VPS13A Gene
protein-coding GIFtS : 57
GC09P078982
vacuolar protein sorting 13 homolog A (S. cerevisiae) (Previous names: chorea acanthocytosis, vacuolar protein sorting 13A (yeast) )Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database (Previous symbol: CHAC )
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Aliases & Descriptions for VPS13A
(According to
1 HGNC ,
2 Entrez Gene ,
3 UniProtKB/Swiss-Prot ,
4 UniProtKB/TrEMBL , 5 OMIM , 6 GeneLoc
, and/or 7 Ensembl ,
8 miRBase )About This Section
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Aliases CHAC 2 , 3 , 5 CHOREIN 2 Chorein 3 FLJ42030 2 KIAA0986 1 , 2 , 3
Descriptions Chorea-acanthocytosis protein 3 chorea acanthocytosis 1 vacuolar protein sorting 13 homolog A (S. cerevisiae) 2 vacuolar protein sorting 13A 2 vacuolar protein sorting 13A (yeast) 1
Search outside databases for aliases for VPS13A genePrevious GC identifers: GC09P075249 GC09P077021
Summaries for VPS13A (According to Entrez Gene ,
Wikipedia's
Gene Wiki ,
UniProtKB/Swiss-Prot ,
and/or
UniProtKB/TrEMBL )
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EntrezGene summary for VPS13A : The protein encoded by this gene may control steps in the cycling of proteins through thetrans-Golgi network to endosomes, lysosomes and the plasma membrane. Mutations in this gene causethe autosomal recessive disorder, chorea-acanthocytosis. Alternative splicing of this gene resultsin multiple transcript variants. [provided by RefSeq] UniProtKB/Swiss-Prot: VP13A_HUMAN, Q96RL7 Function : May play a role in the control of protein cycling through the trans-Golgi network toearly and late endosomes, lysosomes and plasma membrane
Gene Wiki entry for VPS13A
Genomic Location for VPS13A
(According to
GeneLoc and/or
HGNC , and/or
Entrez Gene (NCBI build 36) ,
and/or miRBase ,
Genomic Views according to
UCSC and
Ensembl ,
Transcription factor binding sites according to
SABiosciences )About This Section
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Genomic View : UCSC Golden Path with GeneCards custom track Transcription factor binding sites upstream to the VPS13A gene Entrez Gene cytogenetic band: 9q21 Ensembl cytogenetic band: 9q21.13 HGNC cytogenetic band: 9q21 VPS13A Gene in genomic location: bands according to Ensembl, locations according to
(and/or Entrez Gene and/or Ensembl if different) GeneLoc gene densities for chromosome 9 GeneLoc Exon Structure
GeneLoc location for GC09P078982:
(about GC identifiers )
Start:
78,982,181 bp from pter
End:
79,222,219 bp from pter
Size:
240,039 bases
Orientation:
plus strand
RefSeq DNA sequence: NC_000009.10 NT_023935.17 Proteins for VPS13A
(According to
1 UniProtKB ,
and/or Ensembl ,
Phosphorylation sites according to 2 Phosphosite ,
RefSeq according to NCBI ,
PDB rendering according to OCA and/or Proteopedia ,
Recombinant Proteins
from Invitrogen ,
Millipore ,
Sigma-Aldrich ,
R&D Systems ,
Enzo Life Sciences ,
Abnova ,
OriGene and/or,
Abcam ,
Biochemical Assays by
Invitrogen ,
Millipore ,
R&D Systems ,
Cell Signaling Technology , and/or
Enzo Life Sciences ,
Ontologies according to Gene
Ontology Consortium 01 Apr 2009 and
Entrez Gene ,
Antibodies by Invitrogen ,
Millipore ,
Sigma-Aldrich ,
R&D Systems ,
Cell Signaling Technology ,
Abcam ,
Abnova , and/or
Novus Biologicals )
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UniProtKB/Swiss-Prot: VP13A_HUMAN, Q96RL7 (See
protein sequence )Recommended Name: Vacuolar protein sorting-associated protein 13A Size : 3174 amino acids; 360276 Da
Sequence caution : Sequence=AAH20576.1; Type=Miscellaneous discrepancy; Note=Intron retention;
Secondary accessions : Q5JSX9 Q5JSY0 Q5VYR5 Q702P4 Q709D0 Q86YF8 Q96S61 Q9H995 Q9Y2J1Alternative splicing : 4 isoforms : Q96RL7-1 Q96RL7-2 Q96RL7-3 Q96RL7-4
Post-translational modifications:
View phosphorylation sites using PhosphoSite 2
REFSEQ proteins (4 alternative transcripts):
NP_001018047.1 NP_001018048.1 NP_056001.1 NP_150648.2 ENSEMBL proteins: ENSP00000365821 ENSP00000348011 ENSP00000349985 ENSP00000365834 ENSP00000353422 ENSP00000365823 Human Recombinant Proteins Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 1 Gene Ontology (GO) cellular component term (links to tree view) :
About this table Antibodies for VPS13A: Assays for VPS13A:
Protein
Domains/ Families for VPS13A(According to InterPro , ProtoNet ,
UniProtKB , and/or BLOCKS ,
Sets of similar genes according to GeneDecks )
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Graphical View of Domain Structure for InterPro Entry Q96RL7 ProtoNet protein and cluster: Q96RL7
1 Blocks protein family : IPB009543 Protein of unknown function DUF1162 UniProtKB/Swiss-Prot: VP13A_HUMAN, Q96RL7 Similarity : Belongs to the VPS13 familySimilarity : Contains 10 TPR repeats
Gene Function for VPS13A
(According to MGI Jun 06 2009, UniProtKB ,
IUBMB ,and/or Genatlas ,
shRNA from
OriGene ,
Sigma-Aldrich , RNAi from
Sigma-Aldrich ,
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Clones , and
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from Invitrogen ,
Millipore ,
OriGene , and/or
Abnova ,
siRNAs from
Applied Biosystems ,
SYBR primers from OriGene ,
Cell-based Assays from Millipore ,
Ontologies according to Gene Ontology Consortium 01 Apr 2009 via
Entrez Gene .)
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               OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 4 ): NM_033305 Applied Biosystems Silencer ® siRNAs for VPS13A Sigma-Aldrich siRNA for VPS13A Sigma-Aldrich shRNA for VPS13A Explore Sigma-Aldrich super-pooled esiRNAs                OriGene GFP tagged cDNA clones in CMV expression vector (see all 4 ): NM_001018037                                  Myc/DDK tagged cDNA clones in CMV expression vector (see all 4 ): NM_001018037                                  untagged cDNA clones in CMV expression vector (see all 4 ): NM_001018037  Primers: Browse
Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers               OriGene genome-wide validated SYBR primer pairs: NM_033305 UniProtKB/Swiss-Prot: VP13A_HUMAN, Q96RL7 Function : May play a role in the control of protein cycling through the trans-Golgi network toearly and late endosomes, lysosomes and plasma membrane
3 MGI mutant phenotypes (inferred from 1 allele ) (MGI details for Vps13a) :1 Gene Ontology (GO) molecular function term (links to tree view) :
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Pathways & Interactions for VPS13A
(Pathways according to Invitrogen
(maps by GeneGo ),
Millipore ,
Cell Signaling Technology ,
Sigma-Aldrich ,
KEGG
and/or UniProtKB ,
Sets of similar genes according to GeneDecks ,
Proteins Network according to
SABiosciences ,
Interactions according to 1 UniProtKB ,
2 MINT , and/or
3 STRING ,
with links to IntAct and
Ensembl ,
Ontologies according to Gene Ontology Consortium 01 Apr 2009 via
Entrez Gene .)
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5/10 Interacting proteins for VPS13A (ENSP00000353422 3 Q96RL7 1 ) via UniProtKB, MINT, and/or STRING (see all 10
)About this table 3 Gene Ontology (GO) biological process terms (links to tree view) :
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Drugs & Compounds for VPS13A (Chemical Compounds according to UniProtKB , Enzo Life Sciences ,
Sigma-Aldrich , Tocris Bioscience , and/or
Novoseek and Drugs according to
Enzo Life Sciences and/or
PharmGKB )
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Transcripts for VPS13A(GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 219 Homo sapiens; Jun 2 2009) or GenBank , RefSeq according to Entrez Gene ,
DOTS (version 10), and/or
AceView ,
non coding RNAs according to
RNAdb ,
ESTs according to GeneTide ,
exon structure from GeneLoc ,
alternative splicing isoforms according to ASD and/or
ECgene ,
RNAi Products from Invitrogen ,
Millipore , and/or
Abnova ,
siRNAs from Applied Biosystems ,
Sigma-Aldrich ,
shRNA from
Sigma-Aldrich ,
OriGene ,
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               OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 4 ): NM_033305 Sigma-Aldrich siRNA for VPS13A Sigma-Aldrich shRNA for VPS13A Explore Sigma-Aldrich super-pooled esiRNAs
Applied Biosystems Silencer ® siRNAs: NM_001018037 NM_001018038 NM_015186 NM_033305
REFSEQ mRNAs for VPS13A gene (4 alternative transcripts): NM_001018037.1 NM_001018038.2 NM_015186.3 NM_033305.2
Applied Biosystems TaqMan ® Gene Expression Assays: NM_001018037 NM_001018038 NM_015186 NM_033305
               OriGene GFP tagged cDNA clones in CMV expression vector (see all 4 ): NM_001018037                                  Myc/DDK tagged cDNA clones in CMV expression vector (see all 4 ): NM_001018037                                  untagged cDNA clones in CMV expression vector (see all 4 ): NM_001018037  
Additional cDNA sequence: AB023203.1 AB054005.1 AF337532.1 AJ608769.1 AJ626859.1 AK000273.1 AK022967.1 AK027023.1 AK124024.1 BC020576.1 BC041852.1
10 DOTS entries : DT.100775273 DT.310392 DT.100707617 DT.97795858 DT.440997 DT.97803626 DT.101981083 DT.40208402 DT.86851769 DT.87046558
24/142 AceView cDNA sequences (see all 142
):AA132420 BQ718291 AA702210 AW301250 CB131398 AJ430440 BM126912 BQ011213 AK124024 NM_015186 AW967417 BU902765 AB023203 AI700589 BX111825 AJ608769 CA406082 AA573476 BQ185252 BM837858 AW189007 BE348288 AW301542 AI202451
highest scoring ESTs for VPS13A :AI084224 AA228874 AA328381 AA513312 AA702210 AA830309 AA888785 AB023203 AI218624 AI279826
Unigene Cluster for VPS13A: Vacuolar protein sorting 13 homolog A (S. cerevisiae) Hs.459790 [show with all ESTs ] Unigene Representative Sequence: AF337532 GeneLoc Exon Structure 5/9 Alternative Splicing Database (ASD) splice patterns (SP) for VPS13A (see all 9
) ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19a · 19b ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25a · SP1 :                         -                             SP2 :                                                     SP3 :                                                     SP4 :                                                     SP5 :                                                    
ExUns: 25b ^ 26a · 26b ^ 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32a · 32b ^ 33 ^ 34 SP1 :                         SP2 :                         SP3 :                         SP4 :                         SP5 :                        
About this scheme ECgene alternative splicing isoforms for VPS13A 6 Ensembl transcripts including schematic representations : ENST00000376634
ENST00000355766
ENST00000357409
ENST00000376646
ENST00000360280
ENST00000376636
Expression for VPS13A
(Experimental results according to
1 GeneNote
and GNF BioGPS ,
probe sets-to-genes annotations according to
2 GeneAnnot ,
3 GeneTide ,
Sets of similar genes according to GeneDecks ,
Electronic Northern calculations according to data from
UniGene (Build 219 Homo sapiens),
SAGE tags according to
CGAP ,
plus additional links to
SOURCE , and/or
GNF
BioGPS , and/or
EXPOLDB , and/or
UniProtKB ,
Expression Assays from
Applied Biosystems
)
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VPS13A expression in normal and diseased human tissues Applied Biosystems TaqMan ® Gene Expression Assays for VPS13A 1 / 2 / 3
14 probe-sets matching VPS13A gene Data from
(Publications) and GNF BioGPS About these images About these images CGAP SAGE TAG: --SOURCE GeneReport for Unigene cluster: Hs.459790 Expression variation in blood from EXPOLDB for VPS13A
UniProtKB/Swiss-Prot: VP13A_HUMAN, Q96RL7 Tissue specificity : Widely expressed. Higher expression is found in brain, heart, skeletal muscleand kidney
Orthologs for VPS13A
(Orthologs according to
1,2 HomoloGene (2 older version, for species not in 1 newer version),
3 euGenes ,
4 SGD
and/or
5 MGI Jun 06 2009,
with possible further links to
Flybase
and/or
WormBase ,
Gene Trees according to Ensembl )
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Orthologs for VPS13A gene from 5/16 species (see all 16
)
About this table Species with no ortholog for VPS13A ENSEMBL Gene Tree for VPS13A Paralogs for VPS13A (Paralogs according to 1 HomoloGene and 2 Ensembl , Pseudogenes according to 3 Pseudogene.org )About This Section
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Paralogs for VPS13A gene VPS13D 2 VPS13C 2
SNPs/Variants for VPS13A (According to the
1 NCBI SNP Database ,
2 Ensembl ,
3 PupaSUITE , and
UniProtKB ,
Linkage Disequilibrium by HapMap ,
Genotyping Reagents from
Applied Biosystems )
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HapMap Linkage Disequilibrium images for VPS13A (up to first 250kb)
Disorders & Mutations for VPS13A
(in which this Gene is Involved, According to
OMIM, UniProtKB ,
Novoseek , PharmGKB ,
Genatlas , GeneTests ,
Blood group antigen gene mutations by BGMUT ,
HGMD, GAD ,
HuGE Navigator ,
BCGD ,
and/or TGDB .)
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OMIM: 605978 disorders : 200150 UniProtKB/Swiss-Prot: VP13A_HUMAN, Q96RL7
Defects in VPS13A are the cause of chorea-acanthocytosis (CHAC) [MIM:200150]. CHAC is anautosomal recessive neurodegenerative disorder characterized by the gradual onset of hyperkineticmovements and abnormal erythrocyte morphology. Basal ganglia atrophy in the brain is apathological feature of the disease. Other clinical symptoms include psychiatric features,epilepsy, peripheral neuropathy, myopathy and oral self-mutilation
4 Novoseek disease relationships for VPS13A gene
Disease
Score
Articles
PubMed IDs for Articles with Shared Sentences (# sentences)
chacs
99.02
38
12404112 (7), 14663054 (4), 17345646 (2), 17070500 (2) (see all 13 )
chorea-acanthocytosis
98.59
14
14663054 (2), 12404112 (2), 15293285 (1), 15498460 (1) (see all 8 )
huntington disease
64.94
3
17345646 (1), 15293285 (1), 11761473 (1)
neurodegenerative diseases
59.73
4
15914612 (1), 17070500 (1), 17673232 (1)
About this table GeneTests: VPS13A Chorea-Acanthocytosis Human Gene Mutation Database : VPS13A
Medical News for VPS13A (Possibly Related Articles in
Doctor's Guide )
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--
Publications for VPS13A (in
PubMed .
Associations of this gene to articles via
1 Novoseek ,
2 HGNC ,
3 Entrez Gene ,
4 UniProtKB/Swiss-Prot ,
5 UniProtKB/TrEMBL ,
6 GAD , and/or
7 PharmGKB )
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10/29 PubMed articles for VPS13A gene (see all 29
): A conserved sorting-associated protein is mutant in chorea-acanthocytosis. (PubMed id 11381253) 2, 3, 4 Rampoldi L....Monaco A.P. (2001) Analysis of the human VPS13 gene family. (PubMed id 15498460) 1, 3, 4 Velayos-Baeza A....Monaco A.P. (2004) The gene encoding a newly discovered protein, chorein, is mutated in chorea-acanthocytosis. (PubMed id 11381254) 1, 3, 4 Ueno S.... Sano A. (2001) DNA sequence and analysis of human chromosome 9. (PubMed id 15164053) 3, 4 Humphray S.J.... Dunham I. (2004) The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334) 3, 4 Gerhard D.S....Malek J. (2004) Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039) 3, 4 Ota T....Sugano S. (2004) Prediction of the coding sequences of unidentified human genes. XIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 10231032) 3, 4 Nagase T....Ohara O. (1999) Chorea-acanthocytosis: genetic linkage to chromosome 9q21. (PubMed id 9382101) 2, 3 Rubio J.P....Monaco A.P. (1997) Clinical and molecular genetic assessment of a chorea-acanthocytosis pedigree. (PubMed id 17673232) 1, 3 Ichiba M....Sano A. (2007) Choreoacanthocytosis in a Mexican family. (PubMed id 17998451) 1, 3 Ruiz-Sandoval J.L....Perez-Garcia G. (2007)
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Genome Databases showing VPS13A
(According to
Entrez Gene ,
HGNC ,
AceView ,
euGenes ,
Ensembl ,
miRBase ,
ECgene ,
and/or
H-InvDB )
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Other Databases showing VPS13A
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Specialized Databases showing VPS13A (According to ATLAS , HORDE , IMGT , MTDB, LEIDEN , UniProtKB/Swiss-Prot , and/or UniProtKB/TrEMBL ,Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot )About This Section
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Name Description
GeneReviews http://www.genetests.org/query?gene=VPS13A
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-- Services for VPS13A (Reagents available from Applied Biosystems , Antibodies and assays by Cell
Signaling Technology , Abcam , Novus Biologicals ,Sigma-Aldrich , R&D Systems , Millipore , Abnova , and/or Invitrogen , Clones available from OriGene ,and/or Invitrogen , Drugs and/or compounds by Sigma-Aldrich , Enzo Life Sciences , and/or Tocris Bioscience )About This Section
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