtKB/Swiss-Prot Function:
Acts as guanine nucleotide exchange factor (GEF) specific for the CDC42 GTPase (By similarity). Adapter protein that may provide indirect link between the endocytic membrane traffic and the actin assembly machinery. May regulate the formation of clathrin-coated vesicles. Involved in endocytosis of integrin beta-1 (ITGB1) and transferrin receptor (TFR); internalization of ITGB1 as DAB2-dependent cargo but not TFR may involve association with DAB2. Isoform 1 could be involved in brain-specific synaptic vesicle recycling. Inhibits ARHGAP31 activity toward RAC1.

Gene Ontology (GO) - Molecular Function for ITSN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005085 guanyl-nucleotide exchange factor activity TAS --
GO:0005089 Rho guanyl-nucleotide exchange factor activity TAS --
GO:0005509 calcium ion binding NAS 9799604
GO:0005515 protein binding IPI 10064583
GO:0019209 kinase activator activity IEA --
genes like me logo Genes that share ontologies with ITSN1: view
genes like me logo Genes that share phenotypes with ITSN1: view

Animal Models for ITSN1 Gene

MGI Knock Outs for ITSN1:

Animal Model Products

  • Taconic Biosciences Mouse Models for ITSN1

miRNA for ITSN1 Gene

miRTarBase miRNAs that target ITSN1

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for ITSN1 Gene

Localization for ITSN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ITSN1 Gene

Endomembrane system. Cell junction, synapse, synaptosome. Cell projection, lamellipodium. Membrane, clathrin-coated pit. Note=Colocalizes with SGIP1 at the plasma membrane in structures corresponding most probably to clathrin-coated pits. {ECO:0000305}.

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 ITSN1 gene
Compartment Confidence
plasma membrane 5
cytosol 5
cytoskeleton 2
nucleus 2
endosome 1

Gene Ontology (GO) - Cellular Components for ITSN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
GO:0005886 plasma membrane IDA 20946875
GO:0005905 clathrin-coated pit IEA,IDA 20946875
GO:0012505 endomembrane system IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with ITSN1: view

Pathways & Interactions for ITSN1 Gene

genes like me logo Genes that share pathways with ITSN1: view

Pathways by source for ITSN1 Gene

SIGNOR curated interactions for ITSN1 Gene

Activates:

Gene Ontology (GO) - Biological Process for ITSN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006897 endocytosis IEA --
GO:0007264 small GTPase mediated signal transduction IEA --
GO:0035023 regulation of Rho protein signal transduction IEA --
GO:0035556 intracellular signal transduction IEA --
GO:0042327 positive regulation of phosphorylation IEA --
genes like me logo Genes that share ontologies with ITSN1: view

Drugs & Compounds for ITSN1 Gene

(1) Drugs for ITSN1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with ITSN1: view

Transcripts for ITSN1 Gene

Unigene Clusters for ITSN1 Gene

Intersectin 1 (SH3 domain protein):
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for ITSN1 Gene

No ASD Table

Relevant External Links for ITSN1 Gene

GeneLoc Exon Structure for
ITSN1
ECgene alternative splicing isoforms for
ITSN1

Expression for ITSN1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ITSN1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for ITSN1 Gene

This gene is overexpressed in Heart (25.1) and Brain (9.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for ITSN1 Gene



Protein tissue co-expression partners for ITSN1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ITSN1 Gene:

ITSN1

SOURCE GeneReport for Unigene cluster for ITSN1 Gene:

Hs.160324

mRNA Expression by UniProt/SwissProt for ITSN1 Gene:

Q15811-ITSN1_HUMAN
Tissue specificity: Isoform 2 is ubiquitous in adult and fetal tissues with high expression in skeletal muscle, heart, spleen, ovary, testis and all fetal tissues tested and low expression in thymus, blood, lung, liver and pancreas. Isoform 1 is expressed almost exclusively in the brain, in all brain regions. Not expressed in the spinal cord.
genes like me logo Genes that share expression patterns with ITSN1: view

Primer Products

No data available for mRNA differential expression in normal tissues for ITSN1 Gene

Orthologs for ITSN1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for ITSN1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ITSN1 34 35
  • 99.69 (n)
dog
(Canis familiaris)
Mammalia -- 35
  • 97 (a)
OneToMany
-- 35
  • 97 (a)
OneToMany
LOC100856635 34
  • 92.16 (n)
oppossum
(Monodelphis domestica)
Mammalia ITSN1 35
  • 94 (a)
OneToOne
cow
(Bos Taurus)
Mammalia ITSN1 34 35
  • 91.48 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia ITSN1 35
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Itsn1 34 16 35
  • 88.16 (n)
rat
(Rattus norvegicus)
Mammalia Itsn1 34
  • 87.95 (n)
chicken
(Gallus gallus)
Aves ITSN1 34 35
  • 83.27 (n)
lizard
(Anolis carolinensis)
Reptilia ITSN1 35
  • 91 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia itsn1 34
  • 77.29 (n)
Str.16169 34
African clawed frog
(Xenopus laevis)
Amphibia itsn-A 34
zebrafish
(Danio rerio)
Actinopterygii itsn1 34 35
  • 70.11 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009037 34
  • 48.83 (n)
fruit fly
(Drosophila melanogaster)
Insecta Dap160 34 35
  • 47.34 (n)
worm
(Caenorhabditis elegans)
Secernentea itsn-1 34 35
  • 44.69 (n)
Y116A8C.36 36
  • 34 (a)
ehs-1 36
  • 26 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes EDE1 35
  • 16 (a)
OneToMany
PAN1 37
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 58 (a)
ManyToMany
-- 35
  • 41 (a)
ManyToMany
Species where no ortholog for ITSN1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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 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 ITSN1 Gene

ENSEMBL:
Gene Tree for ITSN1 (if available)
TreeFam:
Gene Tree for ITSN1 (if available)

Paralogs for ITSN1 Gene

Paralogs for ITSN1 Gene

Pseudogenes.org Pseudogenes for ITSN1 Gene

genes like me logo Genes that share paralogs with ITSN1: view

Variants for ITSN1 Gene

Sequence variations from dbSNP and Humsavar for ITSN1 Gene

SNP ID Clin Chr 21 pos Sequence Context AA Info Type
rs755276554 Pathogenic 33,799,852(+) AAGTG(G/T)TGTAT nc-transcript-variant, reference, missense
rs1007429 -- 33,662,347(+) AGTTC(C/T)GAATT intron-variant
rs1007430 -- 33,664,229(+) tgCTT(C/T)CACTC intron-variant
rs10222139 -- 33,815,742(+) TCTGG(A/G)TGAGG intron-variant
rs10222169 -- 33,825,207(+) TTTTT(A/T)TTTTA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for ITSN1 Gene

Variant ID Type Subtype PubMed ID
nsv587400 CNV loss 21841781
nsv587399 CNV gain 21841781
nsv522214 CNV loss 19592680
nsv1144947 CNV deletion 24896259
nsv1139018 CNV deletion 24896259
nsv1117932 CNV deletion 24896259
nsv1114287 CNV deletion 24896259
nsv1072172 CNV deletion 25765185
nsv1059744 CNV loss 25217958
esv3893407 CNV loss 25118596
esv3646910 CNV loss 21293372
esv3557656 CNV deletion 23714750
esv3325016 CNV insertion 20981092
esv2762108 CNV loss 21179565
esv2723363 CNV deletion 23290073
esv2723360 CNV deletion 23290073
esv2723359 CNV deletion 23290073
esv2723358 CNV deletion 23290073
esv2658286 CNV deletion 23128226
esv2419803 CNV deletion 18987734
dgv2382n106 CNV deletion 24896259

Variation tolerance for ITSN1 Gene

Residual Variation Intolerance Score: 0.753% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.74; 66.42% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for ITSN1 Gene

Human Gene Mutation Database (HGMD)
ITSN1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ITSN1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ITSN1 Gene

Disorders for ITSN1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for ITSN1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
tracheomalacia
  • congenital tracheomalacia
- elite association - COSMIC cancer census association via MalaCards
Search ITSN1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for ITSN1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
ITSN1
genes like me logo Genes that share disorders with ITSN1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ITSN1 Gene

Publications for ITSN1 Gene

  1. Two isoforms of a human intersectin (ITSN) protein are produced by brain-specific alternative splicing in a stop codon. (PMID: 9799604) Guipponi M. … Antonarakis S.E. (Genomics 1998) 2 3 4 22 64
  2. The human intersectin genes and their spliced variants are differentially expressed. (PMID: 11690630) Pucharcos C. … de la Luna S. (Biochim. Biophys. Acta 2001) 3 4 22 64
  3. Alu-splice cloning of human intersectin (ITSN), a putative multivalent binding protein expressed in proliferating and differentiating neurons and overexpressed in Down syndrome. (PMID: 10482960) Pucharcos C. … Pritchard M. (Eur. J. Hum. Genet. 1999) 3 4 22 64
  4. The SH3D1A gene maps to human chromosome 21q22.1-->q22.2. (PMID: 9465890) Chen H. … Antonarakis S.E. (Cytogenet. Cell Genet. 1997) 3 4 22 64
  5. The clathrin adaptor Dab2 recruits EH domain scaffold proteins to regulate integrin beta1 endocytosis. (PMID: 22648170) Teckchandani A. … Cooper J.A. (Mol. Biol. Cell 2012) 3 4 64

Products for ITSN1 Gene

Sources for ITSN1 Gene

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