Human Gene CLSTN1 (uc001aqh.3) Description and Page Index
  Description: Homo sapiens calsyntenin 1 (CLSTN1), transcript variant 1, mRNA.
RefSeq Summary (NM_001009566): This gene is a member of the calsyntenin family, a subset of the cadherin superfamily. The encoded transmembrane protein, also known as alcadein-alpha, is thought to bind to kinesin-1 motors to mediate the axonal anterograde transport of certain types of vesicle. Amyloid precursor protein (APP) is trafficked via these vesicles and so this protein is being investigated to see how it might contribute to the mechanisms underlying Alzheimer's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014].
Transcript (Including UTRs)
   Position: hg19 chr1:9,789,079-9,884,550 Size: 95,472 Total Exon Count: 19 Strand: -
Coding Region
   Position: hg19 chr1:9,790,566-9,883,791 Size: 93,226 Coding Exon Count: 19 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr1:9,789,079-9,884,550)mRNA (may differ from genome)Protein (981 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Calsyntenin-1; AltName: Full=Alcadein-alpha; Short=Alc-alpha; AltName: Full=Alzheimer-related cadherin-like protein; AltName: Full=Non-classical cadherin XB31alpha; Contains: RecName: Full=Soluble Alc-alpha; Short=SAlc-alpha; Contains: RecName: Full=CTF1-alpha; AltName: Full=C-terminal fragment 1-alpha; Flags: Precursor;
FUNCTION: Induces KLC1 association with vesicles and functions as a cargo in axonal anterograde transport. Complex formation with APBA2 and APP, stabilizes APP metabolism and enhances APBA2- mediated suppression of beta-APP40 secretion, due to the retardation of intracellular APP maturation. In complex with APBA2 and C99, a C-terminal APP fragment, abolishes C99 interaction with PSEN1 and thus APP C99 cleavage by gamma-secretase, most probably through stabilization of the direct interaction between APBA2 and APP. The intracellular fragment AlcICD suppresses APBB1-dependent transactivation stimulated by APP C-terminal intracellular fragment (AICD), most probably by competing with AICD for APBB1- binding. May modulate calcium-mediated postsynaptic signals (By similarity).
SUBUNIT: Directly interacts with APBA2. Forms a tripartite complex with APBA2 and APP. The CTF1 chain interacts with PSEN1. The intracellular fragment AlcICD interacts with APBB1; this interaction stabilizes AlcICD metabolism. Interacts with KLC1 and APBB1 (By similarity).
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Single-pass type I membrane protein. Golgi apparatus membrane. Cell projection. Cell junction, synapse, postsynaptic cell membrane; Single-pass type I membrane protein (By similarity). Nucleus. Note=Neurite tips. Localized in the postsynaptic membrane of both excitatory and inhibitory synapses (By similarity). The AlcICD fragment is translocated to the nucleus upon interaction with APBB1.
TISSUE SPECIFICITY: Expressed in the brain and, a lower level, in the heart, skeletal muscle, kidney and placenta. Accumulates in dystrophic neurites around the amyloid core of Alzheimer disease senile plaques (at protein level).
DOMAIN: The cytoplasmic domain is involved in interaction with APBA2, as well as the binding of synaptic Ca(2+) (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 presenilin gamma-secretase within the transmembrane domain releases the beta- Alc-alpha 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.
SIMILARITY: Contains 2 cadherin domains.
SEQUENCE CAUTION: Sequence=BAA74934.2; Type=Erroneous initiation;

-  MalaCards Disease Associations
  MalaCards Gene Search: CLSTN1
Diseases sorted by gene-association score: corneal dystrophy, schnyder type (7), alzheimer disease (4)

-  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: 126.10 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 1539.90 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 -435.20759-0.573 Picture PostScript Text
3' UTR -556.061487-0.374 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
PF13385 - Concanavalin A-like lectin/glucanases superfamily

SCOP Domains:
49313 - Cadherin-like
49899 - Concanavalin A-like lectins/glucanases

ModBase Predicted Comparative 3D Structure on O94985
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 Protein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001540 beta-amyloid binding
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0019894 kinesin binding
GO:0042988 X11-like protein binding

Biological Process:
GO:0001558 regulation of cell growth
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:0005576 extracellular region
GO:0005634 nucleus
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:0030054 cell junction
GO:0042995 cell projection
GO:0045202 synapse
GO:0045211 postsynaptic membrane

-  Descriptions from all associated GenBank mRNAs
  LF383932 - JP 2014500723-A/191435: Polycomb-Associated Non-Coding RNAs.
AF438482 - Homo sapiens non-classical cadherin XB31alpha1 (XB31alpha) mRNA, complete cds.
AB020718 - Homo sapiens KIAA0911 mRNA for KIAA0911 protein.
BC033902 - Homo sapiens calsyntenin 1, mRNA (cDNA clone MGC:33741 IMAGE:5263192), complete cds.
AK304813 - Homo sapiens cDNA FLJ61580 complete cds, highly similar to Calsyntenin-1 precursor.
AK289798 - Homo sapiens cDNA FLJ76750 complete cds, highly similar to Homo sapiens calsyntenin 1 (CLSTN1), transcript variant 2, mRNA.
AY753301 - Homo sapiens alcadein alpha-1 mRNA, complete cds.
DQ891263 - Synthetic construct clone IMAGE:100003893; FLH170543.01X; RZPDo839G0798D calsyntenin 1 (CLSTN1) gene, encodes complete protein.
DQ894450 - Synthetic construct Homo sapiens clone IMAGE:100008910; FLH170539.01L; RZPDo839G0797D calsyntenin 1 (CLSTN1) gene, encodes complete protein.
AB587312 - Synthetic construct DNA, clone: pF1KA0911, Homo sapiens CLSTN1 gene for calsyntenin 1, without stop codon, in Flexi system.
MA619509 - JP 2018138019-A/191435: Polycomb-Associated Non-Coding RNAs.
LF206735 - JP 2014500723-A/14238: Polycomb-Associated Non-Coding RNAs.
AK225500 - Homo sapiens mRNA for calsyntenin 1 isoform 1 variant, clone: JTH08932.
AK000605 - Homo sapiens cDNA FLJ20598 fis, clone KAT07882, highly similar to AB020718 Homo sapiens mRNA for KIAA0911 protein.
AK056820 - Homo sapiens cDNA FLJ32258 fis, clone PROST1000272, highly similar to Calsyntenin-1 precursor.
AK001591 - Homo sapiens cDNA FLJ10729 fis, clone NT2RP3001260, highly similar to Calsyntenin-1 precursor.
JD328608 - Sequence 309632 from Patent EP1572962.
LF357463 - JP 2014500723-A/164966: Polycomb-Associated Non-Coding RNAs.
JD063970 - Sequence 44994 from Patent EP1572962.
LF357462 - JP 2014500723-A/164965: Polycomb-Associated Non-Coding RNAs.
JD280686 - Sequence 261710 from Patent EP1572962.
JD396529 - Sequence 377553 from Patent EP1572962.
JD279208 - Sequence 260232 from Patent EP1572962.
JD424603 - Sequence 405627 from Patent EP1572962.
JD118246 - Sequence 99270 from Patent EP1572962.
JD379148 - Sequence 360172 from Patent EP1572962.
JD288714 - Sequence 269738 from Patent EP1572962.
JD231244 - Sequence 212268 from Patent EP1572962.
JD442093 - Sequence 423117 from Patent EP1572962.
JD221282 - Sequence 202306 from Patent EP1572962.
LF357461 - JP 2014500723-A/164964: Polycomb-Associated Non-Coding RNAs.
JD497366 - Sequence 478390 from Patent EP1572962.
JD485517 - Sequence 466541 from Patent EP1572962.
JD518934 - Sequence 499958 from Patent EP1572962.
JD218168 - Sequence 199192 from Patent EP1572962.
JD303658 - Sequence 284682 from Patent EP1572962.
JD415967 - Sequence 396991 from Patent EP1572962.
LF357460 - JP 2014500723-A/164963: Polycomb-Associated Non-Coding RNAs.
JD516520 - Sequence 497544 from Patent EP1572962.
JD111643 - Sequence 92667 from Patent EP1572962.
JD298040 - Sequence 279064 from Patent EP1572962.
JD482247 - Sequence 463271 from Patent EP1572962.
LF357459 - JP 2014500723-A/164962: Polycomb-Associated Non-Coding RNAs.
LF357458 - JP 2014500723-A/164961: Polycomb-Associated Non-Coding RNAs.
LF357457 - JP 2014500723-A/164960: Polycomb-Associated Non-Coding RNAs.
LF357456 - JP 2014500723-A/164959: Polycomb-Associated Non-Coding RNAs.
LF357455 - JP 2014500723-A/164958: Polycomb-Associated Non-Coding RNAs.
LF357454 - JP 2014500723-A/164957: Polycomb-Associated Non-Coding RNAs.
LF357453 - JP 2014500723-A/164956: Polycomb-Associated Non-Coding RNAs.
JD022953 - Sequence 3977 from Patent EP1572962.
AY545556 - Homo sapiens calsyntenin 1-like mRNA, complete sequence.
JD034524 - Sequence 15548 from Patent EP1572962.
LF357452 - JP 2014500723-A/164955: Polycomb-Associated Non-Coding RNAs.
LF357451 - JP 2014500723-A/164954: Polycomb-Associated Non-Coding RNAs.
LF357450 - JP 2014500723-A/164953: Polycomb-Associated Non-Coding RNAs.
LF357449 - JP 2014500723-A/164952: Polycomb-Associated Non-Coding RNAs.
LF357448 - JP 2014500723-A/164951: Polycomb-Associated Non-Coding RNAs.
LF357444 - JP 2014500723-A/164947: Polycomb-Associated Non-Coding RNAs.
LF357443 - JP 2014500723-A/164946: Polycomb-Associated Non-Coding RNAs.
LF357442 - JP 2014500723-A/164945: Polycomb-Associated Non-Coding RNAs.
LF357441 - JP 2014500723-A/164944: Polycomb-Associated Non-Coding RNAs.
LF357440 - JP 2014500723-A/164943: Polycomb-Associated Non-Coding RNAs.
LF357439 - JP 2014500723-A/164942: Polycomb-Associated Non-Coding RNAs.
LF357438 - JP 2014500723-A/164941: Polycomb-Associated Non-Coding RNAs.
LF357437 - JP 2014500723-A/164940: Polycomb-Associated Non-Coding RNAs.
MA442312 - JP 2018138019-A/14238: Polycomb-Associated Non-Coding RNAs.
MA593040 - JP 2018138019-A/164966: Polycomb-Associated Non-Coding RNAs.
MA593039 - JP 2018138019-A/164965: Polycomb-Associated Non-Coding RNAs.
MA593038 - JP 2018138019-A/164964: Polycomb-Associated Non-Coding RNAs.
MA593037 - JP 2018138019-A/164963: Polycomb-Associated Non-Coding RNAs.
MA593036 - JP 2018138019-A/164962: Polycomb-Associated Non-Coding RNAs.
MA593035 - JP 2018138019-A/164961: Polycomb-Associated Non-Coding RNAs.
MA593034 - JP 2018138019-A/164960: Polycomb-Associated Non-Coding RNAs.
MA593033 - JP 2018138019-A/164959: Polycomb-Associated Non-Coding RNAs.
MA593032 - JP 2018138019-A/164958: Polycomb-Associated Non-Coding RNAs.
MA593031 - JP 2018138019-A/164957: Polycomb-Associated Non-Coding RNAs.
MA593030 - JP 2018138019-A/164956: Polycomb-Associated Non-Coding RNAs.
MA593029 - JP 2018138019-A/164955: Polycomb-Associated Non-Coding RNAs.
MA593028 - JP 2018138019-A/164954: Polycomb-Associated Non-Coding RNAs.
MA593027 - JP 2018138019-A/164953: Polycomb-Associated Non-Coding RNAs.
MA593026 - JP 2018138019-A/164952: Polycomb-Associated Non-Coding RNAs.
MA593025 - JP 2018138019-A/164951: Polycomb-Associated Non-Coding RNAs.
MA593021 - JP 2018138019-A/164947: Polycomb-Associated Non-Coding RNAs.
MA593020 - JP 2018138019-A/164946: Polycomb-Associated Non-Coding RNAs.
MA593019 - JP 2018138019-A/164945: Polycomb-Associated Non-Coding RNAs.
MA593018 - JP 2018138019-A/164944: Polycomb-Associated Non-Coding RNAs.
MA593017 - JP 2018138019-A/164943: Polycomb-Associated Non-Coding RNAs.
MA593016 - JP 2018138019-A/164942: Polycomb-Associated Non-Coding RNAs.
MA593015 - JP 2018138019-A/164941: Polycomb-Associated Non-Coding RNAs.
MA593014 - JP 2018138019-A/164940: Polycomb-Associated Non-Coding RNAs.
LF357436 - JP 2014500723-A/164939: Polycomb-Associated Non-Coding RNAs.
LF211968 - JP 2014500723-A/19471: Polycomb-Associated Non-Coding RNAs.
LF212990 - JP 2014500723-A/20493: Polycomb-Associated Non-Coding RNAs.
JD422387 - Sequence 403411 from Patent EP1572962.
JD388613 - Sequence 369637 from Patent EP1572962.
JD470563 - Sequence 451587 from Patent EP1572962.
JD394599 - Sequence 375623 from Patent EP1572962.
JD226480 - Sequence 207504 from Patent EP1572962.
JD253409 - Sequence 234433 from Patent EP1572962.
JD210605 - Sequence 191629 from Patent EP1572962.
JD398237 - Sequence 379261 from Patent EP1572962.
JD341682 - Sequence 322706 from Patent EP1572962.
JD214641 - Sequence 195665 from Patent EP1572962.
JD487768 - Sequence 468792 from Patent EP1572962.
JD060725 - Sequence 41749 from Patent EP1572962.
MA593013 - JP 2018138019-A/164939: Polycomb-Associated Non-Coding RNAs.
MA447545 - JP 2018138019-A/19471: Polycomb-Associated Non-Coding RNAs.
MA448567 - JP 2018138019-A/20493: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K183, CS1, CSTN1_HUMAN, KIAA0911, NM_001009566, NP_001009566, O94985, Q5SR52, Q5UE58, Q71MN0, Q8N4K9
UCSC ID: uc001aqh.3
RefSeq Accession: NM_001009566
Protein: O94985 (aka CSTN1_HUMAN or CLS1_HUMAN)
CCDS: CCDS105.1, CCDS30580.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_001009566.1
exon count: 19CDS single in 3' UTR: no RNA size: 5209
ORF size: 2946CDS single in intron: no Alignment % ID: 99.98
txCdsPredict score: 6032.00frame shift in genome: no % Coverage: 99.67
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.