Igkc (immunoglobulin kappa constant) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Igkc (immunoglobulin kappa constant) Rattus norvegicus
Analyze
Symbol: Igkc
Name: immunoglobulin kappa constant
RGD ID: 1562743
Description: Predicted to be involved in adaptive immune response. Predicted to act upstream of or within B cell differentiation. Predicted to be part of IgG immunoglobulin complex. Orthologous to human IGKC (immunoglobulin kappa constant); INTERACTS WITH 1-naphthyl isothiocyanate; 3-chloropropane-1,2-diol; 4,4'-diaminodiphenylmethane.
Type: protein-coding
Previously known as: D4Mit8; Igk@; immunoglobulin kappa chain; LOC500183; MGC112745; MGC73014; similar to NGF-binding Ig light chain
RGD Orthologs
Human
Mouse
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
NCBI Annotation Information: Genome Annotation Status: not in current annotation release
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
RGSC_v3.44102,208,006 - 102,208,502 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera417,127,845 - 17,128,341 (+)NCBICelera
Cytogenetic Map4q31NCBI


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:6273908   PMID:8080841   PMID:16502470   PMID:22516433   PMID:22664934   PMID:23376485   PMID:23533145   PMID:23580065  


Genomics

Comparative Map Data
Igkc
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
RGSC_v3.44102,208,006 - 102,208,502 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera417,127,845 - 17,128,341 (+)NCBICelera
Cytogenetic Map4q31NCBI
IGKC
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38288,857,361 - 88,857,683 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl288,857,161 - 88,857,683 (-)EnsemblGRCh38hg38GRCh38
GRCh37289,156,874 - 89,157,196 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36288,937,989 - 88,938,311 (-)NCBINCBI36Build 36hg18NCBI36
Celera287,632,104 - 87,632,426 (+)NCBICelera
Cytogenetic Map2p11.2NCBI
HuRef288,075,653 - 88,166,302 (-)NCBIHuRef
CHM1_1289,086,475 - 89,086,797 (-)NCBICHM1_1
T2T-CHM13v2.0288,866,370 - 88,866,692 (-)NCBIT2T-CHM13v2.0
Igkc
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39670,703,419 - 70,703,738 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl670,703,419 - 70,703,950 (+)EnsemblGRCm39 Ensembl
GRCm38670,726,435 - 70,726,754 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl670,726,435 - 70,726,966 (+)EnsemblGRCm38mm10GRCm38
MGSCv37670,676,429 - 70,676,748 (+)NCBIGRCm37MGSCv37mm9NCBIm37
Celera672,811,869 - 72,812,188 (+)NCBICelera
Cytogenetic Map6C1NCBI
cM Map632.04NCBI

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:33
Count of miRNA genes:33
Interacting mature miRNAs:33
Transcripts:ENSRNOT00000074175
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Markers in Region
D4Mit8  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24102,684,777 - 102,684,881 (+)MAPPERmRatBN7.2
Rnor_6.0498,542,003 - 98,542,106RGDRnor6.0
RH127636  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24102,688,085 - 102,688,280 (+)MAPPERmRatBN7.2
Rnor_6.0498,523,071 - 98,523,265NCBIRnor6.0
Rnor_5.04163,308,908 - 163,309,102UniSTSRnor5.0
Celera491,864,152 - 91,864,346UniSTS
RH 3.4 Map4633.8UniSTS
Cytogenetic Map4q32UniSTS
Cytogenetic Map4q31UniSTS


Expression


Sequence

Nucleotide Sequences
GenBank Nucleotide BC062802 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  L22655 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Protein Sequences
GenBank Protein AAA91898 (Get FASTA)   NCBI Sequence Viewer  
  AAH62802 (Get FASTA)   NCBI Sequence Viewer  
  P01836 (Get FASTA)   NCBI Sequence Viewer  
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P01836-F1-model_v2 AlphaFold P01836 1-106 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562743 AgrOrtholog
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:6890409 IMAGE-MGC_LOAD
  IMAGE:7388228 IMAGE-MGC_LOAD
InterPro Ig-like_dom UniProtKB/Swiss-Prot
  Ig-like_dom_sf UniProtKB/Swiss-Prot
  Ig-like_fold UniProtKB/Swiss-Prot
  Ig/MHC_CS UniProtKB/Swiss-Prot
  Ig_C1-set UniProtKB/Swiss-Prot
  MHC/Immunoglobulin UniProtKB/Swiss-Prot
MGC_CLONE MGC:112745 IMAGE-MGC_LOAD
  MGC:73014 IMAGE-MGC_LOAD
NCBI Gene 500183 ENTREZGENE
PANTHER IG-LIKE DOMAIN-CONTAINING PROTEIN UniProtKB/Swiss-Prot
  MHC CLASS II-RELATED UniProtKB/Swiss-Prot
Pfam C1-set UniProtKB/Swiss-Prot
PhenoGen Igkc PhenoGen
PROSITE IG_LIKE UniProtKB/Swiss-Prot
  IG_MHC UniProtKB/Swiss-Prot
SMART IGc1 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot
UniProt KACA_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-04-14 Igkc  immunoglobulin kappa constant  LOC500183  similar to NGF-binding Ig light chain  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 LOC500183  similar to NGF-binding Ig light chain      Symbol and Name status set to provisional 70820 PROVISIONAL