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H-InvDB_8.3 released on March 26, 2013.
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H-Invitational ID: HIT000053681 Accession number: BC051788 Created date: 26-Mar-2013 Last modified: 20-Apr-2012
Definition: Protocadherin gamma-B7 isoform 1 precursor.
 
 

Transcript original information
Accession number BC051788.2
CAGE tag ID NA
EST ID NA
Clone Number MGC:57549 IMAGE:4941167
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (PCDHGB7) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (PCDHGB7);
Sequence data provider Provider:MGC/NCI; 
Annotation project H-Invitational FLcDNA
Length of cDNA 4771[bp] (No. of exon:4)[A:1092 T:1028 G:1263 C:1388]
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: 4757(+)
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 140797260- 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:56099; 
KEGG GENES KEGG GENES(56099); 
GeneCard GeneCardPCDHGB7;  *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 HIP000056703
Predicted CDS 195..2984;  929[aa];  Orientation:+3; 
Codon Adaptation Index (CAI). 0.747
Database links RefSeq NP_061750; 
UniProt Q9Y5F8; 
CCDS CCDS47293; 

Motif information
ORF

length(929),orf(195:2984) MGGSCAQRRRAGPRQVLFPLLLPLFYPTLCEPIRYSIPEELAKGSVVGNL AKDLGLSVLDVSARELRVSAEKLHFSVDAQSGDLLVKDRIDREQICKERR RCELQLEAVVENPLNIFHVIVVIEDVNDHAPQFRKDEINLEISESVSLGM GTILESAEDPDISMNSLSKYQLSPNEYFSLVEKDNPDGGKYPELVLQKTL DRETQSAHHLVLTALDGGDPPRSGTAQIRILVIDANDNPPVFSQDVYRVS LREDVPPGTSILRVKATDQDEGINSEITYSFFGVADKAQHVFSLDYTTGN ILTQQPLDFEEVERYTINIEAKDRGSLSTRCKVIVEVVDENDNSPEIIIT SLSDQIMEDSPPGVVVALFKTRDQDSGENGEVRCSLSRGVPFKIHSSSNN YYKLVTDEALDREQTPEYNVTIAATDRGKPPLSSSKTITLHITDVNDNAP VFGQSAYLVHVPENNQPGASIAQVSASDPDFGLNGRVSYSLIASDLESRT LSSYVSVSAQSGVVFAQRAFDHEQLRTFELTLQARDQGSPALSANVSLRV LVGDRNDNAPRVLYPALGPDGSALFDTVPRAAQPGYLVTKVVAVDADSGH NAWLSYHVVQASEPGLFSLGLRTGEVRMVRALGDKDSVRQRLLVAVRDGG QPPLSATATLHLVFADSLQEVLPDFSDHPTPSDSQAEMQFYLVVALALIS VLFLLAVILAIALRLRQSFSPTAGDCFESVLCSKSGPVGPPNYSEGTLPY AYNFCVPGDQMNPEFNFFTSVDHCPATQDNLNKDSMLLASILTPSVEADK KILKQQAPPNTDWRFSQAQRPGTSGSQNGDDTGTWPNNQFDTEMLQAMIL ASASEAADGSSTLGGGAGTMGLSARYGPQFTLQHVPDYRQNVYIPGSNAT LTNAAGKRDGKAPAGGNGNKKKSGKKEKK* 		a.a.
length		 InterPro Name
length(924), motif(6:929) 924 IPR015492 Protocadherin gamma [Family]
length(103), motif(23:125) 103 IPR015919 Cadherin-like [Domain]
length(81), motif(32:112) 81 IPR013164 Cadherin, N-terminal [Domain]
length(98), motif(32:129) 98 IPR002126 Cadherin [Domain]
length(76), motif(56:131) 76 IPR002126 Cadherin [Domain]
length(20), motif(73:92) 20 IPR002126 Cadherin [Domain]
length(59), motif(75:133) 59 IPR002126 Cadherin [Domain]
length(11), motif(121:131) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(109), motif(126:234) 109 IPR015919 Cadherin-like [Domain]
length(110), motif(130:239) 110 IPR002126 Cadherin [Domain]
length(109), motif(134:242) 109 IPR002126 Cadherin [Domain]
length(92), motif(141:232) 92 IPR002126 Cadherin [Domain]
length(86), motif(155:240) 86 IPR002126 Cadherin [Domain]
length(11), motif(230:240) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(105), motif(235:339) 105 IPR015919 Cadherin-like [Domain]
length(104), motif(240:343) 104 IPR002126 Cadherin [Domain]
length(30), motif(242:271) 30 IPR002126 Cadherin [Domain]
length(105), motif(243:347) 105 IPR002126 Cadherin [Domain]
length(91), motif(247:337) 91 IPR002126 Cadherin [Domain]
length(82), motif(264:345) 82 IPR002126 Cadherin [Domain]
length(13), motif(314:326) 13 IPR002126 Cadherin [Domain]
length(11), motif(335:345) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(105), motif(340:444) 105 IPR015919 Cadherin-like [Domain]
length(105), motif(344:448) 105 IPR002126 Cadherin [Domain]
length(105), motif(348:452) 105 IPR002126 Cadherin [Domain]
length(88), motif(355:442) 88 IPR002126 Cadherin [Domain]
length(82), motif(369:450) 82 IPR002126 Cadherin [Domain]
length(20), motif(431:450) 20 IPR002126 Cadherin [Domain]
length(11), motif(440:450) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(110), motif(445:554) 110 IPR015919 Cadherin-like [Domain]
length(114), motif(449:562) 114 IPR002126 Cadherin [Domain]
length(14), motif(450:463) 14 IPR002126 Cadherin [Domain]
length(110), motif(453:562) 110 IPR002126 Cadherin [Domain]
length(96), motif(457:552) 96 IPR002126 Cadherin [Domain]
length(87), motif(474:560) 87 IPR002126 Cadherin [Domain]
length(27), motif(510:536) 27 IPR002126 Cadherin [Domain]
length(18), motif(544:561) 18 IPR002126 Cadherin [Domain]
length(11), motif(550:560) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(112), motif(555:666) 112 IPR015919 Cadherin-like [Domain]
length(99), motif(577:675) 99 IPR002126 Cadherin [Domain]
length(90), motif(577:666) 90 IPR002126 Cadherin [Domain]
length(82), motif(580:661) 82 IPR002126 Cadherin [Domain]
length(82), motif(591:672) 82 IPR002126 Cadherin [Domain]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000053681
H-Inv cluster ID Locus viewHIX0005252
Accession number BC051788.2
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO;  Splicing isoformSplicing isoform
Coding potential  Help Protein coding; 
Definition Protocadherin gamma-B7 isoform 1 precursor.
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (NP_061750)  [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 PCDHGB7
HGNC aliases NA
HGNC name protocadherin gamma subfamily B, 7
DDBJ PCDHGB7
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 HIP000056703
No. of interaction 2
Interaction partner(s) HIP000042582;  HIP000042582; 
BIND NA
DIP 132891E; 
MINT NA
HPRD NA
IntAct EBI-2001944; 
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:56099; 
KEGG GENES KEGG GENES(56099); 
GeneCard GeneCardPCDHGB7;  *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
34 97 1f5aA1 6e-14 21.7 60/118 d.58.16.1
75 166 2fwuA1 5e-09 19.6 88/157 b.1.27.1
198 602 1dnvA 3e-71 9.7 372/415 b.121.5.3
584 661 1edhA1 2e-12 9.8 78/99 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 AGhsA110116;  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 1552662_a_at;  205717_x_at;  209079_x_at;  211066_x_at;  211876_x_at;  215836_s_at;  216352_x_at; 
HG-U95 1169_at;  657_at; 
HG-U95A 1169_at;  657_at; 
HG-U95B NA
HG-U95C NA
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 2832573;  2832626;  2832627;  2832628;  2832629;  2832646;  2832647;  2832648;  2832649;  2832650;  2832651;  2832751;  2832754;  2832758;  2832759;  2832760;  2832761;  2832762;  2832763;  2832764;  2832765;  2832766;  2832767;  2832768;  2832769;  2878647;  2878649;  2878661; 
HuGeneFL D88799_at;  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:(56099)
Disease Entrez Gene ID:(56099)
Substance Entrez Gene ID:(56099)
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
107 .. 107 A/C rs2240701 + 5'UTR
153 .. 153 C/T rs59981184 + 5'UTR
398 .. 398 T/G rs2015825 + CDS Synonymous[Val68Val]
537 ^ 538 -/C rs11386689 + CDS
1407 .. 1407 G/C rs17208397 + CDS Nonsynonymous[Val405Leu]
1647 .. 1647 G/C rs35892780 + CDS Nonsynonymous[Gly485Arg]
1680 .. 1680 C/T rs111954647 + CDS Synonymous[Leu496Leu]
1760 .. 1760 C/T rs3749766 - CDS Synonymous[His522His]
1840 .. 1840 G/A rs115850576 + CDS Nonsynonymous[Arg549His]
2037 .. 2037 G/A rs116279995 + CDS Nonsynonymous[Gly615Arg]
2580 .. 2580 G/A rs72790042 + CDS Nonsynonymous[Val796Ile]
2814 .. 2814 G/A rs114669158 + CDS Nonsynonymous[Ala874Thr]
2825 .. 2825 A/G rs2233612 + CDS Synonymous[Gly877Gly]
2847 .. 2847 G/A rs116366286 + CDS Nonsynonymous[Val885Met]
2860 .. 2860 G/A rs61749029 + CDS Nonsynonymous[Arg889His]
3014 .. 3014 A/G rs2233613 + 3'UTR
3119 .. 3119 G/A rs76613492 + 3'UTR
3175 .. 3175 T/C rs115159796 + 3'UTR
3439 .. 3439 G/C rs4912608 + 3'UTR
3697 .. 3697 T/C rs113814137 + 3'UTR
4005 .. 4005 G/A rs111365449 + 3'UTR
4196 .. 4196 A/G rs78180647 + 3'UTR
4725 .. 4725 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;