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: HIT000071798 Accession number: AF152494 Created date: 26-Mar-2013 Last modified: 20-Apr-2012
Definition: Protocadherin beta-15 precursor.
 
 

Transcript original information
Accession number AF152494.1
CAGE tag ID NA
EST ID NA
Clone Number NA
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (PCDHB15) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (PCDHB15);
Sequence data provider NA
Annotation project NA
Length of cDNA 2364[bp] (No. of exon:1)[A:535 T:503 G:667 C:659]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type NA
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 HIX0024802
Genomic location  G-integra Help Chromosome 5
Location 5q31.3
Position 140625147- 140627510
Strand +
Possible duplicated location(s) NA
Gene structure 1 exon(s)
Database links RefSeq NM_018935; 
Ensembl ENST00000231173; 
Entrez Gene Entrez Gene ID:56121; 
KEGG GENES KEGG GENES(56121); 
GeneCard GeneCardPCDHB15;  *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 HIP000048753
Predicted CDS 1..2364;  787[aa];  Orientation:+1; 
Codon Adaptation Index (CAI). 0.758
Database links RefSeq NP_061758; 
UniProt Q9Y5E8; 
CCDS CCDS4257; 

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000071798
H-Inv cluster ID Locus viewHIX0024802
Accession number AF152494.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO; 
Coding potential  Help Protein coding; 
Definition Protocadherin beta-15 precursor.
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (NP_061758)  [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 PCDHB15
HGNC aliases NA
HGNC name protocadherin beta 15
DDBJ PCDH-beta15
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 HIP000048753
No. of interaction 1
Interaction partner(s) HIP000049801; 
BIND NA
DIP NA
MINT NA
HPRD NA
IntAct EBI-3446699; 
Database links RefSeq NM_018935; 
Ensembl ENST00000231173; 
Entrez Gene Entrez Gene ID:56121; 
KEGG GENES KEGG GENES(56121); 
GeneCard GeneCardPCDHB15;  *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 endoplasmic;  extracellular;  plasma membrane;  Other; 
Target P signal peptide
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:20-Apr-2012
Start End PDB_ID E-value Identity Coverage SCOP_ID
27 97 1f5aA1 2e-14 15.4 65/118 d.58.16.1
123 217 1p32A 4e-06 6.8 93/182 d.25.1.1
199 616 1dnvA 1e-65 8.6 384/415 b.121.5.3
595 660 1fx3A 3e-04 8.0 64/143 d.33.1.1
Related H-InvDB links GTOP GTOP

Gene expression information  H-ANGEL DNAProbeLocator Last modified:20-Apr-2012
Tissue-specific expression  H-ANGEL NA
Probe
information DNAProbeLocator		 AceGene AGhsA220218; 
Affymetrix
GeneChip		 HG-Focus NA
HG-U133 NA
HG-U133A NA
HG-U133A_2 NA
HG-U133B NA
HG-U133_Plus_2 NA
HG-U95 NA
HG-U95A NA
HG-U95B NA
HG-U95C NA
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 2832502;  2832503;  2832505;  2832506; 
HuGeneFL NA
Agilent Human 1A Oligo Microarray:PGID215 A_23_P121851; 
Whole Human Genome Oligo Microarray:PGID247 A_23_P121851; 
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:(56121)
Disease Entrez Gene ID:(56121)
Substance Entrez Gene ID:(56121)
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
61 .. 61 C/T rs35154204 + CDS Synonymous[Leu21Leu]
188 .. 188 G/A rs2907300 - CDS Nonsynonymous[Gly63Glu]
357 .. 357 T/G rs74906746 + CDS Synonymous[Ala119Ala]
471 .. 471 T/C rs17844620 + CDS Synonymous[Ala157Ala]
529 .. 529 C/T rs76728356 + CDS Nonsynonymous[His177Tyr]
625 .. 625 A/C rs114818434 + CDS Synonymous[Arg209Arg]
795 .. 795 T/C rs117739157 + CDS Synonymous[Ser265Ser]
1079 .. 1079 C/A rs113438705 + CDS Nonsynonymous[Ser360Tyr]
1214 .. 1214 C/G rs116551897 + CDS Nonsynonymous[Thr405Arg]
1233 .. 1233 A/G rs112359544 + CDS Synonymous[Arg411Arg]
1303 .. 1303 C/T rs61743631 + CDS AA-STOP[Gln435*]
1383 .. 1383 C/G rs17844564 + CDS Synonymous[Arg461Arg]
1402 .. 1402 C/A rs58830954 + CDS Nonsynonymous[Leu468Met]
1420 .. 1420 A/C rs61741604 + CDS Nonsynonymous[Ser474Arg]
1420 .. 1420 A/C rs618506 - CDS Nonsynonymous[Ser474Arg]
1425 .. 1425 C/A rs61741603 + CDS Synonymous[Ala475Ala]
1425 .. 1425 C/A rs652104 - CDS Synonymous[Ala475Ala]
1481 .. 1481 G/A rs618096 - CDS Nonsynonymous[Arg494Gln]
1482 .. 1482 G/A rs61742728 + CDS Synonymous[Arg494Arg]
1500 .. 1500 C/A rs61742733 + CDS Synonymous[Leu500Leu]
1501 .. 1501 A/T rs61742734 + CDS Nonsynonymous[Thr501Ser]
1503 .. 1503 C/T rs61742735 + CDS Synonymous[Thr501Thr]
1518 .. 1518 T/C rs61742737 + CDS Synonymous[Ile506Ile]
1522 .. 1522 A/G rs61745117 + CDS Nonsynonymous[Thr508Ala]
1578 .. 1578 T/G rs3776091 - CDS Synonymous[Ala526Ala]
1611 .. 1611 C/G rs17844626 + CDS Synonymous[Gly537Gly]
1613 .. 1613 T/C rs17844627 + CDS Nonsynonymous[Phe538Ser]
1614 .. 1614 C/T rs17844628 + CDS Synonymous[Phe538Phe]
1621 .. 1621 C/T rs3096081 + CDS Synonymous[Leu541Leu]
1632 .. 1632 G/A rs112457389 + CDS Synonymous[Glu544Glu]
1644 .. 1644 A/C rs3096082 + CDS Synonymous[Arg548Arg]
1671 .. 1671 C/T rs17844631 + CDS Synonymous[Asn557Asn]
1709 .. 1709 C/T rs56840646 + CDS Nonsynonymous[Ala570Val]
1782 .. 1782 C/T rs113508999 + CDS Synonymous[Gly594Gly]
1854 .. 1854 G/A rs17844633 + CDS AA-STOP[Trp618*]
1856 .. 1856 C/G rs17844634 + CDS Nonsynonymous[Ala619Gly]
1874 .. 1874 G/T rs77506821 + CDS Nonsynonymous[Arg625Leu]
1904 .. 1904 T/C rs17844635 + CDS Nonsynonymous[Val635Ala]
1920 .. 1920 A/G rs17844636 + CDS Synonymous[Leu640Leu]
1965 .. 1965 C/A rs78481388 + CDS Synonymous[Thr655Thr]
2038 .. 2038 C/G rs79326925 + CDS Nonsynonymous[Gln680Glu]
2363 .. 2363 A/G rs80263204 + CDS Synonymous_atSTOP[*788*]
 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;