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H-InvDB_8.3 released on March 26, 2013.
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H-Invitational ID: HIT000338014 Accession number: BC104926 Created date: 26-Mar-2013 Last modified: 20-Apr-2012
Definition: Protocadherin gamma-A5 isoform 2 precursor.
 
 

Transcript original information
Accession number BC104926.1
CAGE tag ID NA
EST ID NA
Clone Number MGC:132586 IMAGE:8143929
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (PCDHGA5) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (PCDHGA5);
Sequence data provider NA
Annotation project NA
Length of cDNA 2570[bp] (No. of exon:1)[A:608 T:565 G:691 C:706]
Devision HUM
Molecular type mRNA
Library origin Cell type NA
Tissue type Brain, cerebral cortex and lung, 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 HIX0005252
Genomic location  G-integra Help Chromosome 5
Location 5q31.3
Position 140743799- 140746368
Strand +
Possible duplicated location(s) NA
Gene structure 1 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:56110; 
KEGG GENES KEGG GENES(56110); 
GeneCard GeneCardPCDHGA5;  *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 HIP000034338
Predicted CDS 100..2541;  813[aa];  Orientation:+1; 
Codon Adaptation Index (CAI). 0.745
Database links RefSeq NP_114443; 
UniProt NA
CCDS NA

Motif information
ORF

length(813),orf(100:2541) MASPPRGWGCGELLLPFMLLGTLCEPGSGQIRYSMPEELDKGSFVGNIAK DLGLEPQELAERGVRIVSRGRTQLFALNPRSGSLVTAGRIDREELCAQSP LCVVNFNILVENKMKIYGVEVEIIDINDNFPRFRDEELKVKVNENAAAGT RLVLPFARDADVGVNSLRSYQLSSNLHFSLDVVSGTDGQKYPELVLEQPL DREKETVHDLLLTALDGGDPVLSGTTHIRVTVLDANDNAPLFTPSEYSVS VPENIPVGTRLLMLTATDPDEGINGKLTYSFRNEEEKISETFQLDSNLGE ISTLQSLDYEESRFYLMEVVAQDGGALVASAKVVVTVQDVNDNAPEVILT SLTSSISEDCLPGTVIALFSVHDGDSGENGEIACSIPRNLPFKLEKSVDN YYHLLTTRDLDREETSDYNITLTVMDHGTPPLSTESHIPLKVADVNDNPP NFPQASYSTSVTENNPRGVSIFSVTAHDPDSGDNARVTYSLAEDTFQGAP LSSYVSINSDTGVLYALRSFDYEQLRDLQLWVTASDSGNPPLSSNVSLSL FVLDQNDNTPEILYPALPTDGSTGVELAPRSAEPGYLVTKVVAVDKDSGQ NAWLSYRLLKASEPGLFAVGLHTGEVRTARALLDRDALKQSLVVAVEDHG QPPLSATFTVTVAVADRIPDILADLGSIKTPIDPEDLDLTLYLVVAVAAV SCVFLAFVIVLLVLRLRRWHKSRLLQAEGSRLAGVPASHFVGVDGVRAFL QTYSHEVSLTADSRKSHLIFPQPNYADTLLSEESCEKSEPLLMSDKVDAN KEERRVQVSFLFR* 		a.a.
length		 InterPro Name
length(804), motif(1:804) 804 IPR015492 Protocadherin gamma [Family]
length(84), motif(29:112) 84 IPR013164 Cadherin, N-terminal [Domain]
length(96), motif(30:125) 96 IPR015919 Cadherin-like [Domain]
length(100), motif(30:129) 100 IPR002126 Cadherin [Domain]
length(87), motif(45:131) 87 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(109), motif(130:238) 109 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(105), motif(235:339) 105 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(20), motif(326:345) 20 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(107), motif(343:449) 107 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(11), motif(440:450) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(110), motif(445:554) 110 IPR015919 Cadherin-like [Domain]
length(14), motif(450:463) 14 IPR002126 Cadherin [Domain]
length(113), motif(450:562) 113 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(105), motif(579:683) 105 IPR002126 Cadherin [Domain]
length(88), motif(579:666) 88 IPR002126 Cadherin [Domain]
length(83), motif(582:664) 83 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 HIT000338014
H-Inv cluster ID Locus viewHIX0005252
Accession number BC104926.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO; 
Coding potential  Help Protein coding; 
Definition Protocadherin gamma-A5 isoform 2 precursor.
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (NP_114443)  [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 PCDHGA5
HGNC aliases NA
HGNC name protocadherin gamma subfamily A, 5
DDBJ PCDHGA5
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 HIP000034338
No. of interaction NA
Interaction partner(s) NA
BIND NA
DIP NA
MINT NA
HPRD NA
IntAct NA
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:56110; 
KEGG GENES KEGG GENES(56110); 
GeneCard GeneCardPCDHGA5;  *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;  peroxisome;  plasma membrane;  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
5 100 1f5aA1 5e-23 14.9 87/118 d.58.16.1
73 188 1nkgA2 6e-09 9.2 110/171 b.18.1.25
199 524 2nlzA1 4e-65 12.8 304/533 d.153.1.6
584 667 1edhA1 4e-13 14.6 83/99 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 AGhsA110113; 
Affymetrix
GeneChip		 HG-Focus 211875_x_at;  216343_at; 
HG-U133 211875_x_at;  211876_x_at;  211879_x_at;  211880_x_at;  216343_at; 
HG-U133A 211875_x_at;  211876_x_at;  211879_x_at;  211880_x_at;  216343_at; 
HG-U133A_2 211875_x_at;  211876_x_at;  211879_x_at;  211880_x_at;  216343_at; 
HG-U133B NA
HG-U133_Plus_2 211875_x_at;  211876_x_at;  211879_x_at;  211880_x_at;  216343_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 2832575;  2832576;  2832577;  2878651; 
HuGeneFL NA
Agilent Human 1A Oligo Microarray:PGID215 NA
Whole Human Genome Oligo Microarray:PGID247 A_24_P342272; 
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:(56110)
Disease Entrez Gene ID:(56110)
Substance Entrez Gene ID:(56110)
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
597 .. 597 T/C rs57308563 + CDS Synonymous[Ser166Ser]
604 .. 604 A/G rs75267840 + CDS Nonsynonymous[Ser169Gly]
853 .. 853 C/G rs75563633 + CDS Nonsynonymous[Pro252Ala]
908 .. 908 A/C rs75982128 + CDS Nonsynonymous[Asp270Ala]
1155 .. 1155 G/A rs115453161 + CDS Synonymous[Leu352Leu]
1187 ^ 1188 -/G rs34496075 + CDS
1305 .. 1305 T/C rs73792170 + CDS Synonymous[Tyr402Tyr]
1426 .. 1426 G/A rs79266084 + CDS Nonsynonymous[Ala443Thr]
1432 .. 1432 G/C rs117201633 + CDS Nonsynonymous[Val445Leu]
1505 .. 1505 T/C rs78808766 + CDS Nonsynonymous[Val469Ala]
1535 .. 1535 C/T rs6882138 + CDS Nonsynonymous[Pro479Leu]
1836 .. 1836 T/C rs11750908 + CDS Synonymous[Pro579Pro]
1921 .. 1921 C/T rs62378419 + CDS Synonymous[Leu608Leu]
1950 ^ 1951 -/T rs35325687 + CDS
2100 ^ 2101 -/G rs34761299 + CDS
2475 .. 2475 G/T rs75435930 + CDS Synonymous[Leu792Leu]
 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;