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H-InvDB_8.3 released on March 26, 2013.
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H-Invitational ID: HIT000337479 Accession number: BC103927 Created date: 26-Mar-2013 Last modified: 20-Apr-2012
Definition: Protocadherin gamma-B1 isoform 2 precursor.
 
 

Transcript original information
Accession number BC103927.1
CAGE tag ID NA
EST ID NA
Clone Number MGC:119467 IMAGE:40007756
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (PCDHGB1) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (PCDHGB1);
Sequence data provider NA
Annotation project NA
Length of cDNA 2433[bp] (No. of exon:1)[A:580 T:547 G:635 C:671]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type PCR rescued clones
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 HIX0005252
Genomic location  G-integra Help Chromosome 5
Location 5q31.3
Position 140729828- 140732260
Strand +
Possible duplicated location(s) NA
Gene structure 1 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:56104; 
KEGG GENES KEGG GENES(56104); 
GeneCard GeneCardPCDHGB1;  *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 HIP000089773
Predicted CDS 1..2433;  810[aa];  Orientation:+1; 
Codon Adaptation Index (CAI). 0.755
Database links RefSeq NP_115266; 
UniProt NA
CCDS NA

Motif information
ORF

length(810),orf(1:2433) MQRAREAEMMKSQVLFPFLLSLFCGAISQQIRYTIPEELANGSRVGKLAK DLGLSVRELPTRKLRVSAEDYFNVSLESGDLLVNGRIDREKICGRKLECA LEFETVAENPMNVFHVVVVIQDINDNAPRFVAKGIDLEICESALPGVKFS LDSAQDADVEGNSLKLYTINPNQYFSLSTKESPDGSKYPVLLLEKPLDRE HQSSHRLILTAMDGGDPPLSGTTHIWIRVTDANDNAPVFSQEVYRVSLQE NVPWGTSVLRVMATDQDEGINAEITYAFLNSPISTSLFNLNPNTGDITTN GTLDFEETSRYVLSVEAKDGGVHTAHCNVQIEIVDENDNAPEVTFMSFSN QIPEDSDLGTVIALIKVRDKDSGQNGMVTCYTQEEVPFKLESTSKNYYKL VIAGALNREQTADYNVTIIATDKGKPALSSRTSITLHISDINDNAPVFHQ ASYVVHVSENNPPGASIAQVSASDPDLGPNGRVSYSILASDLEPRELLSY VSVSPQSGVVFAQRAFDHEQLRAFELTLQARDQGSPALSANVSLRVLVGD LNDNAPRVLYPALGPDGSALFDMVPRAAEPGYLVTKVVAVDADSGHNAWL SYHVLQASEPGLFSLGLRTGEVRTARALGDRDAARQRLLVAVRDGGQPPL SATATLHLIFADSLQEVLPDLSDRPEPSDPQTELQFYLVVALALISVLFL LAVILAIALRLRRSSSLDTEGCFQTGLCSKSGPGVPPNHSEGTLPYSYNL CIASHSAKTEFNSLNLTPEMAPPQDLLCDDPSMVVCASNEDHKIAYDPSL SSHVSFCKSS* 		a.a.
length		 InterPro Name
length(791), motif(1:791) 791 IPR015492 Protocadherin gamma [Family]
length(96), motif(27:122) 96 IPR015919 Cadherin-like [Domain]
length(103), motif(28:130) 103 IPR002126 Cadherin [Domain]
length(81), motif(29:109) 81 IPR013164 Cadherin, N-terminal [Domain]
length(98), motif(29:126) 98 IPR002126 Cadherin [Domain]
length(84), motif(45:128) 84 IPR002126 Cadherin [Domain]
length(20), motif(70:89) 20 IPR002126 Cadherin [Domain]
length(11), motif(118:128) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(109), motif(123:231) 109 IPR015919 Cadherin-like [Domain]
length(109), motif(127:235) 109 IPR002126 Cadherin [Domain]
length(109), motif(131:239) 109 IPR002126 Cadherin [Domain]
length(94), motif(137:230) 94 IPR002126 Cadherin [Domain]
length(86), motif(152:237) 86 IPR002126 Cadherin [Domain]
length(11), motif(227:237) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(104), motif(232:335) 104 IPR015919 Cadherin-like [Domain]
length(104), motif(236:339) 104 IPR002126 Cadherin [Domain]
length(30), motif(239:268) 30 IPR002126 Cadherin [Domain]
length(104), motif(240:343) 104 IPR002126 Cadherin [Domain]
length(90), motif(244:333) 90 IPR002126 Cadherin [Domain]
length(81), motif(261:341) 81 IPR002126 Cadherin [Domain]
length(13), motif(310:322) 13 IPR002126 Cadherin [Domain]
length(11), motif(331:341) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(105), motif(336:440) 105 IPR015919 Cadherin-like [Domain]
length(106), motif(340:445) 106 IPR002126 Cadherin [Domain]
length(105), motif(344:448) 105 IPR002126 Cadherin [Domain]
length(89), motif(350:438) 89 IPR002126 Cadherin [Domain]
length(82), motif(365:446) 82 IPR002126 Cadherin [Domain]
length(20), motif(427:446) 20 IPR002126 Cadherin [Domain]
length(11), motif(436:446) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(110), motif(441:550) 110 IPR015919 Cadherin-like [Domain]
length(14), motif(446:459) 14 IPR002126 Cadherin [Domain]
length(113), motif(446:558) 113 IPR002126 Cadherin [Domain]
length(110), motif(449:558) 110 IPR002126 Cadherin [Domain]
length(96), motif(453:548) 96 IPR002126 Cadherin [Domain]
length(87), motif(470:556) 87 IPR002126 Cadherin [Domain]
length(27), motif(506:532) 27 IPR002126 Cadherin [Domain]
length(18), motif(540:557) 18 IPR002126 Cadherin [Domain]
length(11), motif(546:556) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(112), motif(551:662) 112 IPR015919 Cadherin-like [Domain]
length(98), motif(574:671) 98 IPR002126 Cadherin [Domain]
length(89), motif(574:662) 89 IPR002126 Cadherin [Domain]
length(80), motif(578:657) 80 IPR002126 Cadherin [Domain]
length(82), motif(587:668) 82 IPR002126 Cadherin [Domain]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000337479
H-Inv cluster ID Locus viewHIX0005252
Accession number BC103927.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO; 
Coding potential  Help Protein coding; 
Definition Protocadherin gamma-B1 isoform 2 precursor.
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (NP_115266)  [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 PCDHGB1
HGNC aliases NA
HGNC name protocadherin gamma subfamily B, 1
DDBJ PCDHGB1
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 HIP000089773
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:56104; 
KEGG GENES KEGG GENES(56104); 
GeneCard GeneCardPCDHGB1;  *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

Gene ontology information
Molecular function calcium ion binding (GO:0005509); 
Biological process homophilic cell adhesion (GO:0007156); 
Cellular component membrane (GO:0016020); 

Subcellular localization information  Last modified:20-Apr-2012
WoLF PSORT extracellular;  plasma membrane;  peroxisome;  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
32 95 1f5aA1 2e-14 16.7 60/118 d.58.16.1
78 179 1fx3A 4e-06 11.0 92/143 d.33.1.1
195 598 1dnvA 1e-69 10.2 372/415 b.121.5.3
580 662 1edhA1 8e-13 11.5 83/99 b.1.6.1
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 AGhsA110119; 
Affymetrix
GeneChip		 HG-Focus 211807_x_at; 
HG-U133 211807_x_at; 
HG-U133A 211807_x_at; 
HG-U133A_2 211807_x_at; 
HG-U133B NA
HG-U133_Plus_2 211807_x_at; 
HG-U95 NA
HG-U95A NA
HG-U95B NA
HG-U95C NA
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 2832560;  2832561;  2832562;  2832563;  2832564; 
HuGeneFL NA
Agilent Human 1A Oligo Microarray:PGID215 NA
Whole Human Genome Oligo Microarray:PGID247 A_23_P310972; 
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:(56104)
Disease Entrez Gene ID:(56104)
Substance Entrez Gene ID:(56104)
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
233 .. 233 G/A rs111465596 + CDS Nonsynonymous[Ser78Asn]
383 .. 383 C/T rs76289268 + CDS Nonsynonymous[Pro128Leu]
557 .. 557 G/T rs62378414 + CDS Nonsynonymous[Ser186Ile]
598 ^ 599 -/G/T rs36001111 + CDS
1195 .. 1195 A/G rs77250251 + CDS Nonsynonymous[Lys399Glu]
1232 .. 1232 C/A rs62623563 + CDS Nonsynonymous[Thr411Lys]
1332 .. 1332 T/C rs78745319 + CDS Synonymous[Asn444Asn]
1530 .. 1530 G/T rs3749778 - CDS Synonymous[Val510Val]
1581 .. 1581 A/G rs3749777 - CDS Synonymous[Thr527Thr]
1759 .. 1759 G/- rs36021732 + CDS
2046 .. 2046 G/A rs73265820 + CDS Synonymous[Thr682Thr]
2294 .. 2294 A/C rs114304577 + CDS Nonsynonymous[Asn765Thr]
2393 .. 2393 C/A rs116608782 + CDS Nonsynonymous[Pro798His]
 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;