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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: 26-Mar-2013
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_002588NM_003735NM_003736NM_014004NM_018912NM_018913NM_018914NM_018915NM_018916NM_018917NM_018918NM_018919NM_018920NM_018921NM_018922NM_018923NM_018924NM_018925NM_018926NM_018927NM_018928NM_018929NM_031993NM_032009NM_032011NM_032053NM_032054NM_032086NM_032087NM_032088NM_032089NM_032090NM_032091NM_032092NM_032094NM_032095NM_032096NM_032097NM_032098NM_032099NM_032100NM_032101NM_032402NM_032403NM_032406NM_032407
Ensembl ENST00000252085ENST00000252087ENST00000253812ENST00000305759ENST00000306593ENST00000308177ENST00000378105ENST00000394576ENST00000398587ENST00000398594ENST00000398604ENST00000398610ENST00000517417ENST00000517434ENST00000518069ENST00000518325ENST00000518882ENST00000520790ENST00000522605ENST00000523390ENST00000528330
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_002588NM_003735NM_003736NM_014004NM_018912NM_018913NM_018914NM_018915NM_018916NM_018917NM_018918NM_018919NM_018920NM_018921NM_018922NM_018923NM_018924NM_018925NM_018926NM_018927NM_018928NM_018929NM_031993NM_032009NM_032011NM_032053NM_032054NM_032086NM_032087NM_032088NM_032089NM_032090NM_032091NM_032092NM_032094NM_032095NM_032096NM_032097NM_032098NM_032099NM_032100NM_032101NM_032402NM_032403NM_032406NM_032407
Ensembl ENST00000252085ENST00000252087ENST00000253812ENST00000305759ENST00000306593ENST00000308177ENST00000378105ENST00000394576ENST00000398587ENST00000398594ENST00000398604ENST00000398610ENST00000517417ENST00000517434ENST00000518069ENST00000518325ENST00000518882ENST00000520790ENST00000522605ENST00000523390ENST00000528330
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:26-Mar-2013
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:26-Mar-2013
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:26-Mar-2013
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:26-Mar-2013
Disease relation Disease name:NA
Related information in OMIM OMIM ID:NA Title:NA
Co-localized orphan diseases OMIM ID:  601888608850611091612554612571
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 ViewerLEGENDALEGENDA

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