H-InvDB x AHG DB
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H-InvDB_9.0 released on May 27, 2015.
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H-Invitational ID: HIT000030595 Accession number: BC001712 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Vesicle-associated membrane protein-associated protein B/C; VAMP-B/VAMP-C; VAMP-associated protein B/C; VAP-B/VAP-C;
 
 

Transcript original information
Accession number BC001712.1
CAGE tag ID NA
EST ID NA
Clone Number MGC:1832 IMAGE:3543354
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ;
Sequence data provider Provider:MGC/NCI; 
Annotation project H-Invitational FLcDNA
Length of cDNA 2262[bp] (No. of exon:6)[A:651 T:571 G:554 C:486]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type Lymph, Burkitt lymphoma
Develpmental stage NA
Mini-G
Sequence quality information
CDS feature Complete CDS
Kozak sequence NA
PolyA Site: 2226(+) Signal: 2220-2224(+)
Vector/adapter sequence NA
Frame shift NA
Remaining intron NA
Splice site acceptor (NAGNAG) NA
Transcript quality feature NA
Notes NA

Gene structure information  G-integra H-DBAS cDNA-genome alignment
H-Inv cluster ID HIX0015950
Genomic location  G-integra Help Chromosome 20
Location 20q13.32
Position 56964338- 57020607
Strand +
Possible duplicated location(s) NA
Gene structure 6 exon(s)
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:9217; 
KEGG GENES KEGG GENES(9217); 
GeneCard NA *GeneCards is provided free to academic non-profit institutions.
Related H-InvDB links H-DBASH-DBAS;  G-integraG-integra;  cDNA-genome alignmentcDNA-genome alignment; 

Predicted CDS information
HIP ID HIP000029075
Predicted CDS 179..910;  243[aa];  Orientation:+2; 
Codon Adaptation Index (CAI). 0.735
Database links RefSeq NP_004729; 
UniProt O95292; 
CCDS CCDS33498; 

Motif information
ORF

length(243),orf(179:910) MAKVEQVLSLEPQHELKFRGPFTDVVTTNLKLGNPTDRNVCFKVKTTAPR RYCVRPNSGIIDAGASINVSVMLQPFDYDPNEKSKHKFMVQSMFAPTDTS DMEAVWKEAKPEDLMDSKLRCVFELPAENDKPHDVEINKIISTTASKTET PIVSKSLSSSLDDTEVKKVMEECKRLQGEVQRLREENKQFKEEDGLRMRK TVQSNSPISALAPTGKEEGLSTRLLALVVLFFIVGVIIGKIAL* 		a.a.
length		 InterPro Name
length(124), motif(1:124) 124 IPR008962 PapD-like [Domain]
length(126), motif(5:130) 126 IPR008962 PapD-like [Domain]
length(118), motif(7:124) 118 IPR000535 MSP domain [Domain]
length(103), motif(8:110) 103 IPR000535 MSP domain [Domain]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000030595
H-Inv cluster ID Locus viewHIX0015950
Accession number BC001712.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO; 
Coding potential  Help Protein coding; 
Definition Vesicle-associated membrane protein-associated protein B/C; VAMP-B/VAMP-C; VAMP-associated protein B/C; VAP-B/VAP-C;
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (O95292)  [Identity/coverage = 100.0%/100.0%] to Homo sapiens (Human). protein.
Experimental evidence Protein evidence
PubMed ID 9920726;  10931946;  11780052;  12665801;  12975309;  15372378;  15489334;  16227268;  16891305;  17081983;  18669648;  18691976;  19289470;  20068231;  20940299;  21269460;  21406692;  22131369;  ALL; 
Gene family/group Gene family H-Inv gene family/group ID NA
Gene family/group name NA
Evidence motif (InterPro) ID NA
Gene symbol/name HGNC symbol NA
HGNC aliases NA
HGNC name NA
DDBJ VAPB
UniProt VAPB
EC number NA
GGDB
(GlycoGene Database)
 Gene symbol NA
Familly NA
Designation NA
Expression NA
KEGG metabolic pathway NA
Protein-protein interaction (PPI) PPI viewer H-Inv protein ID HIP000029075
No. of interaction 2
Interaction partner(s) HIP000019542;  HIP000382003; 
BIND NA
DIP NA
MINT NA
HPRD 01716;  01717;  02812;  03719;  07505; 
IntAct NA
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:9217; 
KEGG GENES KEGG GENES(9217); 
GeneCard NA *GeneCards is provided free to academic non-profit institutions.
etc H-GOLDHuman-Gene diversity Of Life-style related Diseases; 
Curation status Auto-annotated
Notes NA
Related H-InvDB links Gene familyGene family;  Similarity Search ToolSimilarity Search Tool;  TACTTACT; 
fRNAdb (The functional RNA database) : overlapping fRNAdb entries with H-InvDB transcripts based on the location of the genome. 
NA


Subcellular localization information  Last modified:27-May-2015
WoLF PSORT cytosol;  mitochondria;  plasma membrane;  Other; 
Target P Other
SOSUI membrane protein
TMHMM membrane protein
PTS1 Not targeted
Related H-InvDB links LIFEdb LIFEdb; 
JRE-1.4.0 or later is required. Download JRE at Sun's web site.

Protein structure information (GTOP) GTOP Last modified:27-May-2015
Start End PDB_ID E-value Identity Coverage SCOP_ID
6 132 1wicA 7e-32 27.4 124/152 b.1.11.2
Related H-InvDB links GTOP GTOP

Gene expression information  H-ANGEL DNAProbeLocator Last modified:27-May-2015
Tissue-specific expression  H-ANGEL NA
Probe
information DNAProbeLocator		 AceGene AGhsA131103; 
Affymetrix
GeneChip		 HG-Focus 202550_s_at; 
HG-U133 202550_s_at; 
HG-U133A 202550_s_at; 
HG-U133A_2 202550_s_at; 
HG-U133B NA
HG-U133_Plus_2 202550_s_at; 
HG-U95 41757_at; 
HG-U95A 41757_at; 
HG-U95B NA
HG-U95C NA
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 3890916;  3890917;  3890918;  3890922;  3890929;  3890931;  3890933;  3890934;  3890936;  3890937;  3890938;  3890939;  3890940;  3911464;  3911472;  3911474; 
HuGeneFL NA
Agilent Human 1A Oligo Microarray:PGID215 A_23_P91293; 
Whole Human Genome Oligo Microarray:PGID247 A_23_P91293; 
Related H-InvDB links H-ANGELH-ANGEL;  DNAProbeLocatorDNAProbeLocator; 

Disease/pathology information  DiseaseInfo Viewer LEGENDA Last modified:27-May-2015
Disease relation Disease name: Amyotrophic lateral sclerosis 8 (608627);  Disease name: Spinal muscular atrophy, late-onset, Finkel type (182980); 
Related information in OMIM OMIM ID:  605704;  Title: VESICLE-ASSOCIATED MEMBRANE PROTEIN-ASSOCIATED PROTEIN B
Co-localized orphan diseases NA
Disease related mutation MutationView:  605704; 
JRE-1.4.0 or later is required.Download JRE at Sun's web site.
Literature-Extracted GENe-Disease Associations (LEGENDA) LEGENDA Gene name Entrez Gene ID:(9217)
Disease Entrez Gene ID:(9217)
Substance Entrez Gene ID:(9217)
Related H-InvDB links DiseaseInfo ViewerDiseaseInfo Viewer;  LEGENDALEGENDA; 

Polymorphism (SNP, indel), microsatellite (Short Tandem Repeat, STR) and repeat information  VaryGene Repeat mask viewer
 Single Nucleotide Polymorphism (SNP) and indel  VaryGene
Location Variation dbSNP ID Strand CDS/UTR Translation
64 .. 64 G/A rs111312823 + 5'UTR
146 .. 146 C/G rs201547974 + 5'UTR
246 .. 246 C/T rs113533827 + CDS Nonsynonymous[Thr23Ile]
283 .. 283 G/A rs141383583 + CDS Synonymous[Pro35Pro]
341 .. 341 A/C rs150761013 + CDS Synonymous[Arg55Arg]
344 .. 344 C/T rs74315431 + CDS Nonsynonymous[Pro56Ser]
352 .. 352 C/T rs139149560 + CDS Synonymous[Ser58Ser]
397 .. 397 A/G rs144027663 + CDS Synonymous[Leu73Leu]
407 .. 407 G/A rs200276908 + CDS Nonsynonymous[Asp77Asn]
568 .. 568 T/G rs146459055 + CDS Nonsynonymous[Asp130Glu]
670 .. 670 C/T rs139884809 + CDS Synonymous[Thr164Thr]
688 .. 688 G/A rs143144050 + CDS Nonsynonymous[Met170Ile]
706 .. 706 G/A rs199921117 + CDS Synonymous[Leu176Leu]
729 .. 729 G/A rs145483046 + CDS Nonsynonymous[Arg184Gln]
836 .. 836 C/T rs142370781 + CDS Nonsynonymous[Leu220Phe]
845 .. 845 C/T rs144718603 + CDS Nonsynonymous[Arg223Trp]
878 .. 878 G/A rs149215094 + CDS Nonsynonymous[Val234Ile]
934 .. 934 A/T rs201048706 + 3'UTR
985 .. 985 G/A rs138521885 + 3'UTR
1110 .. 1110 A/G rs199923819 + 3'UTR
1123 .. 1123 G/A rs202245892 - 3'UTR
1124 ^ 1125 -/AAAG rs199588133 + 3'UTR
1254 .. 1254 A/T rs11557086 + 3'UTR
1258 .. 1258 C/T rs182950622 + 3'UTR
1377 .. 1377 G/A rs141496875 + 3'UTR
1506 .. 1506 C/T rs118055109 + 3'UTR
1626 .. 1626 T/G rs150303699 + 3'UTR
1663 .. 1663 C/G rs6070466 + 3'UTR
1684 .. 1684 G/A rs138920779 + 3'UTR
1686 .. 1686 G/A rs149433608 + 3'UTR
1725 .. 1725 A/T rs187590871 + 3'UTR
1794 .. 1794 A/G rs3746398 - 3'UTR
1847 .. 1847 G/C rs1059794 + 3'UTR
1849 ^ 1850 -/G rs34626267 + 3'UTR
1905 .. 1905 T/G rs76895132 + 3'UTR
1963 .. 1963 C/T rs12512 - 3'UTR
1974 .. 1974 C/T rs1059809 + 3'UTR
2009 .. 2009 G/A rs191660921 + 3'UTR
2090 .. 2090 A/G rs182712704 + 3'UTR
2130 .. 2130 C/T rs1802460 + 3'UTR
2175 .. 2175 G/C rs7400 - 3'UTR
2192 .. 2192 A/G rs1802459 + 3'UTR
 Microsatellite (Short Tandem Repeat, STR)
No data available
 Microsatellite: Human-Gene diversity Of Life-style related Diseases (H-GOLD)
No data available
 Repeat  Repeat mask viewer
No data available
Database links H-GOLDHuman-Gene diversity Of Life-style related Diseases(H-GOLD); 
Related H-InvDB links VaryGeneVaryGene;  Repeat mask viewerRepeat Mask Viewer;