H-InvDB x AHG DB
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H-InvDB_9.0 released on May 27, 2015.
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H-Invitational ID: HIT000337479 Accession number: BC103927 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Similar to Protocadherin gamma-B1; PCDH-gamma-B1; 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 ;
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 HIX0216344
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 NA
Ensembl NA
Entrez Gene Entrez Gene ID:56104
KEGG GENES KEGG GENES(56104)
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 HIP000089773
Predicted CDS 1..2433;  810[aa];  Orientation:+1; 
Codon Adaptation Index (CAI). 0.754
Database links RefSeq NP_115266
UniProt NA
CCDS CCDS75330

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(103), motif(28:130) 103 IPR002126 Cadherin [Domain]
length(72), motif(29:100) 72 IPR015919 Cadherin-like [Domain]
length(81), motif(29:109) 81 IPR013164 Cadherin, N-terminal [Domain]
length(97), motif(30:126) 97 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(108), motif(124:231) 108 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(103), motif(233:335) 103 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(104), motif(337:440) 104 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(123), motif(437:559) 123 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(108), motif(552:659) 108 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 viewHIX0216344
Accession number BC103927.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO; 
Coding potential  Help Protein coding; 
Definition Similar to Protocadherin gamma-B1; PCDH-gamma-B1; Precursor;
Similarity category  Help Category: Similar to known protein(Category II).
Similar to known protein (Q9Y5G3)  [Identity/coverage = 100.0%/86.62%] to Homo sapiens (Human). protein.
Experimental evidence Protein evidence
PubMed ID 1038092915489334ALL
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 PCDHGB1
UniProt PCDHGB1
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 NA
Ensembl NA
Entrez Gene Entrez Gene ID:56104
KEGG GENES KEGG GENES(56104)
GeneCard NA *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 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

Gene ontology information
Molecular function calcium ion binding (GO:0005509); 
Biological process cell adhesion (GO:0007155);  homophilic cell adhesion (GO:0007156); 
Cellular component membrane (GO:0016020);  plasma membrane (GO:0005886); 

Subcellular localization information  Last modified:27-May-2015
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:27-May-2015
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:27-May-2015
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

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
22 .. 22 G/A rs199858823 + CDS Nonsynonymous[Glu8Lys]
38 .. 38 A/G rs180956402 + CDS Nonsynonymous[Gln13Arg]
172 .. 172 G/C rs139554138 + CDS Nonsynonymous[Glu58Gln]
233 .. 233 G/A rs111465596 + CDS Nonsynonymous[Ser78Asn]
331 .. 331 A/G rs202231783 + CDS Nonsynonymous[Met111Val]
383 .. 383 C/T rs76289268 + CDS Nonsynonymous[Pro128Leu]
557 .. 557 G/T rs62378414 + CDS Nonsynonymous[Ser186Ile]
598 ^ 599 -/G/T rs36001111 + CDS
647 .. 647 A/C rs199920590 + CDS Nonsynonymous[Asp216Ala]
662 .. 662 G/A rs199977912 + CDS Nonsynonymous[Gly221Asp]
840 .. 840 T/C rs146569254 + CDS Synonymous[Asn280Asn]
847 .. 847 A/G rs183514769 + CDS Nonsynonymous[Ile283Val]
921 .. 921 G/A rs200349180 + CDS Synonymous[Glu307Glu]
961 .. 961 G/A rs201087525 + CDS Nonsynonymous[Gly321Arg]
1016 .. 1016 A/G rs202007643 + CDS Nonsynonymous[Asn339Ser]
1088 .. 1088 C/G rs200422536 + CDS Nonsynonymous[Ala363Gly]
1195 .. 1195 A/G rs77250251 + CDS Nonsynonymous[Lys399Glu]
1216 .. 1216 C/T rs189413445 + CDS Synonymous[Leu406Leu]
1218 .. 1218 A/G rs199832341 + CDS Synonymous[Leu406Leu]
1222 .. 1222 C/A rs148748054 + CDS Synonymous[Arg408Arg]
1232 .. 1232 C/A rs62623563 + CDS Nonsynonymous[Thr411Lys]
1281 .. 1281 C/T rs186005750 + CDS Synonymous[Ala427Ala]
1298 .. 1298 G/A rs200369157 + CDS Nonsynonymous[Ser433Asn]
1309 .. 1309 C/A rs191804700 + CDS Nonsynonymous[His437Asn]
1332 .. 1332 T/C rs78745319 + CDS Synonymous[Asn444Asn]
1359 .. 1359 T/C rs200864490 + CDS Synonymous[Tyr453Tyr]
1518 .. 1518 G/C rs181453842 + CDS Nonsynonymous[Gln506His]
1530 .. 1530 G/T rs3749778 - CDS Synonymous[Val510Val]
1548 .. 1548 C/T rs186558249 + CDS Synonymous[Phe516Phe]
1567 .. 1567 G/T rs191017713 + CDS Nonsynonymous[Ala523Ser]
1580 .. 1580 C/T rs182346627 + CDS Nonsynonymous[Thr527Ile]
1581 .. 1581 A/G rs3749777 - CDS Synonymous[Thr527Thr]
1602 .. 1602 C/T rs150984625 + CDS Synonymous[Gly534Gly]
1634 .. 1634 G/C rs146243220 + CDS Nonsynonymous[Arg545Pro]
1758 .. 1758 G/- rs36021732 + CDS
1942 .. 1942 C/G rs147767080 + CDS Nonsynonymous[Pro648Ala]
1956 .. 1956 C/T rs200739845 + CDS Synonymous[Ala652Ala]
1991 .. 1991 T/C rs201454130 + CDS Nonsynonymous[Leu664Pro]
2046 .. 2046 G/A rs73265820 + CDS Synonymous[Thr682Thr]
2106 .. 2106 G/T rs186670703 + CDS Synonymous[Ala702Ala]
2162 .. 2162 G/T rs191134866 + CDS Nonsynonymous[Gly721Val]
2276 .. 2276 C/A rs199727665 + CDS Nonsynonymous[Thr759Lys]
2294 .. 2294 A/C rs183312809 + CDS Nonsynonymous[Asn765Thr]
2365 .. 2365 A/C rs201522550 + CDS Nonsynonymous[Asn789His]
2383 .. 2383 G/A rs199530238 + CDS Nonsynonymous[Ala795Thr]
2393 .. 2393 C/A rs200777796 + 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