Human Gene CLSTN2 (ENST00000458420.7) from GENCODE V44
  Description: Homo sapiens calsyntenin 2 (CLSTN2), mRNA. (from RefSeq NM_022131)
Gencode Transcript: ENST00000458420.7
Gencode Gene: ENSG00000158258.16
Transcript (Including UTRs)
   Position: hg38 chr3:139,935,185-140,577,397 Size: 642,213 Total Exon Count: 17 Strand: +
Coding Region
   Position: hg38 chr3:139,935,375-140,566,253 Size: 630,879 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr3:139,935,185-140,577,397)mRNA (may differ from genome)Protein (955 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Calsyntenin-2; AltName: Full=Alcadein-gamma; Short=Alc-gamma; Flags: Precursor;
FUNCTION: May modulate calcium-mediated postsynaptic signals (By similarity).
SUBCELLULAR LOCATION: Cell membrane; Single-pass type I membrane protein (Potential). Endoplasmic reticulum membrane. Golgi apparatus membrane. Note=Most prominent in the postsynaptic specializations of asymmetric (type I) synapses with both axodendritic and axospinous localization (By similarity).
TISSUE SPECIFICITY: Restricted to the brain.
DOMAIN: Binds synaptic Ca(2+) with its cytoplasmic domain (By similarity).
PTM: Proteolytically processed under normal cellular conditions. A primary zeta-cleavage generates a large extracellular (soluble) N- terminal domain (sAlc) and a short C-terminal transmembrane fragment (CTF1). A secondary cleavage catalyzed by gamma-secretase within the transmembrane domain releases the beta-Alc-gamma chain in the extracellular milieu and produces an intracellular fragment (AlcICD). This processing is strongly suppressed in the tripartite complex formed with APBA2 and APP, which seems to prevent the association with PSEN1 (By similarity).
SIMILARITY: Contains 2 cadherin domains.

-  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: CLSTN2
Diseases sorted by gene-association score: keratinizing squamous cell carcinoma (7), connective tissue cancer (1)

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 39.26 RPKM in Ovary
Total median expression: 135.06 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 -111.50190-0.587 Picture PostScript Text
3' UTR -3439.2011144-0.309 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
IPR002126 - Cadherin
IPR015919 - Cadherin-like
IPR008985 - ConA-like_lec_gl_sf
IPR013320 - ConA-like_subgrp

Pfam Domains:
PF00028 - Cadherin domain

ModBase Predicted Comparative 3D Structure on Q9H4D0
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
Genome BrowserGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005509 calcium ion binding

Biological Process:
GO:0007155 cell adhesion
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules
GO:0050806 positive regulation of synaptic transmission
GO:0051965 positive regulation of synapse assembly

Cellular Component:
GO:0000139 Golgi membrane
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0005886 plasma membrane
GO:0009986 cell surface
GO:0014069 postsynaptic density
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0045211 postsynaptic membrane

-  Descriptions from all associated GenBank mRNAs
  AK315308 - Homo sapiens cDNA, FLJ96337, highly similar to Homo sapiens calsyntenin 2 (CLSTN2), mRNA.
AK096432 - Homo sapiens cDNA FLJ39113 fis, clone NTONG2005897, highly similar to Calsyntenin-2 precursor.
BC103496 - Homo sapiens calsyntenin 2, mRNA (cDNA clone MGC:119559 IMAGE:40008317), complete cds.
AJ278018 - Homo sapiens mRNA for calsyntenin-2 (CS2 gene).
BC103506 - Homo sapiens calsyntenin 2, mRNA (cDNA clone MGC:119561 IMAGE:40008319), complete cds.
BC104485 - Homo sapiens calsyntenin 2, mRNA (cDNA clone MGC:119560 IMAGE:40008318), complete cds.
KJ903050 - Synthetic construct Homo sapiens clone ccsbBroadEn_12444 CLSTN2 gene, encodes complete protein.
AY753303 - Homo sapiens alcadein gamma mRNA, complete cds.
AK056411 - Homo sapiens cDNA FLJ31849 fis, clone NT2RP7000586, highly similar to Calsyntenin-2 precursor.
JD272577 - Sequence 253601 from Patent EP1572962.
JD341293 - Sequence 322317 from Patent EP1572962.
DL492665 - Novel nucleic acids.
BC004871 - Homo sapiens calsyntenin 2, mRNA (cDNA clone IMAGE:3938696), partial cds.
BC007943 - Homo sapiens calsyntenin 2, mRNA (cDNA clone IMAGE:4130487), partial cds.
AK096818 - Homo sapiens cDNA FLJ39499 fis, clone PROST2016777, highly similar to Calsyntenin-2 precursor.
JD207062 - Sequence 188086 from Patent EP1572962.
JD488332 - Sequence 469356 from Patent EP1572962.
JD232279 - Sequence 213303 from Patent EP1572962.
JD117876 - Sequence 98900 from Patent EP1572962.
JD280659 - Sequence 261683 from Patent EP1572962.
JD500104 - Sequence 481128 from Patent EP1572962.
JD234439 - Sequence 215463 from Patent EP1572962.
JD291557 - Sequence 272581 from Patent EP1572962.
JD123779 - Sequence 104803 from Patent EP1572962.
JD403763 - Sequence 384787 from Patent EP1572962.
JD432278 - Sequence 413302 from Patent EP1572962.
JD421171 - Sequence 402195 from Patent EP1572962.
JD443709 - Sequence 424733 from Patent EP1572962.
JD425487 - Sequence 406511 from Patent EP1572962.
JD272420 - Sequence 253444 from Patent EP1572962.
JD061757 - Sequence 42781 from Patent EP1572962.
JD438381 - Sequence 419405 from Patent EP1572962.
JD068177 - Sequence 49201 from Patent EP1572962.
JD078474 - Sequence 59498 from Patent EP1572962.
JD479127 - Sequence 460151 from Patent EP1572962.
JD155550 - Sequence 136574 from Patent EP1572962.
JD450489 - Sequence 431513 from Patent EP1572962.
JD092126 - Sequence 73150 from Patent EP1572962.
JD100197 - Sequence 81221 from Patent EP1572962.
JD124139 - Sequence 105163 from Patent EP1572962.
JD137490 - Sequence 118514 from Patent EP1572962.
JD074474 - Sequence 55498 from Patent EP1572962.
AK056386 - Homo sapiens cDNA FLJ31824 fis, clone NT2RP6000060.
JD054410 - Sequence 35434 from Patent EP1572962.
JD023764 - Sequence 4788 from Patent EP1572962.
JD028815 - Sequence 9839 from Patent EP1572962.
JD033434 - Sequence 14458 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B2RCW5, CS2, CSTN2_HUMAN, D3DNF4, ENST00000458420.1, ENST00000458420.2, ENST00000458420.3, ENST00000458420.4, ENST00000458420.5, ENST00000458420.6, NM_022131, Q3SX54, Q3ZB76, Q5UE56, Q96HZ2, Q9BSS0, Q9H4D0, uc003etn.1, uc003etn.2, uc003etn.3, uc003etn.4
UCSC ID: ENST00000458420.7
RefSeq Accession: NM_022131
Protein: Q9H4D0 (aka CSTN2_HUMAN or CLS2_HUMAN)
CCDS: CCDS3112.1

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