Ly6g5c (lymphocyte antigen 6 family member G5C) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Ly6g5c (lymphocyte antigen 6 family member G5C) Rattus norvegicus
Analyze
Symbol: Ly6g5c
Name: lymphocyte antigen 6 family member G5C
RGD ID: 735180
Description: Predicted to enable identical protein binding activity. Predicted to be located in extracellular region. Predicted to be part of protein-containing complex. Predicted to colocalize with external side of plasma membrane. Orthologous to human LY6G5C (lymphocyte antigen 6 family member G5C); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; ammonium chloride; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: epididymal secretory protein 8; lymphocyte antigen 6 complex locus protein G5c; lymphocyte antigen 6 complex, locus G5C; re8
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2203,709,426 - 3,713,940 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl203,709,529 - 3,713,608 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx204,408,433 - 4,412,527 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0203,770,489 - 3,774,583 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0204,308,362 - 4,312,653 (-)NCBIRnor_WKY
Rnor_6.0205,100,415 - 5,104,631 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl205,100,415 - 5,104,494 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0207,173,674 - 7,177,753 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4203,773,183 - 3,777,262 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1203,773,409 - 3,777,489 (-)NCBI
Celera204,312,034 - 4,316,113 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
megacolon  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

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. The genomic sequence and comparative analysis of the rat major histocompatibility complex. Hurt P, etal., Genome Res 2004 Apr;14(4):631-9.
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:17008713  


Genomics

Comparative Map Data
Ly6g5c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2203,709,426 - 3,713,940 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl203,709,529 - 3,713,608 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx204,408,433 - 4,412,527 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0203,770,489 - 3,774,583 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0204,308,362 - 4,312,653 (-)NCBIRnor_WKY
Rnor_6.0205,100,415 - 5,104,631 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl205,100,415 - 5,104,494 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0207,173,674 - 7,177,753 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4203,773,183 - 3,777,262 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1203,773,409 - 3,777,489 (-)NCBI
Celera204,312,034 - 4,316,113 (+)NCBICelera
Cytogenetic Map20p12NCBI
LY6G5C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38631,676,684 - 31,681,067 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl631,676,684 - 31,684,040 (-)EnsemblGRCh38hg38GRCh38
GRCh37631,644,461 - 31,648,844 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36631,752,440 - 31,756,120 (-)NCBINCBI36Build 36hg18NCBI36
Build 34631,752,439 - 31,756,120NCBI
Celera633,242,682 - 33,246,372 (-)NCBICelera
Cytogenetic Map6p21.33NCBI
HuRef631,430,686 - 31,434,376 (-)NCBIHuRef
CHM1_1631,646,597 - 31,650,286 (-)NCBICHM1_1
T2T-CHM13v2.0631,529,718 - 31,534,101 (-)NCBIT2T-CHM13v2.0
Ly6g5c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391735,327,270 - 35,331,149 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1735,327,255 - 35,330,967 (+)EnsemblGRCm39 Ensembl
GRCm381735,108,294 - 35,112,173 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1735,108,279 - 35,111,991 (+)EnsemblGRCm38mm10GRCm38
MGSCv371735,245,245 - 35,248,898 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361734,716,356 - 34,720,009 (+)NCBIMGSCv36mm8
Celera1738,204,977 - 38,208,905 (+)NCBICelera
Cytogenetic Map17B1NCBI
Ly6g5c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955437220,428 - 223,636 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955437220,603 - 223,636 (-)NCBIChiLan1.0ChiLan1.0
LY6G5C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1632,227,629 - 32,233,058 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl632,227,629 - 32,231,409 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0631,337,846 - 31,343,226 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
LY6G5C
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1121,159,598 - 1,163,526 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl121,159,598 - 1,163,526 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha121,296,174 - 1,300,102 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0121,304,967 - 1,309,728 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl121,304,969 - 1,308,899 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1121,164,273 - 1,168,198 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0121,231,445 - 1,235,371 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0121,298,663 - 1,302,592 (-)NCBIUU_Cfam_GSD_1.0
Ly6g5c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494635,708,691 - 35,714,120 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367271,848,505 - 1,852,398 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049367271,848,502 - 1,852,659 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LY6G5C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl723,791,198 - 23,795,734 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1723,791,160 - 23,795,967 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2727,451,630 - 27,460,718 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LY6G5C
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11740,342,875 - 40,348,537 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1740,344,510 - 40,348,254 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604431,587,130 - 31,592,410 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ly6g5c
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475424,526,003 - 24,528,280 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ly6g5c
70 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:42
Count of miRNA genes:34
Interacting mature miRNAs:38
Transcripts:ENSRNOT00000001122
Prediction methods:Miranda, Rnahybrid, Targetscan
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015279595304575Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
61448Ciaa1CIA Autoantibody QTL 1300.001blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)2026463954597031Rat
61472Aia1Adjuvant induced arthritis QTL 1180.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2026463954597031Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2036216499243559Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)20362164910078919Rat
737973Pia21Pristane induced arthritis QTL 214.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2036216564606812Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system hemolymphoid system integumental system musculoskeletal system nervous system reproductive system respiratory system appendage
High
Medium
Low
Below cutoff 2 1 1 1 2 5 3 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000001122   ⟹   ENSRNOP00000001122
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl203,709,529 - 3,713,608 (-)Ensembl
Rnor_6.0 Ensembl205,100,415 - 5,104,494 (+)Ensembl
RefSeq Acc Id: NM_198739   ⟹   NP_942034
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,709,529 - 3,713,608 (-)NCBI
Rnor_6.0205,100,415 - 5,104,494 (+)NCBI
Rnor_5.0207,173,674 - 7,177,753 (+)NCBI
RGSC_v3.4203,773,183 - 3,777,262 (-)RGD
Celera204,312,034 - 4,316,113 (+)RGD
Sequence:
RefSeq Acc Id: XM_008772716   ⟹   XP_008770938
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,709,426 - 3,713,940 (-)NCBI
Rnor_6.0205,100,420 - 5,104,631 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_942034 (Get FASTA)   NCBI Sequence Viewer  
  XP_008770938 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAD56202 (Get FASTA)   NCBI Sequence Viewer  
  CAE83992 (Get FASTA)   NCBI Sequence Viewer  
  EDL83518 (Get FASTA)   NCBI Sequence Viewer  
  Q8CHN2 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_942034   ⟸   NM_198739
- UniProtKB: G3V630 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008770938   ⟸   XM_008772716
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000001122   ⟸   ENSRNOT00000001122
Protein Domains
UPAR/Ly6

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8CHN2-F1-model_v2 AlphaFold Q8CHN2 1-145 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13701392
Promoter ID:EPDNEW_R11914
Type:single initiation site
Name:Ly6g5c_1
Description:lymphocyte antigen 6 family member G5C
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0205,100,416 - 5,100,476EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:735180 AgrOrtholog
BioCyc Gene G2FUF-4644 BioCyc
Ensembl Genes ENSRNOG00000000846 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000001122 ENTREZGENE
  ENSRNOP00000001122.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000001122 ENTREZGENE
  ENSRNOT00000001122.3 UniProtKB/TrEMBL
InterPro LY6G5C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:294245 UniProtKB/TrEMBL
NCBI Gene 294245 ENTREZGENE
PANTHER PTHR14909 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ly6g5c PhenoGen
UniProt G3V630 ENTREZGENE, UniProtKB/TrEMBL
  LY65C_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q6MG54 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-02-01 Ly6g5c  lymphocyte antigen 6 family member G5C  Ly6g5c  lymphocyte antigen 6 complex, locus G5C  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Ly6g5c  lymphocyte antigen 6 complex, locus G5C    epididymal secretory protein 8  Name updated 1299863 APPROVED
2004-09-10 Ly6g5c  epididymal secretory protein 8  re8    Symbol and Name updated 1299863 APPROVED