Human Gene CLVS1 (uc003xuh.3)
  Description: Homo sapiens clavesin 1 (CLVS1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr8:62,200,525-62,414,204 Size: 213,680 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr8:62,212,387-62,412,101 Size: 199,715 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:62,200,525-62,414,204)mRNA (may differ from genome)Protein (354 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsGeneNetworkH-INV
HGNCHPRDLynxMGIneXtProtOMIM
PubMedReactomeTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CLVS1_HUMAN
DESCRIPTION: RecName: Full=Clavesin-1; AltName: Full=Cellular retinaldehyde-binding protein-like; AltName: Full=Retinaldehyde-binding protein 1-like 1;
FUNCTION: Required for normal morphology of late endosomes and/or lysosomes in neurons (By similarity). Binds phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2).
SUBUNIT: Forms a complex with clathrin heavy chain and gamma- adaptin.
SUBCELLULAR LOCATION: Golgi apparatus, trans-Golgi network membrane; Peripheral membrane protein (By similarity). Cytoplasmic vesicle, clathrin-coated vesicle (By similarity). Early endosome membrane; Peripheral membrane protein.
TISSUE SPECIFICITY: Expressed mainly in the brain.
DOMAIN: The CRAL-TRIO domain is required for targeting to the membrane and for binding PtdIns(3,5)P2.
MISCELLANEOUS: Binding to PtdIns(3,5)P2 is not required for localization.
SIMILARITY: Contains 1 CRAL-TRIO domain.

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CLVS1
CDC HuGE Published Literature: CLVS1
Positive Disease Associations: Alzheimer Disease , Erythrocyte Count , Hemoglobins
Related Studies:
  1. Alzheimer Disease
    S J Furney et al. Molecular psychiatry 2011, Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease., Molecular psychiatry. [PubMed 21116278]
  2. Erythrocyte Count
    , , . [PubMed 0]
  3. Erythrocyte Count
    , , . [PubMed 0]
           more ... click here to view the complete list

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 2.19 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 14.29 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 -100.30324-0.310 Picture PostScript Text
3' UTR -512.732103-0.244 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
IPR001071 - CRAL-bd_toc_tran
IPR001251 - CRAL-TRIO_dom
IPR011074 - CRAL/TRIO_N_dom

Pfam Domains:
PF00650 - CRAL/TRIO domain
PF03765 - CRAL/TRIO, N-terminal domain
PF13716 - Divergent CRAL/TRIO domain

SCOP Domains:
46938 - CRAL/TRIO N-terminal domain
52087 - CRAL/TRIO domain

ModBase Predicted Comparative 3D Structure on Q8IUQ0
FrontTopSide
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 orthologGenome BrowserNo orthologNo ortholog
Gene Details  Gene Details  
Gene Sorter  Gene Sorter  
   FlyBase  
   Protein Sequence  
   Alignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0008289 lipid binding
GO:0080025 phosphatidylinositol-3,5-bisphosphate binding

Biological Process:
GO:0007040 lysosome organization

Cellular Component:
GO:0005768 endosome
GO:0005794 Golgi apparatus
GO:0005802 trans-Golgi network
GO:0016020 membrane
GO:0030136 clathrin-coated vesicle
GO:0031410 cytoplasmic vesicle
GO:0031901 early endosome membrane
GO:0032588 trans-Golgi network membrane


-  Descriptions from all associated GenBank mRNAs
  AF445194 - Homo sapiens unknown mRNA.
BC048992 - Homo sapiens cDNA clone IMAGE:5284856, containing frame-shift errors.
AK091641 - Homo sapiens cDNA FLJ34322 fis, clone FEBRA2008861.
AX747107 - Sequence 632 from Patent EP1308459.
BC042617 - Homo sapiens retinaldehyde binding protein 1-like 1, mRNA (cDNA clone MGC:34646 IMAGE:5192332), complete cds.
AY094971 - Homo sapiens cellular retinaldehyde-binding protein-like protein mRNA, complete cds.
AK313040 - Homo sapiens cDNA, FLJ93513.
CU692106 - Synthetic construct Homo sapiens gateway clone IMAGE:100021088 5' read RLBP1L1 mRNA.
HQ448548 - Synthetic construct Homo sapiens clone IMAGE:100071984; CCSB011093_03 hypothetical protein MGC34646 (RLBP1L1) gene, encodes complete protein.
KJ905019 - Synthetic construct Homo sapiens clone ccsbBroadEn_14413 CLVS1 gene, encodes complete protein.
AK125153 - Homo sapiens cDNA FLJ43163 fis, clone FCBBF3000168.
AK094567 - Homo sapiens cDNA FLJ37248 fis, clone BRAMY2006459.
JD507266 - Sequence 488290 from Patent EP1572962.
JD349350 - Sequence 330374 from Patent EP1572962.
JD076725 - Sequence 57749 from Patent EP1572962.
JD277957 - Sequence 258981 from Patent EP1572962.
JD216259 - Sequence 197283 from Patent EP1572962.
JD189211 - Sequence 170235 from Patent EP1572962.
JD515538 - Sequence 496562 from Patent EP1572962.
JD254992 - Sequence 236016 from Patent EP1572962.
JD510145 - Sequence 491169 from Patent EP1572962.
JD115736 - Sequence 96760 from Patent EP1572962.
JD073777 - Sequence 54801 from Patent EP1572962.
JD045887 - Sequence 26911 from Patent EP1572962.
JD529319 - Sequence 510343 from Patent EP1572962.
JD183284 - Sequence 164308 from Patent EP1572962.
JD197426 - Sequence 178450 from Patent EP1572962.
JD041085 - Sequence 22109 from Patent EP1572962.
JD440123 - Sequence 421147 from Patent EP1572962.
JD563209 - Sequence 544233 from Patent EP1572962.
JD387341 - Sequence 368365 from Patent EP1572962.
JD245366 - Sequence 226390 from Patent EP1572962.
JD376907 - Sequence 357931 from Patent EP1572962.
JD348446 - Sequence 329470 from Patent EP1572962.
JD512410 - Sequence 493434 from Patent EP1572962.
JD536086 - Sequence 517110 from Patent EP1572962.
JD093908 - Sequence 74932 from Patent EP1572962.

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

Protein Q8IUQ0 (Reactome details) participates in the following event(s):

R-HSA-5333658 CLAT:AP1:CLVS bind PI(3,5)P2
R-HSA-432720 Lysosome Vesicle Biogenesis
R-HSA-421837 Clathrin derived vesicle budding
R-HSA-199992 trans-Golgi Network Vesicle Budding
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: B2R7M5, C8UZT3, CLVS1_HUMAN, CRALBPL, NM_173519, NP_775790, Q8IUQ0, Q8NB32, RLBP1L1
UCSC ID: uc003xuh.3
RefSeq Accession: NM_173519
Protein: Q8IUQ0 (aka CLVS1_HUMAN)
CCDS: CCDS6176.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_173519.2
exon count: 6CDS single in 3' UTR: no RNA size: 3506
ORF size: 1065CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2250.00frame shift in genome: no % Coverage: 99.60
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
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.