H-InvDB x AHG DB
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H-InvDB_8.3 released on March 26, 2013.
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H-Invitational ID: HIT000000208 Accession number: AB007961 Created date: 26-Mar-2013 Last modified: 20-Apr-2012
Definition: Similar to Metalloproteinase, extracellular matrix glycoprotein VMP3;
 
 

Transcript original information
Accession number AB007961.1
CAGE tag ID NA
EST ID NA
Clone Number HH1162
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ;
Sequence data provider Provider:KDRI; 
Annotation project H-Invitational FLcDNA
Length of cDNA 5929[bp] (No. of exon:1)[A:1628 T:1936 G:1255 C:1110]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type brain
Develpmental stage NA
Mini-G
Sequence quality information
CDS feature Complete CDS
Kozak sequence NA
PolyA NA
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 HIX0114185
Genomic location  G-integra Help Chromosome 1
Location 1q25.1
Position 173985581- 173991508
Strand -
Possible duplicated location(s) NA
Gene structure 1 exon(s)
Database links RefSeq NA
Ensembl NA
Entrez Gene NA
KEGG GENES NA
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 HIP000031044
Predicted CDS 2148..2354;  68[aa];  Orientation:+3; 
Codon Adaptation Index (CAI). 0.683

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000000208
H-Inv cluster ID Locus viewHIX0114185
Accession number AB007961.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help Representative H-Inv IDRepresentative transcript; 
Coding potential  Help Protein coding; 
Definition Similar to Metalloproteinase, extracellular matrix glycoprotein VMP3;
Similarity category  Help Category: Similar to known protein(Category II).
Similar to known protein (D8TPL0)  [Identity/coverage = 51.042%/27.93%] to Volvox carteri f. nagariensis. protein.
Experimental evidence Protein evidence
PubMed ID 20616280;  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 NA
UniProt vmp3
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 HIP000031044
No. of interaction NA
Interaction partner(s) NA
BIND NA
DIP NA
MINT NA
HPRD NA
IntAct NA
Database links RefSeq NA
Ensembl NA
Entrez Gene NA
KEGG GENES NA
GeneCard NA *GeneCards is provided free to academic non-profit institutions.
etc H-GOLDHuman-Gene diversity Of Life-style related Diseases; 
Curation status Human curated
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:20-Apr-2012
WoLF PSORT cytosol;  extracellular;  nuclear;  Other; 
Target P Not predicted
SOSUI soluble protein
TMHMM soluble 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.

Gene expression information  H-ANGEL DNAProbeLocator Last modified:20-Apr-2012
Tissue-specific expression  H-ANGEL NA
Probe
information DNAProbeLocator		 AceGene NA
Affymetrix
GeneChip		 HG-Focus NA
HG-U133 215109_at; 
HG-U133A 215109_at; 
HG-U133A_2 215109_at; 
HG-U133B NA
HG-U133_Plus_2 215109_at; 
HG-U95 34902_at; 
HG-U95A 34902_at; 
HG-U95B NA
HG-U95C NA
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 2367953;  2367955;  2367957;  2444620;  2444621;  2444622; 
HuGeneFL NA
Agilent Human 1A Oligo Microarray:PGID215 NA
Whole Human Genome Oligo Microarray:PGID247 A_24_P560992; 
Related H-InvDB links H-ANGELH-ANGEL;  DNAProbeLocatorDNAProbeLocator; 

Disease/pathology information  DiseaseInfo Viewer LEGENDA Last modified:20-Apr-2012
Disease relation Disease name:NA
Related information in OMIM OMIM ID:NA Title:NA
Co-localized orphan diseases OMIM ID:  115665;  116600;  155600;  600975;  605225;  605606;  606788;  606852;  606928;  607317;  607671;  608543;  608553;  608995;  610320;  612367;  612596; 
Disease related mutation NA
Literature-Extracted GENe-Disease Associations (LEGENDA) LEGENDA Gene name NA
Disease NA
Substance NA
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
292 .. 292 C/G rs117896783 - 5'UTR
881 .. 881 C/A rs117741584 - 5'UTR
1245 .. 1245 C/T rs77169234 - 5'UTR
1420 .. 1420 C/T rs12070869 - 5'UTR
1476 .. 1476 C/T rs12070863 - 5'UTR
1838 .. 1838 A/G rs1321637 - 5'UTR
2220 ^ 2221 -/T rs67286737 - CDS
2221 .. 2221 A/T rs117085887 - CDS Nonsynonymous[Asp25Val]
2221 ^ 2222 -/T rs11393317 - CDS
2228 ^ 2229 -/T rs71685934 - CDS
2229 ^ 2230 -/T rs66723035 - CDS
2237 .. 2237 C/T rs115422006 - CDS Synonymous[Phe30Phe]
2291 .. 2291 G/A rs12565973 - CDS Nonsynonymous[Met48Ile]
2495 .. 2495 G/T rs76930468 - 3'UTR
2501 .. 2501 G/A rs75401514 - 3'UTR
2553 .. 2553 T/C rs72711438 - 3'UTR
2563 .. 2563 T/G rs4297348 - 3'UTR
3077 .. 3077 C/T rs76390087 - 3'UTR
3176 .. 3176 T/C rs74126489 - 3'UTR
3227 .. 3227 A/G rs73027423 - 3'UTR
3483 .. 3483 G/C rs10912717 - 3'UTR
3553 ^ 3554 -/C rs34138445 - 3'UTR
3586 .. 3586 T/C rs73027415 - 3'UTR
3654 .. 3654 A/G rs79011787 - 3'UTR
3713 .. 3713 T/C rs10798302 - 3'UTR
3735 .. 3735 G/A rs112430365 - 3'UTR
3892 .. 3892 T/G rs116676418 - 3'UTR
3939 .. 3939 A/G rs72711437 - 3'UTR
4051 .. 4051 T/A rs12562588 - 3'UTR
4058 .. 4058 C/A rs116281061 - 3'UTR
4348 .. 4348 G/A rs61826823 - 3'UTR
4444 .. 4444 A/G rs12120395 - 3'UTR
4469 .. 4469 T/A rs117622865 - 3'UTR
4474 ^ 4475 -/TATTA rs113452743 - 3'UTR
4518 .. 4518 C/A rs12122992 - 3'UTR
4563 .. 4563 T/- rs61239660 - 3'UTR
4569 .. 4569 T/G rs74126487 - 3'UTR
4570 .. 4570 T/G rs55733322 - 3'UTR
4588 .. 4588 T/G rs116412484 - 3'UTR
4751 .. 4751 G/A rs73027407 - 3'UTR
5038 .. 5038 T/A rs12060401 - 3'UTR
5497 .. 5497 A/C rs59846661 - 3'UTR
5854 .. 5854 G/A rs1133673 + 3'UTR
5928 ^ 5929 -/A rs67675128 - 3'UTR
 Microsatellite (Short Tandem Repeat, STR)
Location Variation Strand
194..208 (cgg)5 +
 Microsatellite: Human-Gene diversity Of Life-style related Diseases (H-GOLD)
No data available
 Repeat  Repeat mask viewer
Type Start End Strand
AluSx1 1348 1644 -
MIR3 2875 2982 -
AluJr 4195 4432 -
L1MB5 4648 4857 -
AluJr 5815 5929 +
Database links H-GOLDHuman-Gene diversity Of Life-style related Diseases(H-GOLD); 
Related H-InvDB links VaryGeneVaryGene;  Repeat mask viewerRepeat Mask Viewer;