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: HIT000071759 Accession number: AF152333 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Protocadherin gamma-B4; PCDH-gamma-B4; Cadherin-20; Fibroblast cadherin-2; Precursor;
 
 

Transcript original information
Accession number AF152333.1
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 (PCDHGC5) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (PCDHGC5);
Sequence data provider NA
Annotation project NA
Length of cDNA 4578[bp] (No. of exon:4)[A:1042 T:1015 G:1202 C:1319]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type brain
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) 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 140767452- 140892546
Strand +
Possible duplicated location(s) NA
Gene structure 4 exon(s)
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:8641
KEGG GENES KEGG GENES(8641)
GeneCard GeneCardPCDHGC5*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 HIP000060466
Predicted CDS 1..2772;  923[aa];  Orientation:+1; 
Codon Adaptation Index (CAI). 0.746
Database links RefSeq NP_003727
UniProt Q9UN71
CCDS CCDS54928

Motif information
ORF

length(923),orf(1:2772)
MGSGAGELGRAERLPVLFLFLLSLFCPALCEQIRYRIPEEMPKGSVVGNL
ATDLGFSVQELPTRKLRVSSEKPYFTVSAESGELLVSSRLDREEICGKKP
ACALEFEAVAENPLNFYHVNVEIEDINDHTPKFTQNSFELQISESAQPGT
RFILGSAHDADIGSNTLQNYQLSPSDHFSLINKEKSDGSKYPEMVLKTPL
DREKQKSYHLTLTALDFGAPPLSSTAQIHVLVTDANDNAPVFSQDVYRVS
LSENVYPGTTVLQVTATDQDEGVNAEITFSFSEASQITQFDLNSNTGEIT
VLNTLDFEEVKEYSIVLEARDGGGMIAQCTVEVEVIDENDNAPEVIFQSL
PNLIMEDAELGTHIALLKVRDKDSRHNGEVTCKLEGDVPFKILTSSRNTY
KLVTDAVLDREQNPEYNITVTATDRGKPPLSSSSSITLHIGDVNDNAPVF
SQSSYIVHVAENNPPGASISQVRASDPDLGPNGQVSYCIMASDLEQRELS
SYVSISAESGVVFAQRAFDHEQLRAFELTLQARDQGSPALSANVSLRVLV
DDRNDNAPRVLYPALGPDGSALFDMVPHAAEPGYLVTKVVAVDADSGHNA
WLSYHVLQASEPGLFSLGLRTGEVRTARALGDRDAVRQRLLVAVRDGGQP
PLSATATLHLVFADSLQEVLPDITDRPDPSDLQAELQFYLVVALALISVL
FLVAMILAIALRLRRSSSPASWSCFQPGLCVKSESVVPPNYSEGTLPYSY
NLCVAHTGKTEFNFLKCSEQLSSGQDILCGDSSGALFPLCNSSELTSHQQ
APPNTDWRFSQAQRPGTSGSQNGDDTGTWPNNQFDTEMLQAMILASASEA
ADGSSTLGGGAGTMGLSARYGPQFTLQHVPDYRQNVYIPGSNATLTNAAG
KRDGKAPAGGNGNKKKSGKKEKK*
a.a.
length
InterPro Name
length(82), motif(31:112) 82 IPR013164 Cadherin, N-terminal [Domain]
length(94), motif(32:125) 94 IPR015919 Cadherin-like [Domain]
length(98), motif(32:129) 98 IPR002126 Cadherin [Domain]
length(97), motif(37:133) 97 IPR002126 Cadherin [Domain]
length(86), motif(46:131) 86 IPR002126 Cadherin [Domain]
length(20), motif(73:92) 20 IPR002126 Cadherin [Domain]
length(11), motif(121:131) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(108), motif(127:234) 108 IPR015919 Cadherin-like [Domain]
length(109), motif(130:238) 109 IPR002126 Cadherin [Domain]
length(109), motif(134:242) 109 IPR002126 Cadherin [Domain]
length(95), motif(139:233) 95 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(117), motif(230:346) 117 IPR015919 Cadherin-like [Domain]
length(107), motif(239:345) 107 IPR002126 Cadherin [Domain]
length(30), motif(242:271) 30 IPR002126 Cadherin [Domain]
length(103), motif(243:345) 103 IPR002126 Cadherin [Domain]
length(89), motif(247:335) 89 IPR002126 Cadherin [Domain]
length(80), motif(264:343) 80 IPR002126 Cadherin [Domain]
length(13), motif(312:324) 13 IPR002126 Cadherin [Domain]
length(11), motif(333:343) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(104), motif(339:442) 104 IPR015919 Cadherin-like [Domain]
length(87), motif(354:440) 87 IPR002126 Cadherin [Domain]
length(94), motif(354:447) 94 IPR002126 Cadherin [Domain]
length(97), motif(354:450) 97 IPR002126 Cadherin [Domain]
length(82), motif(367:448) 82 IPR002126 Cadherin [Domain]
length(20), motif(429:448) 20 IPR002126 Cadherin [Domain]
length(11), motif(438:448) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(123), motif(439:561) 123 IPR015919 Cadherin-like [Domain]
length(113), motif(448:560) 113 IPR002126 Cadherin [Domain]
length(14), motif(448:461) 14 IPR002126 Cadherin [Domain]
length(110), motif(451:560) 110 IPR002126 Cadherin [Domain]
length(95), motif(456:550) 95 IPR002126 Cadherin [Domain]
length(87), motif(472:558) 87 IPR002126 Cadherin [Domain]
length(27), motif(508:534) 27 IPR002126 Cadherin [Domain]
length(18), motif(542:559) 18 IPR002126 Cadherin [Domain]
length(11), motif(548:558) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(109), motif(554:662) 109 IPR015919 Cadherin-like [Domain]
length(98), motif(576:673) 98 IPR002126 Cadherin [Domain]
length(89), motif(576:664) 89 IPR002126 Cadherin [Domain]
length(81), motif(579:659) 81 IPR002126 Cadherin [Domain]
length(82), motif(589:670) 82 IPR002126 Cadherin [Domain]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000071759
H-Inv cluster ID Locus viewHIX0005252
Accession number AF152333.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO;  Splicing isoformSplicing isoform
Coding potential  Help Protein coding; 
Definition Protocadherin gamma-B4; PCDH-gamma-B4; Cadherin-20; Fibroblast cadherin-2; Precursor;
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (Q9UN71)  [Identity/coverage = 100.0%/100.0%] to Homo sapiens (Human). protein.
Experimental evidence Protein evidence
PubMed ID 91991961038092915489334ALL
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 PCDHGC5
HGNC aliases NA
HGNC name protocadherin gamma subfamily C, 5
DDBJ PCDH-gamma-B4
UniProt PCDHGB4
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 HIP000060466
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:8641
KEGG GENES KEGG GENES(8641)
GeneCard GeneCardPCDHGC5*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 plasma membrane;  extracellular;  endoplasmic;  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
34 100 1f5aA1 3e-15 19.0 63/118 d.58.16.1
128 215 1l3wA4 8e-10 21.6 83/107 b.1.6.1
199 600 1dnvA 1e-66 11.6 371/415 b.121.5.3
582 659 1edhA1 1e-12 13.3 77/99 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 AGhsA061122;  AGhsB190717; 
Affymetrix
GeneChip
HG-Focus 211807_x_at;  215836_s_at; 
HG-U133 205717_x_at;  209079_x_at;  211066_x_at;  211807_x_at;  211876_x_at;  215836_s_at;  216352_x_at; 
HG-U133A 205717_x_at;  209079_x_at;  211066_x_at;  211807_x_at;  211876_x_at;  215836_s_at;  216352_x_at; 
HG-U133A_2 205717_x_at;  209079_x_at;  211066_x_at;  211807_x_at;  211876_x_at;  215836_s_at;  216352_x_at; 
HG-U133B NA
HG-U133_Plus_2 205717_x_at;  209079_x_at;  211066_x_at;  211807_x_at;  211876_x_at;  215836_s_at;  216352_x_at; 
HG-U95 1690_at;  657_at; 
HG-U95A 1690_at;  657_at; 
HG-U95B NA
HG-U95C NA
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 2832599;  2832600;  2832616;  2832618;  2832619;  2832751;  2832754;  2832758;  2832759;  2832760;  2832761;  2832762;  2832763;  2832764;  2832765;  2832766;  2832767;  2832768;  2832769;  2878642;  2878647;  2878661; 
HuGeneFL AB000896_at;  L11373_at; 
Agilent Human 1A Oligo Microarray:PGID215 A_23_P354734; 
Whole Human Genome Oligo Microarray:PGID247 A_23_P354734;  A_23_P359588; 
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
52 .. 52 T/G rs200817766 + CDS Nonsynonymous[Phe18Val]
451 .. 451 C/A rs67622091 + CDS Synonymous[Arg151Arg]
506 .. 506 A/C rs202036029 + CDS Nonsynonymous[Asn169Thr]
538 .. 538 C/T rs68033444 + CDS Synonymous[Leu180Leu]
540 .. 540 G/A rs77505166 + CDS Synonymous[Leu180Leu]
681 .. 681 G/C rs149167054 + CDS Nonsynonymous[Gln227His]
682 .. 682 A/T rs145399301 + CDS Nonsynonymous[Ile228Leu]
695 .. 695 T/A rs113550354 + CDS Nonsynonymous[Val232Glu]
767 .. 767 A/G rs186708822 + CDS Nonsynonymous[Tyr256Cys]
818 .. 818 T/G rs201901866 + CDS Nonsynonymous[Val273Gly]
857 .. 857 A/C rs200109598 + CDS Nonsynonymous[Gln286Pro]
984 .. 984 A/G rs138074064 + CDS Synonymous[Gln328Gln]
991 .. 991 G/T rs201053346 + CDS Nonsynonymous[Val331Leu]
1057 .. 1057 C/T rs191165529 + CDS Synonymous[Leu353Leu]
1071 .. 1071 C/T rs183330174 + CDS Synonymous[Asp357Asp]
1126 .. 1126 C/G rs141101630 + CDS Nonsynonymous[His376Asp]
1129 .. 1129 A/G rs187666474 + CDS Nonsynonymous[Asn377Asp]
1225 .. 1225 G/A rs144915863 + CDS Nonsynonymous[Asp409Asn]
1258 .. 1258 G/A rs72790030 + CDS Nonsynonymous[Val420Ile]
1273 .. 1273 C/T rs192156139 + CDS Nonsynonymous[Arg425Trp]
1316 .. 1316 A/G rs202220616 + CDS Nonsynonymous[His439Arg]
1390 .. 1390 C/G rs183257097 + CDS Nonsynonymous[Pro464Ala]
1393 .. 1393 C/T rs148279287 + CDS Nonsynonymous[Pro465Ser]
1472 .. 1472 C/T rs188323445 + CDS Nonsynonymous[Ala491Val]
1490 .. 1490 G/A rs192606668 + CDS Nonsynonymous[Arg497Gln]
1545 .. 1545 G/A rs201662463 + CDS Synonymous[Gln515Gln]
1555 .. 1555 G/T rs201120335 + CDS Nonsynonymous[Asp519Tyr]
1632 .. 1632 G/C rs200072718 + CDS Synonymous[Val544Val]
1644 .. 1644 G/T rs200792478 + CDS Synonymous[Val548Val]
1652 .. 1652 A/G rs199537783 + CDS Nonsynonymous[Asp551Gly]
1677 .. 1677 G/A rs115696241 + CDS Synonymous[Arg559Arg]
1775 .. 1775 T/G rs201900584 + CDS Nonsynonymous[Val592Gly]
1838 .. 1838 G/C rs141134077 + CDS Nonsynonymous[Gly613Ala]
1842 .. 1842 C/T rs150721796 + CDS Synonymous[Leu614Leu]
1874 .. 1874 G/T rs201153580 + CDS Nonsynonymous[Arg625Leu]
1987 .. 1987 G/C rs199638280 + CDS Nonsynonymous[Ala663Pro]
2125 .. 2125 A/G rs200734314 + CDS Nonsynonymous[Ile709Val]
2339 .. 2339 G/T rs137959577 + CDS Nonsynonymous[Gly780Val]
2434 .. 2434 G/A rs201391904 + CDS Nonsynonymous[Ala812Thr]
2446 .. 2446 G/A rs200418116 + CDS Nonsynonymous[Gly816Ser]
2502 .. 2502 T/C rs149352680 + CDS Synonymous[Phe834Phe]
2601 .. 2601 C/T rs143630962 + CDS Synonymous[Ser867Ser]
2602 .. 2602 G/A rs114669158 + CDS Nonsynonymous[Ala868Thr]
2605 .. 2605 C/T rs148119281 + CDS Nonsynonymous[Arg869Cys]
2610 .. 2610 C/T rs141873183 + CDS Synonymous[Tyr870Tyr]
2613 .. 2613 A/G rs2233612 + CDS Synonymous[Gly871Gly]
2635 .. 2635 G/A rs116366286 + CDS Nonsynonymous[Val879Met]
2648 .. 2648 G/A rs61749029 + CDS Nonsynonymous[Arg883His]
2675 .. 2675 A/G rs201009079 + CDS Nonsynonymous[Asn892Ser]
2691 .. 2691 C/T rs143362044 + CDS Synonymous[Asn897Asn]
2734 .. 2734 G/A rs200541479 + CDS Nonsynonymous[Gly912Ser]
2750 .. 2750 C/T rs202071188 + CDS Nonsynonymous[Ser917Leu]
2769 .. 2769 G/A rs147534370 + CDS Synonymous[Lys923Lys]
2801 .. 2801 C/T rs201024828 + 3'UTR
2802 .. 2802 G/A rs2233613 + 3'UTR
2907 .. 2907 G/A rs76613492 + 3'UTR
2963 .. 2963 T/C rs115159796 + 3'UTR
2973 .. 2973 C/A rs191106767 + 3'UTR
3209 .. 3209 C/A rs146235929 + 3'UTR
3227 .. 3227 G/C rs4912608 + 3'UTR
3302 .. 3302 T/G rs148447880 + 3'UTR
3464 .. 3464 G/A rs142624814 + 3'UTR
3485 .. 3485 T/C rs113814137 + 3'UTR
3491 .. 3491 C/T rs150999050 + 3'UTR
3498 .. 3498 T/G rs187622252 + 3'UTR
3687 .. 3687 A/G rs192947391 + 3'UTR
3770 .. 3770 T/C rs140884268 + 3'UTR
3793 .. 3793 G/A rs111365449 + 3'UTR
3984 .. 3984 A/G rs78180647 + 3'UTR
4052 .. 4052 G/A rs185198109 + 3'UTR
4145 .. 4145 C/T rs147780926 + 3'UTR
4438 .. 4438 C/T rs141207714 + 3'UTR
4457 .. 4457 G/T rs189734474 + 3'UTR
4513 .. 4513 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