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: HIT000052733 Accession number: BC042650 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Similar to Protocadherin gamma-C4; PCDH-gamma-C4; Precursor;
 
 

Transcript original information
Accession number BC042650.1
CAGE tag ID NA
EST ID NA
Clone Number IMAGE:4914375
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 Provider:MGC/NCI
Annotation project H-Invitational FLcDNA
Length of cDNA 3470[bp] (No. of exon:2)[A:771 T:789 G:918 C:992]
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: 3458(+) Signal: 3440-3444(+)
Vector/adapter sequence NA
Frame shift 1532-1532[bp] Insertion(T); 1534-1535[bp] Insertion(AC);
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 140864649- 140892539
Strand +
Possible duplicated location(s) NA
Gene structure 2 exon(s)
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:56098
KEGG GENES KEGG GENES(56098)
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 HIP000216802
Predicted CDS 93..1907;  604[aa];  Orientation:+3; 
Codon Adaptation Index (CAI). 0.76

Motif information
ORF

length(604),orf(93:1907)
MLRKVRSWTEIWRWATLLFLFYHLGYVCGQIRYPVPEESQEGTFVGNVAQ
DFLLDTDSLSARRLQVAGEVNQRHFRVDLDSGALLIKNPIDREALCGLSA
SCIVPLEFVTEGPLEMYRAEVEIVDVNDHAPRFPRQQLDLEIGEAAPPGQ
RFPLEKAQDADVGSNSISSYRLSSNEHFALDVKKRSDGSLVPELLLEKPL
DREKQSDYRLVLTAVDGGNPPRSGTAELRVSVLDVNDNAPAFQQSSYRIS
VLESAPAGMVLIQLNASDPDLGPSGNVTFYFSGHTPDRVRNLFSLHPTTG
KLTLLGPLDFESENYYEFDVRARDGGSPAMEQHCSLRVDLLDVNDNAPYI
TVTSELGTLPESAEPGTVVALISVQDPDSGSNGDVSLRIPDHLPFALKSA
FRNQFSLVTAGPLDREAKSSYDIMVTASDAGNPPLSTHRTIFLNISDVND
NPPSFFQRSHEVFVPENNRPGDLLCSLAASPECLHPRQQCHTDQRSWQAG
WQGPSRWQWQQEEVGQEGEEVTWRPGQEPQGSLSPTSPASPYLHPGLRVS
GLTPRILVGAKAMLPLGNRNKCPVSTYPFPPRGLNMQKQFRWEPPSNQLL
YPWG*
a.a.
length
InterPro Name
length(83), motif(29:111) 83 IPR013164 Cadherin, N-terminal [Domain]
length(67), motif(30:96) 67 IPR015919 Cadherin-like [Domain]
length(83), motif(31:113) 83 IPR002126 Cadherin [Domain]
length(99), motif(35:133) 99 IPR002126 Cadherin [Domain]
length(81), motif(51:131) 81 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(115), motif(125:239) 115 IPR002126 Cadherin [Domain]
length(108), motif(127:234) 108 IPR015919 Cadherin-like [Domain]
length(30), motif(133:162) 30 IPR002126 Cadherin [Domain]
length(109), motif(134:242) 109 IPR002126 Cadherin [Domain]
length(93), motif(141:233) 93 IPR002126 Cadherin [Domain]
length(86), motif(155:240) 86 IPR002126 Cadherin [Domain]
length(13), motif(207:219) 13 IPR002126 Cadherin [Domain]
length(20), motif(221:240) 20 IPR002126 Cadherin [Domain]
length(11), motif(230:240) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(125), motif(230:354) 125 IPR015919 Cadherin-like [Domain]
length(14), motif(240:253) 14 IPR002126 Cadherin [Domain]
length(107), motif(240:346) 107 IPR002126 Cadherin [Domain]
length(108), motif(243:350) 108 IPR002126 Cadherin [Domain]
length(94), motif(247:340) 94 IPR002126 Cadherin [Domain]
length(85), motif(264:348) 85 IPR002126 Cadherin [Domain]
length(27), motif(298:324) 27 IPR002126 Cadherin [Domain]
length(18), motif(332:349) 18 IPR002126 Cadherin [Domain]
length(11), motif(338:348) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(134), motif(338:471) 134 IPR015919 Cadherin-like [Domain]
length(110), motif(347:456) 110 IPR002126 Cadherin [Domain]
length(105), motif(351:455) 105 IPR002126 Cadherin [Domain]
length(84), motif(358:441) 84 IPR002126 Cadherin [Domain]
length(82), motif(372:453) 82 IPR002126 Cadherin [Domain]
length(11), motif(443:453) 11 IPR020894 Cadherin conserved site [Conserved_site]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000052733
H-Inv cluster ID Locus viewHIX0005252
Accession number BC042650.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO;  Splicing isoformSplicing isoform
Coding potential  Help Protein coding; 
Definition Similar to Protocadherin gamma-C4; PCDH-gamma-C4; Precursor;
Similarity category  Help Category: Similar to known protein(Category II).
Similar to known protein (Q9Y5F7)  [Identity/coverage = 99.793%/51.49%] 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 PCDHGC5
HGNC aliases NA
HGNC name protocadherin gamma subfamily C, 5
DDBJ NA
UniProt PCDHGC4
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 HIP000216802
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:56098
KEGG GENES KEGG GENES(56098)
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. 
FR ID FR062174
Accession
Description
Location
PMID

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;  mitochondria;  cytosol;  Other; 
Target P signal peptide
SOSUI soluble protein
TMHMM soluble 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
12 99 1f5aA1 3e-14 22.0 82/118 d.58.16.1
70 163 1fx3A 3e-04 8.4 86/143 d.33.1.1
190 479 2nlzA1 4e-47 10.2 275/533 d.153.1.6
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 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 205717_x_at;  209079_x_at;  211066_x_at;  211876_x_at;  215836_s_at;  216352_x_at; 
HG-U95 657_at; 
HG-U95A 657_at; 
HG-U95B NA
HG-U95C NA
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 2832725;  2832726;  2832727;  2832728;  2832729;  2832730;  2832760;  2832761;  2832762;  2832763;  2832764;  2832765;  2832766;  2832767;  2832768;  2832769;  2878661; 
HuGeneFL 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

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
29 ^ 30 -/G rs145099347 + 5'UTR
63 .. 63 G/C rs199625514 + 5'UTR
136 .. 136 C/T rs138463062 + CDS Nonsynonymous[Ala15Val]
194 .. 194 G/A rs77402299 + CDS Synonymous[Pro34Pro]
210 .. 210 C/A rs114678203 + CDS Nonsynonymous[Gln40Lys]
234 .. 234 G/A rs201756706 + CDS Nonsynonymous[Val48Ile]
256 .. 256 A/G rs147409155 + CDS Nonsynonymous[Asp55Gly]
259 .. 259 C/T rs139641513 + CDS Nonsynonymous[Thr56Met]
357 .. 357 C/T rs143779180 + CDS Nonsynonymous[Pro89Ser]
575 .. 575 T/C rs147216126 + CDS Synonymous[Asp161Asp]
616 .. 616 A/G rs76923861 + CDS Nonsynonymous[Asn175Ser]
711 .. 711 G/A rs114766079 + CDS Nonsynonymous[Asp207Asn]
763 .. 763 G/A rs201857404 + CDS Nonsynonymous[Gly224Asp]
829 .. 829 G/C rs142273728 + CDS Nonsynonymous[Ser246Thr]
899 .. 899 G/A rs151239937 + CDS Synonymous[Pro269Pro]
915 .. 915 G/A rs114142606 + CDS Nonsynonymous[Gly275Ser]
938 .. 938 T/C rs2078071 - CDS Synonymous[Ser282Ser]
941 .. 941 T/C rs146615755 + CDS Synonymous[Gly283Gly]
978 .. 978 C/T rs141349392 + CDS Nonsynonymous[His296Tyr]
984 .. 984 A/G rs145186028 + CDS Nonsynonymous[Thr298Ala]
1009 .. 1009 G/T rs190955361 + CDS Nonsynonymous[Gly306Val]
1054 .. 1054 G/A rs145871538 + CDS Nonsynonymous[Arg321Gln]
1172 .. 1172 C/T rs148995268 + CDS Synonymous[Pro360Pro]
1183 .. 1183 A/C rs201073884 + CDS Nonsynonymous[Glu364Ala]
1188 .. 1188 G/A rs111842066 + CDS Nonsynonymous[Gly366Ser]
1190 .. 1190 C/G rs143039217 + CDS Synonymous[Gly366Gly]
1238 .. 1238 C/T rs148184642 + CDS Synonymous[Asn382Asn]
1256 .. 1256 C/T rs116799150 + CDS Synonymous[Arg388Arg]
1403 .. 1403 C/G rs200150307 + CDS Synonymous[Thr437Thr]
1419 .. 1419 C/T rs114847835 + CDS Nonsynonymous[Leu443Phe]
1427 .. 1427 T/G rs187495695 + CDS Nonsynonymous[Ile445Met]
1472 .. 1472 T/C rs200580042 + CDS Synonymous[His460His]
1495 .. 1495 A/G rs142766421 + CDS Nonsynonymous[Asn468Ser]
1532 .. 1532 G/A rs61749029 + CDS Synonymous[Ser480Ser]
1559 .. 1559 A/G rs201009079 + CDS Synonymous[Gln489Gln]
1575 .. 1575 C/T rs143362044 + CDS Nonsynonymous[Arg495Cys]
1618 .. 1618 G/A rs200541479 + CDS AA-STOP[Trp509*]
1634 .. 1634 C/T rs202071188 + CDS Synonymous[Val514Val]
1653 .. 1653 G/A rs147534370 + CDS Nonsynonymous[Val521Ile]
1685 .. 1685 C/T rs201024828 + CDS Synonymous[Gly531Gly]
1686 .. 1686 A/G rs2233613 + CDS Nonsynonymous[Ser532Gly]
1791 .. 1791 G/A rs76613492 + CDS Nonsynonymous[Gly567Arg]
1847 .. 1847 T/C rs115159796 + CDS Synonymous[Asn585Asn]
1857 .. 1857 C/A rs191106767 + CDS Nonsynonymous[Gln589Lys]
2093 .. 2093 C/A rs146235929 + 3'UTR
2111 .. 2111 G/C rs4912608 + 3'UTR
2186 .. 2186 T/G rs148447880 + 3'UTR
2348 .. 2348 G/A rs142624814 + 3'UTR
2369 .. 2369 T/C rs113814137 + 3'UTR
2375 .. 2375 C/T rs150999050 + 3'UTR
2382 .. 2382 T/G rs187622252 + 3'UTR
2571 .. 2571 A/G rs192947391 + 3'UTR
2654 .. 2654 T/C rs140884268 + 3'UTR
2677 .. 2677 G/A rs111365449 + 3'UTR
2868 .. 2868 A/G rs78180647 + 3'UTR
2936 .. 2936 G/A rs185198109 + 3'UTR
3029 .. 3029 C/T rs147780926 + 3'UTR
3322 .. 3322 C/T rs141207714 + 3'UTR
3341 .. 3341 G/T rs189734474 + 3'UTR
3397 .. 3397 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