H-InvDB x AHG DB
Transcript view
H-InvDB_9.0 released on May 27, 2015.
Search by for Advanced Search
Home Quick guide Navi BLAST Site map Download Contact us Help
H-Invitational ID: HIT000433666 Accession number: AK314800 Created date: 26-Mar-2013 Last modified: 27-May-2015
Definition: Cadherin-12; Brain cadherin; BR-cadherin; Neural type cadherin 2; N-cadherin 2; Precursor;
 
 

Transcript original information
Accession number AK314800.1
CAGE tag ID NA
EST ID NA
Clone Number TESTI4015463
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (CDH12) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (CDH12);
Sequence data provider NA
Annotation project NA
Length of cDNA 2843[bp] (No. of exon:12)[A:862 T:696 G:646 C:639]
Devision HTC
Molecular type mRNA
Library origin Cell type NA
Tissue type testis
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 HIX0004774
Genomic location  G-integra Help Chromosome 5
Location 5p14.3
Position 21751846- 22212878
Strand -
Possible duplicated location(s) NA
Gene structure 12 exon(s)
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:1010
KEGG GENES KEGG GENES(1010)
GeneCard GeneCardCDH12*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 HIP000076769
Predicted CDS 459..2843;  794[aa];  Orientation:+3; 
Codon Adaptation Index (CAI). 0.72
Database links RefSeq NP_004052
UniProt P55289
CCDS CCDS3890

Motif information
ORF

length(794),orf(459:2843)
MLTRNCLSLLLWVLFDGGLLTPLQPQPQQTLATEPRENVIHLPGQRSHFQ
RVKRGWVWNQFFVLEEYVGSEPQYVGKLHSDLDKGEGTVKYTLSGDGAGT
VFTIDETTGDIHAIRSLDREEKPFYTLRAQAVDIETRKPLEPESEFIIKV
QDINDNEPKFLDGPYVATVPEMSPVGAYVLQVKATDADDPTYGNSARVVY
SILQGQPYFSIDPKTGVIRTALPNMDREVKEQYQVLIQAKDMGGQLGGLA
GTTIVNITLTDVNDNPPRFPKSIFHLKVPESSPIGSAIGRIRAVDPDFGQ
NAEIEYNIVPGDGGNLFDIVTDEDTQEGVIKLKKPLDFETKKAYTFKVEA
SNLHLDHRFHSAGPFKDTATVKISVLDVDEPPVFSKPLYTMEVYEDTPVG
TIIGAVTAQDLDVGSSAVRYFIDWKSDGDSYFTIDGNEGTIATNELLDRE
STAQYNFSIIASKVSNPLLTSKVNILINVLDVNEFPPEISVPYETAVCEN
AKPGQIIQIVSAADRDLSPAGQQFSFRLSPEAAIKPNFTVRDFRNNTAGI
ETRRNGYSRRQQELYFLPVVIEDSSYPVQSSTNTMTIRVCRCDSDGTILS
CNVEAIFLPVGLSTGALIAILLCIVILLAIVVLYVALRRQKKKDTLMTSK
EDIRDNVIHYDDEGGGEEDTQAFDIGALRNPKVIEENKIRRDIKPDSLCL
PRQRPPMEDNTDIRDFIHQRLQENDVDPTAPPYDSLATYAYEGSGSVAES
LSSIDSLTTEADQDYDYLTDWGPRFKVLADMFGEEESYNPDKVT*
a.a.
length
InterPro Name
length(89), motif(63:151) 89 IPR002126 Cadherin [Domain]
length(87), motif(74:160) 87 IPR015919 Cadherin-like [Domain]
length(82), motif(77:158) 82 IPR002126 Cadherin [Domain]
length(77), motif(80:156) 77 IPR002126 Cadherin [Domain]
length(81), motif(80:160) 81 IPR002126 Cadherin [Domain]
length(20), motif(100:119) 20 IPR002126 Cadherin [Domain]
length(11), motif(148:158) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(109), motif(153:261) 109 IPR015919 Cadherin-like [Domain]
length(109), motif(157:265) 109 IPR002126 Cadherin [Domain]
length(30), motif(160:189) 30 IPR002126 Cadherin [Domain]
length(109), motif(161:269) 109 IPR002126 Cadherin [Domain]
length(95), motif(165:259) 95 IPR002126 Cadherin [Domain]
length(86), motif(182:267) 86 IPR002126 Cadherin [Domain]
length(13), motif(232:244) 13 IPR002126 Cadherin [Domain]
length(20), motif(248:267) 20 IPR002126 Cadherin [Domain]
length(11), motif(257:267) 11 IPR020894 Cadherin conserved site [Conserved_site]
length(117), motif(262:378) 117 IPR015919 Cadherin-like [Domain]
length(117), motif(266:382) 117 IPR002126 Cadherin [Domain]
length(14), motif(267:280) 14 IPR002126 Cadherin [Domain]
length(115), motif(270:384) 115 IPR002126 Cadherin [Domain]
length(102), motif(275:376) 102 IPR002126 Cadherin [Domain]
length(93), motif(291:383) 93 IPR002126 Cadherin [Domain]
length(27), motif(326:352) 27 IPR002126 Cadherin [Domain]
length(122), motif(373:494) 122 IPR015919 Cadherin-like [Domain]
length(107), motif(383:489) 107 IPR002126 Cadherin [Domain]
length(105), motif(385:489) 105 IPR002126 Cadherin [Domain]
length(92), motif(389:480) 92 IPR002126 Cadherin [Domain]
length(82), motif(406:487) 82 IPR002126 Cadherin [Domain]
length(18), motif(471:488) 18 IPR002126 Cadherin [Domain]
length(109), motif(482:590) 109 IPR015919 Cadherin-like [Domain]
length(119), motif(489:607) 119 IPR002126 Cadherin [Domain]
length(98), motif(492:589) 98 IPR002126 Cadherin [Domain]
length(98), motif(493:590) 98 IPR002126 Cadherin [Domain]
length(88), motif(510:597) 88 IPR002126 Cadherin [Domain]
length(147), motif(638:784) 147 IPR000233 Cadherin, cytoplasmic domain [Domain]
length(94), motif(694:787) 94 IPR027397 Catenin binding domain [Domain]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000433666
H-Inv cluster ID Locus viewHIX0004774
Accession number AK314800.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help NO;  Splicing isoformSplicing isoform
Coding potential  Help Protein coding; 
Definition Cadherin-12; Brain cadherin; BR-cadherin; Neural type cadherin 2; N-cadherin 2; Precursor;
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (P55289)  [Identity/coverage = 100.0%/100.0%] to Homo sapiens (Human). protein.
Experimental evidence Protein evidence
PubMed ID 773196879820331470203915489334ALL
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 CDH12
HGNC aliases NA
HGNC name cadherin 12, type 2 (N-cadherin 2)
DDBJ NA
UniProt CDH12
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 HIP000076769
No. of interaction 7
Interaction partner(s) HIP000021401HIP000021401HIP000095593HIP000099536HIP000099536HIP000117036HIP000117036
BIND NA
DIP NA
MINT NA
HPRD 04314;  12049; 
IntAct NA
Database links RefSeq NA
Ensembl NA
Entrez Gene Entrez Gene ID:1010
KEGG GENES KEGG GENES(1010)
GeneCard GeneCardCDH12*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 extracellular;  peroxisome;  endoplasmic;  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:27-May-2015
Start End PDB_ID E-value Identity Coverage SCOP_ID
80 118 1f15A 6e-04 14.3 39/157 b.121.4.5
102 526 1dnvA 1e-54 6.2 386/415 b.121.5.3
499 603 1f15A 9e-06 12.4 94/157 b.121.4.5
Related H-InvDB links GTOP GTOP

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
67 .. 67 A/G rs62350675 - 5'UTR
247 .. 247 T/C rs72636100 - 5'UTR
247 .. 247 T/C rs4301201 - 5'UTR
260 .. 260 A/G rs151053331 - 5'UTR
260 .. 260 A/G rs10065908 - 5'UTR
450 .. 450 C/A rs201028667 - 5'UTR
518 .. 518 A/G rs150281223 - CDS Synonymous[Leu20Leu]
520 .. 520 C/T rs142596033 - CDS Nonsynonymous[Thr21Ile]
532 .. 532 C/A rs201969238 - CDS Nonsynonymous[Pro25Gln]
534 ^ 535 -/C rs146023607 - CDS
548 .. 548 T/G rs147719621 - CDS Synonymous[Thr30Thr]
558 .. 558 G/C rs117878510 - CDS Nonsynonymous[Glu34Gln]
594 .. 594 C/T rs147080212 - CDS Nonsynonymous[Arg46Trp]
619 .. 619 G/A rs141662751 - CDS Nonsynonymous[Arg54His]
621 .. 621 G/A rs147912407 - CDS Nonsynonymous[Gly55Ser]
638 .. 638 A/G rs142320441 - CDS Synonymous[Gln60Gln]
660 .. 660 G/A rs4371716 - CDS Nonsynonymous[Val68Met]
671 .. 671 G/C rs147803091 - CDS Nonsynonymous[Glu71Asp]
749 .. 749 C/T rs111835226 - CDS Synonymous[Gly97Gly]
942 .. 942 G/C rs145189313 - CDS Nonsynonymous[Asp162His]
1023 .. 1023 G/A rs200251715 - CDS Nonsynonymous[Asp189Asn]
1026 .. 1026 C/G rs201503504 - CDS Nonsynonymous[Pro190Ala]
1097 .. 1097 C/G rs112146213 - CDS Synonymous[Pro213Pro]
1106 .. 1106 T/C rs17839323 - CDS Synonymous[Gly216Gly]
1125 .. 1125 C/T rs115178807 - CDS Nonsynonymous[Pro223Ser]
1238 .. 1238 C/T rs76592602 - CDS Synonymous[Thr260Thr]
1308 .. 1308 A/G rs17328673 - CDS Nonsynonymous[Ile284Val]
1427 .. 1427 G/A rs150544028 - CDS Synonymous[Glu323Glu]
1505 .. 1505 G/T rs112632478 - CDS Nonsynonymous[Glu349Asp]
1524 .. 1524 G/C rs200835943 - CDS Nonsynonymous[Asp356His]
1548 .. 1548 C/T rs191030425 - CDS Nonsynonymous[Pro364Ser]
1567 .. 1567 C/T rs201729605 - CDS Nonsynonymous[Thr370Met]
1629 .. 1629 A/G rs147983357 - CDS Nonsynonymous[Met391Val]
1632 .. 1632 G/C rs201550912 - CDS Nonsynonymous[Glu392Gln]
1634 .. 1634 G/A rs144416688 - CDS Synonymous[Glu392Glu]
1640 .. 1640 T/C rs186008008 - CDS Synonymous[Tyr394Tyr]
1644 .. 1644 G/A rs199790838 - CDS Nonsynonymous[Asp396Asn]
1646 ^ 1647 -/AAAA rs10698212 - CDS
1670 .. 1670 C/T rs199520573 - CDS Synonymous[Gly404Gly]
1703 .. 1703 C/T rs144117760 - CDS Synonymous[Ser415Ser]
1704 .. 1704 A/G rs1135751 + CDS Nonsynonymous[Ser416Gly]
1710 .. 1710 G/T rs138517275 - CDS Nonsynonymous[Val418Phe]
1759 .. 1759 T/C rs200459087 - CDS Nonsynonymous[Ile434Thr]
1781 .. 1781 C/T rs112884095 - CDS Synonymous[Ile441Ile]
1816 .. 1816 C/T rs143124599 - CDS Nonsynonymous[Ala453Val]
1819 .. 1819 A/G rs147110131 - CDS Nonsynonymous[Gln454Arg]
1839 .. 1839 G/A rs201414975 - CDS Nonsynonymous[Ala461Thr]
1882 .. 1882 T/C rs12108814 - CDS Nonsynonymous[Ile475Thr]
1940 .. 1940 G/A rs138890010 - CDS Synonymous[Glu494Glu]
1946 .. 1946 C/T rs200815361 - CDS Synonymous[Ala496Ala]
1947 .. 1947 G/A rs150229492 - CDS Nonsynonymous[Val497Met]
2027 .. 2027 A/G rs2303749 - CDS Synonymous[Gln523Gln]
2043 .. 2043 T/C rs143459013 - CDS Nonsynonymous[Ser529Pro]
2054 .. 2054 T/C rs111616437 - CDS Synonymous[Ala532Ala]
2076 .. 2076 G/A rs140423691 - CDS Nonsynonymous[Val540Ile]
2080 .. 2080 G/A rs200808789 - CDS Nonsynonymous[Arg541His]
2099 .. 2099 A/G rs151084481 - CDS Synonymous[Thr547Thr]
2102 .. 2102 G/A rs201811162 - CDS Synonymous[Ala548Ala]
2104 .. 2104 G/C rs143462106 - CDS Nonsynonymous[Gly549Ala]
2306 .. 2306 G/A rs139945013 - CDS Synonymous[Ala616Ala]
2340 .. 2340 T/C rs13173286 - CDS Synonymous[Leu628Leu]
2431 .. 2431 T/A rs77887979 - CDS Nonsynonymous[Ile658Asn]
2434 .. 2434 A/T rs143993546 - CDS Nonsynonymous[His659Leu]
2527 .. 2527 G/A rs199892587 - CDS Nonsynonymous[Arg690His]
2532 .. 2532 G/A rs201679120 - CDS Nonsynonymous[Asp692Asn]
2546 .. 2546 C/G rs149905162 - CDS Nonsynonymous[Asp696Glu]
2563 .. 2563 G/A rs139076535 - CDS Nonsynonymous[Arg702His]
2633 .. 2633 C/T rs6451993 - CDS Synonymous[Asp725Asp]
2639 .. 2639 C/T rs6451992 - CDS Synonymous[Asp727Asp]
2681 .. 2681 C/T rs138634556 - CDS Synonymous[Tyr741Tyr]
2728 .. 2728 T/C rs147548175 - CDS Nonsynonymous[Leu757Pro]
2798 .. 2798 C/T rs201750582 - CDS Synonymous[Asp780Asp]
2817 .. 2817 A/T rs142721168 - CDS Nonsynonymous[Ser787Cys]
 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