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H-InvDB_9.0 released on May 27, 2015.
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H-Invitational ID: HIT000071754 Accession number: AF152328 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Protocadherin gamma-A8; PCDH-gamma-A8; Precursor;
 
 

Transcript original information
Accession number AF152328.1
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 4605[bp] (No. of exon:4)[A:1070 T:993 G:1198 C:1344]
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 140772381- 140892546
Strand +
Possible duplicated location(s) NA
Gene structure 4 exon(s)
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:9708
KEGG GENES KEGG GENES(9708)
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 HIP000023156
Predicted CDS 1..2799;  932[aa];  Orientation:+1; 
Codon Adaptation Index (CAI). 0.758
Database links RefSeq NP_114477
UniProt Q9Y5G5
CCDS CCDS47291

Motif information
ORF

length(932),orf(1:2799)
MAAPQSRPRRGELILLCALLGTLWEIGRGQIRYSVPEETDKGSFVGNISK
DLGLDPRKLAKHGVRIVSRGRTQLFALNPRSGSLITAGRIDREELCAQSP
RCLININTLVEDKGKLFGVEIEIIDINDNNPKFQVEDLEVKINEIAVPGA
RYPLPEAVDPDVGVNSLQSYQLSPNHHFSLDVQTGDNGAINPELVLERAL
DREEEAAHHLVLTASDGGKPPRSSTVRIHVTVLDTNDNAPVFPHPIYRVK
VLENMPPGTRLLTVTASDPDEGINGKVAYKFRKINEKQTPLFQLNENTGE
ISIAKSLDYEECSFYEMEIQAEDVGALLGRTKLLISVEDVNDNRPEVIIT
SLFSPVLENSLPGTVIAFLSVHDQDSGKNGQVVCYTRDNLPFKLEKSIGN
YYRLVTRKYLDRENVSIYNITVMASDLGTPPLSTETQIALHVADINDNPP
TFPHASYSAYILENNLRGASIFSLTAHDPDSQENAQVTYSVTEDTLQGAP
LSSYISINSDTGVLYALQSFDYEQIRDLQLLVTASDSGDPPLSSNMSLSL
FVLDQNDNAPEILYPALPTDGSTGVELAPRSAERGYLVTKVVAVDRDSGQ
NAWLSYRLLKASEPGLFSVGLHTGEVRTARALLDRDALKQSLVVAVQDHG
QPPLSATVTLTVAVADSIPEVLTELGSLKPSVDPNDSSLTLYLVVAVAAI
SCVFLAFVAVLLGLRLRRWHKSRLLQDSGGRLVGVPASHFVGVEEVQAFL
QTYSQEVSLTADSRKSHLIFPQPNYADMLISQEGCEKNDSLLTSVDFHEY
KNEADHGQQAPPNTDWRFSQAQRPGTSGSQNGDDTGTWPNNQFDTEMLQA
MILASASEAADGSSTLGGGAGTMGLSARYGPQFTLQHVPDYRQNVYIPGS
NATLTNAAGKRDGKAPAGGNGNKKKSGKKEKK*
a.a.
length
InterPro Name
length(113), motif(19:131) 113 IPR002126 Cadherin [Domain]
length(87), motif(29:115) 87 IPR015919 Cadherin-like [Domain]
length(84), motif(29:112) 84 IPR013164 Cadherin, N-terminal [Domain]
length(105), motif(29:133) 105 IPR002126 Cadherin [Domain]
length(99), motif(30:128) 99 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(110), motif(129:238) 110 IPR002126 Cadherin [Domain]
length(109), motif(134:242) 109 IPR002126 Cadherin [Domain]
length(94), motif(140:233) 94 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(104), motif(239:342) 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(106), motif(343:448) 106 IPR002126 Cadherin [Domain]
length(87), motif(356:442) 87 IPR002126 Cadherin [Domain]
length(97), motif(356:452) 97 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(125), motif(441:565) 125 IPR015919 Cadherin-like [Domain]
length(115), motif(449:563) 115 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(111), motif(556:666) 111 IPR015919 Cadherin-like [Domain]
length(104), motif(579:682) 104 IPR002126 Cadherin [Domain]
length(87), motif(580:666) 87 IPR002126 Cadherin [Domain]
length(82), motif(583:664) 82 IPR002126 Cadherin [Domain]
length(79), motif(591:669) 79 IPR002126 Cadherin [Domain]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000071754
H-Inv cluster ID Locus viewHIX0005252
Accession number AF152328.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO;  Splicing isoformSplicing isoform
Coding potential  Help Protein coding; 
Definition Protocadherin gamma-A8; PCDH-gamma-A8; Precursor;
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (Q9Y5G5)  [Identity/coverage = 100.0%/100.0%] to Homo sapiens (Human). protein.
Experimental evidence Protein evidence
PubMed ID 92058411038092915489334ALL
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-A8
UniProt PCDHGA8
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 HIP000023156
No. of interaction 3
Interaction partner(s) HIP000044820HIP000138610HIP000138610
BIND NA
DIP NA
MINT NA
HPRD NA
IntAct NA
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:9708
KEGG GENES KEGG GENES(9708)
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; 
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
36 100 1f5aA1 8e-17 22.0 59/118 d.58.16.1
131 234 1edhA2 4e-10 22.8 98/112 b.1.6.1
208 525 2nlzA1 1e-63 11.8 296/533 d.153.1.6
504 666 1o75A3 8e-18 8.0 152/191 b.120.1.1
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 AGhsA110112;  AGhsB190717; 
Affymetrix
GeneChip
HG-Focus 215836_s_at;  216343_at; 
HG-U133 205717_x_at;  209079_x_at;  211066_x_at;  211876_x_at;  211879_x_at;  211880_x_at;  215836_s_at;  216343_at;  216352_x_at; 
HG-U133A 205717_x_at;  209079_x_at;  211066_x_at;  211876_x_at;  211879_x_at;  211880_x_at;  215836_s_at;  216343_at;  216352_x_at; 
HG-U133A_2 205717_x_at;  209079_x_at;  211066_x_at;  211876_x_at;  211879_x_at;  211880_x_at;  215836_s_at;  216343_at;  216352_x_at; 
HG-U133B NA
HG-U133_Plus_2 205717_x_at;  209079_x_at;  211066_x_at;  211876_x_at;  211879_x_at;  211880_x_at;  215836_s_at;  216343_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 2832604;  2832605;  2832606;  2832607;  2832751;  2832754;  2832758;  2832759;  2832760;  2832761;  2832762;  2832763;  2832764;  2832765;  2832766;  2832767;  2832768;  2832769;  2878647;  2878651;  2878661; 
HuGeneFL L11373_at; 
Agilent Human 1A Oligo Microarray:PGID215 A_23_P354734; 
Whole Human Genome Oligo Microarray:PGID247 A_23_P354734;  A_24_P308851; 
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
30 .. 30 C/T rs77141792 + CDS Synonymous[Arg10Arg]
31 .. 31 G/C rs201895231 + CDS Nonsynonymous[Gly11Arg]
47 .. 47 T/G rs726684 + CDS Nonsynonymous[Leu16Arg]
193 .. 193 C/T rs182052960 + CDS Nonsynonymous[Arg65Cys]
299 .. 299 C/T rs148589854 + CDS Nonsynonymous[Pro100Leu]
307 .. 307 C/T rs142751758 + CDS Synonymous[Leu103Leu]
356 .. 356 T/C rs113280752 + CDS Nonsynonymous[Val119Ala]
429 .. 429 C/T rs151037104 + CDS Synonymous[Asn143Asn]
442 .. 442 C/G rs201229959 + CDS Nonsynonymous[Pro148Ala]
519 .. 519 C/- rs3214276 + CDS
561 .. 561 T/G rs11575958 + CDS Nonsynonymous[Asn187Lys]
601 .. 601 G/C rs199973289 + CDS Nonsynonymous[Asp201His]
639 .. 639 G/T rs189963623 + CDS Synonymous[Thr213Thr]
645 .. 645 G/A rs181214352 + CDS Synonymous[Ser215Ser]
662 .. 662 C/G rs200282311 + CDS Nonsynonymous[Pro221Arg]
669 .. 669 T/C rs116240246 + CDS Synonymous[Ser223Ser]
701 .. 701 A/T rs72492419 + CDS Nonsynonymous[Asp234Val]
731 .. 731 A/G rs72790032 + CDS Nonsynonymous[His244Arg]
779 .. 779 G/A rs200863279 + CDS Nonsynonymous[Arg260Gln]
845 .. 845 G/A rs141295392 + CDS Nonsynonymous[Arg282Gln]
897 .. 897 G/T rs143738602 + CDS Synonymous[Gly299Gly]
905 .. 905 C/G rs185464441 + CDS AA-STOP[Ser302*]
916 .. 916 A/G rs189824439 + CDS Nonsynonymous[Ser306Gly]
1008 .. 1008 G/T rs2240700 + CDS Synonymous[Ser336Ser]
1081 .. 1081 C/G rs201697840 + CDS Nonsynonymous[Leu361Val]
1085 .. 1085 C/T rs182092307 + CDS Nonsynonymous[Pro362Leu]
1130 .. 1130 G/A rs186465469 + CDS Nonsynonymous[Gly377Glu]
1182 .. 1182 A/C rs201832611 + CDS Nonsynonymous[Leu394Phe]
1270 .. 1270 G/A rs146481056 + CDS Nonsynonymous[Ala424Thr]
1339 .. 1339 G/A rs141035845 + CDS Nonsynonymous[Asp447Asn]
1358 .. 1358 C/T rs115102808 + CDS Nonsynonymous[Pro453Leu]
1432 .. 1432 G/A rs144796076 + CDS Nonsynonymous[Asp478Asn]
1474 .. 1474 A/C rs199519740 + CDS Nonsynonymous[Thr492Pro]
1476 .. 1476 C/A rs191844335 + CDS Synonymous[Thr492Thr]
1508 .. 1508 C/G rs11575959 + CDS Nonsynonymous[Ser503Trp]
1554 .. 1554 A/G rs201573539 + CDS Synonymous[Gln518Gln]
1556 .. 1556 C/T rs183754735 + CDS Nonsynonymous[Ser519Phe]
1580 .. 1580 A/G rs201461446 + CDS Nonsynonymous[Asp527Gly]
1615 .. 1615 G/A rs199658498 + CDS Nonsynonymous[Asp539Asn]
1637 .. 1637 T/A rs188283892 + CDS Nonsynonymous[Met546Lys]
1751 .. 1751 G/C rs200338108 + CDS Nonsynonymous[Arg584Pro]
1752 .. 1752 T/C rs199836246 + CDS Synonymous[Arg584Arg]
1824 .. 1824 G/C rs201732776 + CDS Synonymous[Leu608Leu]
1890 .. 1890 A/C rs138625114 + CDS Synonymous[Arg630Arg]
1908 .. 1908 T/C rs4912749 + CDS Synonymous[Asp636Asp]
1927 .. 1927 G/A rs148904388 + CDS Nonsynonymous[Val643Met]
1990 .. 1990 G/A rs143444747 + CDS Nonsynonymous[Val664Met]
2011 .. 2011 G/C rs200702899 + CDS Nonsynonymous[Val671Leu]
2023 .. 2023 T/G rs116789057 + CDS Nonsynonymous[Leu675Val]
2281 .. 2281 G/C rs192995605 + CDS Nonsynonymous[Ala761Pro]
2309 .. 2309 T/C rs72790033 + CDS Nonsynonymous[Phe770Ser]
2325 .. 2325 C/T rs147992300 + CDS Synonymous[Tyr775Tyr]
2369 .. 2369 C/T rs143509166 + CDS Nonsynonymous[Ser790Phe]
2397 .. 2397 A/G rs200048432 + CDS Synonymous[Glu799Glu]
2461 .. 2461 G/A rs201391904 + CDS Nonsynonymous[Ala821Thr]
2473 .. 2473 G/A rs200418116 + CDS Nonsynonymous[Gly825Ser]
2529 .. 2529 T/C rs149352680 + CDS Synonymous[Phe843Phe]
2628 .. 2628 C/T rs143630962 + CDS Synonymous[Ser876Ser]
2629 .. 2629 G/A rs114669158 + CDS Nonsynonymous[Ala877Thr]
2632 .. 2632 C/T rs148119281 + CDS Nonsynonymous[Arg878Cys]
2637 .. 2637 C/T rs141873183 + CDS Synonymous[Tyr879Tyr]
2640 .. 2640 A/G rs2233612 + CDS Synonymous[Gly880Gly]
2662 .. 2662 G/A rs116366286 + CDS Nonsynonymous[Val888Met]
2675 .. 2675 G/A rs61749029 + CDS Nonsynonymous[Arg892His]
2702 .. 2702 A/G rs201009079 + CDS Nonsynonymous[Asn901Ser]
2718 .. 2718 C/T rs143362044 + CDS Synonymous[Asn906Asn]
2761 .. 2761 G/A rs200541479 + CDS Nonsynonymous[Gly921Ser]
2777 .. 2777 C/T rs202071188 + CDS Nonsynonymous[Ser926Leu]
2796 .. 2796 G/A rs147534370 + CDS Synonymous[Lys932Lys]
2828 .. 2828 C/T rs201024828 + 3'UTR
2829 .. 2829 G/A rs2233613 + 3'UTR
2934 .. 2934 G/A rs76613492 + 3'UTR
2990 .. 2990 T/C rs115159796 + 3'UTR
3000 .. 3000 C/A rs191106767 + 3'UTR
3236 .. 3236 C/A rs146235929 + 3'UTR
3254 .. 3254 G/C rs4912608 + 3'UTR
3329 .. 3329 T/G rs148447880 + 3'UTR
3491 .. 3491 G/A rs142624814 + 3'UTR
3512 .. 3512 T/C rs113814137 + 3'UTR
3518 .. 3518 C/T rs150999050 + 3'UTR
3525 .. 3525 T/G rs187622252 + 3'UTR
3714 .. 3714 A/G rs192947391 + 3'UTR
3797 .. 3797 T/C rs140884268 + 3'UTR
3820 .. 3820 G/A rs111365449 + 3'UTR
4011 .. 4011 A/G rs78180647 + 3'UTR
4079 .. 4079 G/A rs185198109 + 3'UTR
4172 .. 4172 C/T rs147780926 + 3'UTR
4465 .. 4465 C/T rs141207714 + 3'UTR
4484 .. 4484 G/T rs189734474 + 3'UTR
4540 .. 4540 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