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H-InvDB_8.3 released on March 26, 2013.
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H-Invitational ID: HIT000334151 Accession number: BC069015 Created date: 26-Mar-2013 Last modified: 26-Mar-2013
Definition: Ig kappa chain C region;
 
 

Transcript original information
Accession number BC069015.1
CAGE tag ID NA
EST ID NA
Clone Number IMAGE:4854409
Experimental resources NBRC: NITE Biological Resource Center  NBRC ; HGPD: Human Gene and Protein Database HGPD ; Antibody: searching human antibodies at "BIO-kaimono.com" Antibody (IGKC) ; Catalog: searching experimental product catalogs at "BIO-kaimono.com" Catalog (IGKC);
Sequence data provider NA
Annotation project NA
Length of cDNA 877[bp] (No. of exon:5)[A:257 T:180 G:205 C:235]
Devision HTC
Molecular type mRNA
Library origin Cell type NA
Tissue type Primary B-Cells from Tonsils
Develpmental stage NA
Mini-G
Sequence quality information
CDS feature Complete CDS
Kozak sequence NA
PolyA Site: 830(+) Signal: 808-812(+)
Vector/adapter sequence NA
Frame shift NA
Remaining intron NA
Splice site acceptor (NAGNAG) NA
Transcript quality feature NMD predicted; 
Notes NA

Gene structure information  G-integra H-DBAS cDNA-genome alignment
H-Inv cluster ID HIX0021121
Genomic location  G-integra Help Chromosome 2
Location 2p11.2
Position 89156676- 89345980
Strand -
Possible duplicated location(s) NA
Gene structure 5 exon(s)
Database links RefSeq NA
Ensembl ENST00000390237ENST00000390238ENST00000390239ENST00000390240ENST00000390241ENST00000390242ENST00000390252ENST00000390256ENST00000390264ENST00000390265ENST00000418209ENST00000429992ENST00000430694ENST00000434790ENST00000442736ENST00000448155ENST00000452230ENST00000453184ENST00000464162ENST00000465170ENST00000468494ENST00000473726ENST00000479981ENST00000480492ENST00000482769ENST00000483158ENST00000484817ENST00000490686ENST00000492167ENST00000493819ENST00000495489ENST00000496168ENST00000498435ENST00000498574ENST00000509129ENST00000518305ENST00000521304ENST00000521705ENST00000523070
Entrez Gene NA
KEGG GENES NA
GeneCard GeneCardIGKC*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 HIP000146945
Predicted CDS 18..728;  236[aa];  Orientation:+3; 
Codon Adaptation Index (CAI). 0.788

Motif information
ORF

length(236),orf(18:728)
MDMRVPAQLLGLLLLWLPGARCAIQLTQSPSSLSASVGDRVTITCRASQG
ISSALAWYQQKPGKAPKLLIYDASSLESGVPSRFSGSGSGTDFTLTISSL
QPEDFATYYCQQFNNYPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSG
TASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC*
a.a.
length
InterPro Name
length(116), motif(18:133) 116 IPR007110 Immunoglobulin-like [Domain]
length(104), motif(24:127) 104 IPR013106 Immunoglobulin V-set [Domain]
length(105), motif(25:129) 105 IPR013783 Immunoglobulin-like fold [Domain]
length(100), motif(30:129) 100 IPR003599 Immunoglobulin subtype [Domain]
length(73), motif(40:112) 73 IPR003596 Immunoglobulin V-set, subgroup [Domain]
length(103), motif(130:232) 103 IPR013783 Immunoglobulin-like fold [Domain]
length(98), motif(135:232) 98 IPR007110 Immunoglobulin-like [Domain]
length(92), motif(141:232) 92 IPR003599 Immunoglobulin subtype [Domain]
length(87), motif(141:227) 87 IPR003597 Immunoglobulin C1-set [Domain]
length(76), motif(151:226) 76 IPR003597 Immunoglobulin C1-set [Domain]
length(7), motif(214:220) 7 IPR003006 Immunoglobulin/major histocompatibility complex, conserved site [Conserved_site]

Gene function information  Gene family PPI viewer Similarity Search Tool TACT
H-Inv ID HIT000334151
H-Inv cluster ID Locus viewHIX0021121
Accession number BC069015.1
CAGE tag ID NA
EST ID NA
Transcript feature  Help Representative H-Inv IDRepresentative transcript; 
Coding potential  Help Protein coding; 
Definition Ig kappa chain C region;
Similarity category  Help Category: Identical to known human protein(Category I).
Identical to known human protein (P01834)  [Identity/coverage = 100.0%/100.0%] to Homo sapiens (Human). protein.
Experimental evidence Protein evidence
PubMed ID 48936824923144502770354475315489770558692367758189588180ALL
Gene family/group Gene family H-Inv gene family/group ID HIF0000001
Gene family/group name Immunoglobulin (Ig).
Evidence motif (InterPro) ID NA
Gene symbol/name HGNC symbol IGKC
HGNC aliases NA
HGNC name immunoglobulin kappa constant
DDBJ NA
UniProt IGKC
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 HIP000146945
No. of interaction NA
Interaction partner(s) NA
BIND NA
DIP NA
MINT NA
HPRD NA
IntAct NA
Database links RefSeq NA
Ensembl ENST00000390237ENST00000390238ENST00000390239ENST00000390240ENST00000390241ENST00000390242ENST00000390252ENST00000390256ENST00000390264ENST00000390265ENST00000418209ENST00000429992ENST00000430694ENST00000434790ENST00000442736ENST00000448155ENST00000452230ENST00000453184ENST00000464162ENST00000465170ENST00000468494ENST00000473726ENST00000479981ENST00000480492ENST00000482769ENST00000483158ENST00000484817ENST00000490686ENST00000492167ENST00000493819ENST00000495489ENST00000496168ENST00000498435ENST00000498574ENST00000509129ENST00000518305ENST00000521304ENST00000521705ENST00000523070
Entrez Gene NA
KEGG GENES NA
GeneCard GeneCardIGKC*GeneCards is provided free to academic non-profit institutions.
etc H-GOLDHuman-Gene diversity Of Life-style related Diseases
Curation status Human curated
Notes NA
Related H-InvDB links Gene 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


Subcellular localization information  Last modified:26-Mar-2013
WoLF PSORT extracellular; 
Target P signal peptide
SOSUI membrane 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:26-Mar-2013
Start End PDB_ID E-value Identity Coverage SCOP_ID
18 170 1ksiA1 2e-23 5.2 153/441 b.30.2.1
150 229 1jrhL2 4e-07 29.1 55/61 b.1.1.2
Related H-InvDB links GTOP GTOP

Gene expression information  H-ANGEL DNAProbeLocator Last modified:26-Mar-2013
Tissue-specific expression  H-ANGEL NA
Probe
information DNAProbeLocator
AceGene NA
Affymetrix
GeneChip
HG-Focus NA
HG-U133 214669_x_at;  214768_x_at;  214836_x_at;  216207_x_at;  221651_x_at;  221671_x_at;  224795_x_at; 
HG-U133A 214669_x_at;  214768_x_at;  214836_x_at;  216207_x_at;  221651_x_at;  221671_x_at; 
HG-U133A_2 214669_x_at;  214768_x_at;  214836_x_at;  216207_x_at;  221651_x_at;  221671_x_at; 
HG-U133B 224795_x_at; 
HG-U133_Plus_2 214669_x_at;  214768_x_at;  214836_x_at;  216207_x_at;  221651_x_at;  221671_x_at;  224795_x_at; 
HG-U95 31512_at;  31586_f_at;  38194_s_at; 
HG-U95A 31512_at;  31586_f_at;  38194_s_at; 
HG-U95B NA
HG-U95C NA
HG-U95D NA
HG-U95E NA
HG-U95Av2 NA
HuEx-1_0 2493062;  2493064;  2493065;  2493090;  2493116;  2493239;  2493340;  2493354;  2493355;  2493356;  2495066;  2563789;  2563790;  2563791;  2563792;  2563872;  2563873;  2563874;  2563875;  2563876;  2564080; 
HuGeneFL M63438_s_at;  Z00010_at; 
Agilent Human 1A Oligo Microarray:PGID215 NA
Whole Human Genome Oligo Microarray:PGID247 A_24_P494425; 
Related H-InvDB links H-ANGELH-ANGEL DNAProbeLocatorDNAProbeLocator

Disease/pathology information  DiseaseInfo Viewer LEGENDA Last modified:26-Mar-2013
Disease relation Disease name:NA
Related information in OMIM OMIM ID:NA Title:NA
Co-localized orphan diseases OMIM ID:  600666607329609402
Disease related mutation
JRE-1.4.0 or later is required.Download JRE at Sun's web site.
Literature-Extracted GENe-Disease Associations (LEGENDA) LEGENDA Gene name NA
Disease NA
Substance NA
Related H-InvDB links DiseaseInfo ViewerDiseaseInfo ViewerLEGENDALEGENDA

Evolutionary information  Evola Help Last modified:26-Mar-2013
Relationship Species Accession number MGI Links
Orthology Mus sp. (Mouse) BC091754 G-integraG-integra
Orthology Canis sp. (Dog) ENSCAFT00000011790 G-integraG-integra
Orthology Danio sp. (Zebrafish) ENSDART00000086733 G-integraG-integra
Orthology Macaca sp. (Macaque) ENSMMUT00000029842 G-integraG-integra
Orthology Monodelphis sp. (Opossum) ENSMODT00000012494 G-integraG-integra
Orthology Pan sp. (Chimpanzee) ENSPTRT00000022626 G-integraG-integra
Orthology Bos sp. (Cow) XM_001254705 G-integraG-integra
Phylogenetic tree [View by ATV]
Neighbor-joining (phb) 
Related H-InvDB links EvolaEvoladN/dS (under constraction); 

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
32 .. 32 C/G rs113094008 - CDS Synonymous[Val5Val]
188 .. 188 G/A rs2693165 - CDS AA-STOP[Trp57*]
404 .. 404 A/C rs78964890 - CDS Nonsynonymous[Lys129Asn]
509 .. 509 A/G rs17852840 - CDS Synonymous[Arg164Arg]
571 .. 571 T/C rs11546027 + CDS Nonsynonymous[Val185Ala]
616 .. 616 C/T rs11546030 - CDS Nonsynonymous[Thr200Ile]
654 .. 654 G/C rs232230 + CDS Nonsynonymous[Val213Leu]
689 .. 689 C/T rs3210130 + CDS Synonymous[Ser224Ser]
692 .. 692 G/T rs12191 + CDS Synonymous[Ser225Ser]
696 .. 696 G/A rs14246 + CDS Nonsynonymous[Val227Ile]
733 .. 733 A/G rs1136331 + 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