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: HIT000040259 Accession number: BC027451 Created date: 26-Mar-2013 Last modified: 20-Apr-2012
Definition: Protocadherin gamma-C3 isoform 3.
 
 

Transcript original information
Accession number BC027451.1
CAGE tag ID NA
EST ID NA
Clone Number IMAGE:4944432
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (PCDHGC3) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (PCDHGC3);
Sequence data provider NA
Annotation project NA
Length of cDNA 2305[bp] (No. of exon:4)[A:508 T:486 G:600 C:711]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type Brain, anaplastic oligodendroglioma with 1p/19q loss
Develpmental stage NA
Mini-G
Sequence quality information
CDS feature Complete CDS
Kozak sequence NA
PolyA Site: 2291(+)
Vector/adapter sequence NA
Frame shift NA
Remaining intron NA
Splice site acceptor (NAGNAG) CAGAAG; 
Transcript quality feature NA
Notes NA

Gene structure information  G-integra H-DBAS cDNA-genome alignment
H-Inv cluster ID HIX0005252
Genomic location  G-integra Help Chromosome 5
Location 5q31.3
Position 140855571- 140892513
Strand +
Possible duplicated location(s) NA
Gene structure 4 exon(s)
Database links RefSeq NM_002588;  NM_003735;  NM_003736;  NM_014004;  NM_018912;  NM_018913;  NM_018914;  NM_018915;  NM_018916;  NM_018917;  NM_018918;  NM_018919;  NM_018920;  NM_018921;  NM_018922;  NM_018923;  NM_018924;  NM_018925;  NM_018926;  NM_018927;  NM_018928;  NM_018929;  NM_031993;  NM_032009;  NM_032011;  NM_032053;  NM_032054;  NM_032086;  NM_032087;  NM_032088;  NM_032089;  NM_032090;  NM_032091;  NM_032092;  NM_032094;  NM_032095;  NM_032096;  NM_032097;  NM_032098;  NM_032099;  NM_032100;  NM_032101;  NM_032402;  NM_032403;  NM_032406;  NM_032407; 
Ensembl ENST00000252085;  ENST00000252087;  ENST00000253812;  ENST00000305759;  ENST00000306593;  ENST00000308177;  ENST00000378105;  ENST00000394576;  ENST00000398587;  ENST00000398594;  ENST00000398604;  ENST00000398610;  ENST00000517417;  ENST00000517434;  ENST00000518069;  ENST00000518325;  ENST00000518882;  ENST00000520790;  ENST00000522605;  ENST00000523390;  ENST00000528330; 
Entrez Gene Entrez Gene ID:5098; 
KEGG GENES KEGG GENES(5098); 
GeneCard GeneCardPCDHGC3;  *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 HIP000112490
Predicted CDS 114..518;  134[aa];  Orientation:+3; 
Codon Adaptation Index (CAI). 0.844
Database links RefSeq NP_115779; 
UniProt Q9BR81; 
CCDS NA

Motif information
ORF

length(134),orf(114:518) MVPEAWRSGLQAPPNTDWRFSQAQRPGTSGSQNGDDTGTWPNNQFDTEML QAMILASASEAADGSSTLGGGAGTMGLSARYGPQFTLQHVPDYRQNVYIP GSNATLTNAAGKRDGKAPAGGNGNKKKSGKKEKK* 		a.a.
length		 InterPro Name
length(124), motif(11:134) 124 IPR015492 Protocadherin gamma [Family]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000040259
H-Inv cluster ID Locus viewHIX0005252
Accession number BC027451.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO; 
Coding potential  Help Protein coding; 
Definition Protocadherin gamma-C3 isoform 3.
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (NP_115779)  [Identity/coverage = 100.0%/100.0%] to Homo sapiens protein.
Experimental evidence Protein evidence
PubMed ID NA
Gene family/group Gene family H-Inv gene family/group ID HIF0000005
Gene family/group name Putative Zinc finger, C2H2-type (IPR007087).
Evidence motif (InterPro) ID IPR007087
Gene symbol/name HGNC symbol PCDHGC3
HGNC aliases NA
HGNC name protocadherin gamma subfamily C, 3
DDBJ PCDHGC3
UniProt NA
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 HIP000112490
No. of interaction NA
Interaction partner(s) NA
BIND NA
DIP NA
MINT NA
HPRD NA
IntAct NA
Database links RefSeq NM_002588;  NM_003735;  NM_003736;  NM_014004;  NM_018912;  NM_018913;  NM_018914;  NM_018915;  NM_018916;  NM_018917;  NM_018918;  NM_018919;  NM_018920;  NM_018921;  NM_018922;  NM_018923;  NM_018924;  NM_018925;  NM_018926;  NM_018927;  NM_018928;  NM_018929;  NM_031993;  NM_032009;  NM_032011;  NM_032053;  NM_032054;  NM_032086;  NM_032087;  NM_032088;  NM_032089;  NM_032090;  NM_032091;  NM_032092;  NM_032094;  NM_032095;  NM_032096;  NM_032097;  NM_032098;  NM_032099;  NM_032100;  NM_032101;  NM_032402;  NM_032403;  NM_032406;  NM_032407; 
Ensembl ENST00000252085;  ENST00000252087;  ENST00000253812;  ENST00000305759;  ENST00000306593;  ENST00000308177;  ENST00000378105;  ENST00000394576;  ENST00000398587;  ENST00000398594;  ENST00000398604;  ENST00000398610;  ENST00000517417;  ENST00000517434;  ENST00000518069;  ENST00000518325;  ENST00000518882;  ENST00000520790;  ENST00000522605;  ENST00000523390;  ENST00000528330; 
Entrez Gene Entrez Gene ID:5098; 
KEGG GENES KEGG GENES(5098); 
GeneCard GeneCardPCDHGC3;  *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 Putative Zinc finger, C2H2-type (IPR007087). 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 nuclear;  cytosol; 
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 AGhsB190717; 
Affymetrix
GeneChip		 HG-Focus 215836_s_at; 
HG-U133 205717_x_at;  209079_x_at;  211066_x_at;  211876_x_at;  215836_s_at;  216352_x_at; 
HG-U133A 205717_x_at;  209079_x_at;  211066_x_at;  211876_x_at;  215836_s_at;  216352_x_at; 
HG-U133A_2 205717_x_at;  209079_x_at;  211066_x_at;  211876_x_at;  215836_s_at;  216352_x_at; 
HG-U133B NA
HG-U133_Plus_2 205717_x_at;  209079_x_at;  211066_x_at;  211876_x_at;  215836_s_at;  216352_x_at; 
HG-U95 657_at; 
HG-U95A 657_at; 
HG-U95B NA
HG-U95C NA
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 2832711;  2832751;  2832754;  2832758;  2832759;  2832760;  2832761;  2832762;  2832763;  2832764;  2832765;  2832766;  2832767;  2832768;  2832769;  2878647;  2878661; 
HuGeneFL L11373_at; 
Agilent Human 1A Oligo Microarray:PGID215 A_23_P354734; 
Whole Human Genome Oligo Microarray:PGID247 A_23_P354734; 
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:  601888;  608850;  611091;  612554;  612571; 
Disease related mutation NA
Literature-Extracted GENe-Disease Associations (LEGENDA) LEGENDA Gene name Entrez Gene ID:(5098)
Disease Entrez Gene ID:(5098)
Substance Entrez Gene ID:(5098)
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
28 .. 28 C/A rs72790062 + 5'UTR
348 .. 348 G/A rs114669158 + CDS Nonsynonymous[Ala79Thr]
359 .. 359 A/G rs2233612 + CDS Synonymous[Gly82Gly]
381 .. 381 G/A rs116366286 + CDS Nonsynonymous[Val90Met]
394 .. 394 G/A rs61749029 + CDS Nonsynonymous[Arg94His]
548 .. 548 A/G rs2233613 + 3'UTR
653 .. 653 G/A rs76613492 + 3'UTR
709 .. 709 T/C rs115159796 + 3'UTR
973 .. 973 G/C rs4912608 + 3'UTR
1231 .. 1231 T/C rs113814137 + 3'UTR
1539 .. 1539 G/A rs111365449 + 3'UTR
1730 .. 1730 A/G rs78180647 + 3'UTR
2259 .. 2259 C/T rs112402554 + 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;