Human Gene ITSN2 (ENST00000355123.9_13) from GENCODE V47lift37
  Description: intersectin 2, transcript variant 1 (from RefSeq NM_006277.3)
Gencode Transcript: ENST00000355123.9_13
Gencode Gene: ENSG00000198399.16_18
Transcript (Including UTRs)
   Position: hg19 chr2:24,425,733-24,583,405 Size: 157,673 Total Exon Count: 40 Strand: -
Coding Region
   Position: hg19 chr2:24,426,495-24,550,951 Size: 124,457 Coding Exon Count: 39 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:24,425,733-24,583,405)mRNA (may differ from genome)Protein (1697 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ITSN2_HUMAN
DESCRIPTION: RecName: Full=Intersectin-2; AltName: Full=SH3 domain-containing protein 1B; AltName: Full=SH3P18; AltName: Full=SH3P18-like WASP-associated protein;
FUNCTION: 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 (CCPs). Seems to be involved in CCPs maturation including invagination or budding. Involved in endocytosis of integrin beta-1 (ITGB1) and transferrin receptor (TFR).
SUBUNIT: Belongs to a complex that may contain multimers of ITSN1, ITSN2 and EPS15, and different partners according to the step in the endocytic process. Interacts with ADAM15. Interacts with FASLG. Interacts with ANKRD54 (By similarity). Interacts with FCHO2.
SUBCELLULAR LOCATION: Cytoplasm.
TISSUE SPECIFICITY: Ubiquitous. Isoform 1 is primarily expressed in adult heart and liver.
MISCELLANEOUS: Overexpression results in the inhibition of the transferrin uptake and the blockage of the clathrin-mediated endocytosis.
SIMILARITY: Contains 1 C2 domain.
SIMILARITY: Contains 1 DH (DBL-homology) domain.
SIMILARITY: Contains 2 EF-hand domains.
SIMILARITY: Contains 2 EH domains.
SIMILARITY: Contains 1 PH domain.
SIMILARITY: Contains 5 SH3 domains.
CAUTION: It is uncertain whether Met-1 or Met-2 is the initiator.
CAUTION: Studies in clathrin-mediated endocytosis of ITGB1 and TFR used a siRNA mixture of ISTN1 and ISTN2 suggesting a partially overlapping role of the EH domain-containing proteins (PubMed:22648170).
SEQUENCE CAUTION: Sequence=AAF59903.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAF59904.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAF63600.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=BAA86570.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: ITSN2
Diseases sorted by gene-association score: landau-kleffner syndrome (9), intestinal schistosomiasis (7), cataract 3, multiple types (6)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 17.48 RPKM in Thyroid
Total median expression: 349.65 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -131.90266-0.496 Picture PostScript Text
3' UTR -217.10762-0.285 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000008 - C2_Ca-dep
IPR008973 - C2_Ca/lipid-bd_dom_CaLB
IPR018029 - C2_membr_targeting
IPR000219 - DH-domain
IPR011992 - EF-hand-like_dom
IPR018247 - EF_Hand_1_Ca_BS
IPR018249 - EF_HAND_2
IPR002048 - EF_hand_Ca-bd
IPR000261 - EPS15_homology
IPR000108 - p67phox
IPR011993 - PH_like_dom
IPR001849 - Pleckstrin_homology
IPR011511 - SH3_2
IPR001452 - SH3_domain

Pfam Domains:
PF00018 - SH3 domain
PF00168 - C2 domain
PF00621 - RhoGEF domain
PF07653 - Variant SH3 domain
PF12763 - Cytoskeletal-regulatory complex EF hand
PF14604 - Variant SH3 domain
PF16652 - Pleckstrin homology domain

SCOP Domains:
47473 - EF-hand
48065 - DBL homology domain (DH-domain)
50044 - SH3-domain
50729 - PH domain-like
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1J3T - NMR MuPIT 1UDL - NMR MuPIT 1UE9 - NMR MuPIT 1UFF - NMR MuPIT 1UHF - NMR MuPIT 3GF9 - X-ray MuPIT 3JZY - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9NZM3
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005070 SH3/SH2 adaptor activity
GO:0005089 Rho guanyl-nucleotide exchange factor activity
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0046872 metal ion binding

Biological Process:
GO:0006897 endocytosis
GO:0009967 positive regulation of signal transduction
GO:0030154 cell differentiation
GO:0035023 regulation of Rho protein signal transduction
GO:1903861 positive regulation of dendrite extension

Cellular Component:
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  BC146779 - Homo sapiens intersectin 2, mRNA (cDNA clone MGC:166861 IMAGE:9007231), complete cds.
AB033082 - Homo sapiens KIAA1256 mRNA for KIAA1256 protein.
AF182198 - Homo sapiens intersectin 2 long isoform (ITSN2) mRNA, complete cds.
LF384838 - JP 2014500723-A/192341: Polycomb-Associated Non-Coding RNAs.
AF248540 - Homo sapiens intersectin 2 (SH3D1B) mRNA, complete cds.
KJ901063 - Synthetic construct Homo sapiens clone ccsbBroadEn_10457 ITSN2 gene, encodes complete protein.
AB384587 - Synthetic construct DNA, clone: pF1KA1256, Homo sapiens ITSN2 gene for intersectin-2, complete cds, without stop codon, in Flexi system.
AF182199 - Homo sapiens intersectin 2 short isoform (ITSN2) mRNA, complete cds.
AK021545 - Homo sapiens cDNA FLJ11483 fis, clone HEMBA1001822, highly similar to Mus musculus Ese2L protein mRNA.
AK127858 - Homo sapiens cDNA FLJ45961 fis, clone PLACE7013055.
BC038963 - Homo sapiens, Similar to intersectin 2, clone IMAGE:6055200, mRNA, partial cds.
MA620415 - JP 2018138019-A/192341: Polycomb-Associated Non-Coding RNAs.
AK025400 - Homo sapiens cDNA: FLJ21747 fis, clone COLF5160, highly similar to AF182198 Homo sapiens intersectin 2 long isoform (ITSN2) mRNA.
AK000302 - Homo sapiens cDNA FLJ20295 fis, clone HEP05888.
AK091859 - Homo sapiens cDNA FLJ34540 fis, clone HLUNG2008521, moderately similar to Homo sapiens intersectin 2 (SH3D1B) mRNA.
AX747227 - Sequence 752 from Patent EP1308459.
JD528454 - Sequence 509478 from Patent EP1572962.
JD526638 - Sequence 507662 from Patent EP1572962.
JD551763 - Sequence 532787 from Patent EP1572962.
JD483699 - Sequence 464723 from Patent EP1572962.
JD364745 - Sequence 345769 from Patent EP1572962.
JD084481 - Sequence 65505 from Patent EP1572962.
JD377877 - Sequence 358901 from Patent EP1572962.
JD294602 - Sequence 275626 from Patent EP1572962.
JD259928 - Sequence 240952 from Patent EP1572962.
JD362098 - Sequence 343122 from Patent EP1572962.
JD335119 - Sequence 316143 from Patent EP1572962.
JD220996 - Sequence 202020 from Patent EP1572962.
AF001630 - Homo sapiens SH3P18-like WASP associated protein (SWAP) mRNA, partial cds.
AF038189 - Homo sapiens clone 23554 mRNA sequence.
U61167 - Homo sapiens SH3 domain-containing protein SH3P18 mRNA, partial cds.
LF328759 - JP 2014500723-A/136262: Polycomb-Associated Non-Coding RNAs.
LF328758 - JP 2014500723-A/136261: Polycomb-Associated Non-Coding RNAs.
LF328757 - JP 2014500723-A/136260: Polycomb-Associated Non-Coding RNAs.
AK097890 - Homo sapiens cDNA FLJ40571 fis, clone THYMU2006160.
MA564336 - JP 2018138019-A/136262: Polycomb-Associated Non-Coding RNAs.
MA564335 - JP 2018138019-A/136261: Polycomb-Associated Non-Coding RNAs.
MA564334 - JP 2018138019-A/136260: Polycomb-Associated Non-Coding RNAs.
LF328754 - JP 2014500723-A/136257: Polycomb-Associated Non-Coding RNAs.
BC020921 - Homo sapiens intersectin 2, mRNA (cDNA clone IMAGE:4244766), complete cds.
LF328753 - JP 2014500723-A/136256: Polycomb-Associated Non-Coding RNAs.
LF328752 - JP 2014500723-A/136255: Polycomb-Associated Non-Coding RNAs.
DQ570219 - Homo sapiens piRNA piR-30331, complete sequence.
LF328751 - JP 2014500723-A/136254: Polycomb-Associated Non-Coding RNAs.
JD361662 - Sequence 342686 from Patent EP1572962.
MA564331 - JP 2018138019-A/136257: Polycomb-Associated Non-Coding RNAs.
MA564330 - JP 2018138019-A/136256: Polycomb-Associated Non-Coding RNAs.
MA564329 - JP 2018138019-A/136255: Polycomb-Associated Non-Coding RNAs.
MA564328 - JP 2018138019-A/136254: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9NZM3 (Reactome details) participates in the following event(s):

R-HSA-8862280 FCHo proteins bind nascent clathrin-coated pit
R-HSA-8866283 ARBB recruits GPCRs into clathrin-coated pits
R-HSA-8867756 CLASP proteins and cargo are recruited to the nascent clathrin-coated pit
R-HSA-8856813 AAK1 phosphorylates AP-2 mu subunit at T156
R-HSA-8856808 Recruitment of AP-2 complex and clathrin
R-HSA-8871194 RAB5 and GAPVD1 bind AP-2
R-HSA-8868658 HSPA8-mediated ATP hydrolysis promotes vesicle uncoating
R-HSA-8868659 Clathrin recruits auxilins to the clathrin-coated vesicle
R-HSA-8868661 Dynamin-mediated GTP hydrolysis promotes vesicle scission
R-HSA-8868660 Auxilin recruits HSPA8:ATP to the clathrin-coated vesicle
R-HSA-8868648 SYNJ hydrolyze PI(4,5)P2 to PI(4)P
R-HSA-8868071 Clathrin recruits PIK3C2A
R-HSA-8868230 SNX9 recruits components of the actin polymerizing machinery
R-HSA-8867754 F- and N- BAR domain proteins bind the clathrin-coated pit
R-HSA-8868236 BAR domain proteins recruit dynamin
R-HSA-8868072 Clathrin-associated PIK3C2A phosphorylates PI(4)P to PI(3,4)P2
R-HSA-8868651 Endophilins recruit synaptojanins to the clathrin-coated pit
R-HSA-8856828 Clathrin-mediated endocytosis
R-HSA-8856825 Cargo recognition for clathrin-mediated endocytosis
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000355123.1, ENST00000355123.2, ENST00000355123.3, ENST00000355123.4, ENST00000355123.5, ENST00000355123.6, ENST00000355123.7, ENST00000355123.8, ITSN2_HUMAN, KIAA1256, NM_006277, O95062, Q15812, Q9HAK4, Q9NXE6, Q9NYG0, Q9NZM2, Q9NZM3, Q9ULG4, SH3D1B, SWAP, uc317yyf.1, uc317yyf.2
UCSC ID: ENST00000355123.9_13
RefSeq Accession: NM_006277.3
Protein: Q9NZM3 (aka ITSN2_HUMAN or ITN2_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.