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

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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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8203,714,094 - 3,718,861 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl203,714,197 - 3,718,276 (-)EnsemblGRCr8
mRatBN7.2203,709,426 - 3,713,940 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl203,709,529 - 3,713,608 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx204,408,433 - 4,412,527 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0203,770,489 - 3,774,583 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0204,308,362 - 4,312,653 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0205,100,415 - 5,104,631 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl205,100,415 - 5,104,494 (+)Ensemblrn6Rnor6.0
Rnor_5.0207,173,674 - 7,177,753 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4203,773,183 - 3,777,262 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera204,312,034 - 4,316,113 (+)NCBICelera
RGSC_v3.1203,773,409 - 3,777,489 (-)NCBI
Cytogenetic Map20p12NCBI
JBrowse:




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
GRCr8203,714,094 - 3,718,861 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl203,714,197 - 3,718,276 (-)EnsemblGRCr8
mRatBN7.2203,709,426 - 3,713,940 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl203,709,529 - 3,713,608 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx204,408,433 - 4,412,527 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0203,770,489 - 3,774,583 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0204,308,362 - 4,312,653 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0205,100,415 - 5,104,631 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl205,100,415 - 5,104,494 (+)Ensemblrn6Rnor6.0
Rnor_5.0207,173,674 - 7,177,753 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4203,773,183 - 3,777,262 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera204,312,034 - 4,316,113 (+)NCBICelera
RGSC_v3.1203,773,409 - 3,777,489 (-)NCBI
Cytogenetic Map20p12NCBI
LY6G5C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38631,676,684 - 31,681,067 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl631,676,684 - 31,684,040 (-)Ensemblhg38GRCh38
GRCh37631,644,461 - 31,648,844 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36631,752,440 - 31,756,120 (-)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm381735,108,294 - 35,112,173 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1735,108,279 - 35,111,991 (+)Ensemblmm10GRCm38
MGSCv371735,245,245 - 35,248,898 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361734,716,356 - 34,720,009 (+)NCBIMGSCv36mm8
Celera1738,204,977 - 38,208,905 (+)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1718.59NCBI
Ly6g5c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955437220,428 - 223,636 (-)Ensembl
ChiLan1.0NW_004955437220,603 - 223,636 (-)NCBIChiLan1.0ChiLan1.0
LY6G5C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2546,153,713 - 46,164,355 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1642,115,061 - 42,125,868 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0631,337,846 - 31,343,226 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1632,227,629 - 32,233,058 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl632,227,629 - 32,231,409 (-)EnsemblpanPan2panpan1.1
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 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha121,296,174 - 1,300,102 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0121,304,967 - 1,309,728 (-)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 Ensembl
SpeTri2.0NW_0049367271,848,502 - 1,852,659 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LY6G5C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl723,791,241 - 23,795,734 (-)EnsemblsusScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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 1.0HetGla 1.0hetGla2
Ly6g5c
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1187,707,998 - 7,712,085 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Ly6g5c
107 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015332005306452Rat
61474Eae1Experimental allergic encephalomyelitis QTL 13nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)2016693431Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20126925056Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20133724594Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20126128279Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600300Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20153308346533083Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124164241Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20134066551Rat
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)20362632310078622Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129193376Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)2016693431Rat
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20127341128Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2036263239244918Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129193376Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129193376Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129193376Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129193376Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20114100378Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127341128Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127341128Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578510Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600300Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
ectoderm
endocrine system
endoderm
hemolymphoid system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
2 1 6 1 3 3 8 4 5 1 10 3 2 2

Sequence


Ensembl Acc Id: ENSRNOT00000001122   ⟹   ENSRNOP00000001122
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl203,714,197 - 3,718,276 (-)Ensembl
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
GRCr8203,714,197 - 3,718,276 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,714,094 - 3,718,861 (-)NCBI
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  
Ensembl Protein ENSRNOP00000001122
GenBank Protein Q8CHN2 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_942034   ⟸   NM_198739
- UniProtKB: Q8CHN2 (UniProtKB/Swiss-Prot),   Q6MG54 (UniProtKB/Swiss-Prot),   G3V630 (UniProtKB/TrEMBL),   A6KTT8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008770938   ⟸   XM_008772716
- Peptide Label: isoform X1
- UniProtKB: Q8CHN2 (UniProtKB/Swiss-Prot),   Q6MG54 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl 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
Ensembl Transcript ENSRNOT00000001122 ENTREZGENE
InterPro LY6_UPA_recep-like UniProtKB/Swiss-Prot
  LY6G5C UniProtKB/Swiss-Prot
NCBI Gene 294245 ENTREZGENE
PANTHER LYMPHOCYTE ANTIGEN 6 COMPLEX LOCUS PROTEIN G5C UniProtKB/Swiss-Prot
  PTHR14909 UniProtKB/Swiss-Prot
Pfam UPAR_LY6 UniProtKB/Swiss-Prot
PhenoGen Ly6g5c PhenoGen
RatGTEx ENSRNOG00000000846 RatGTEx
UniProt A6KTT8 ENTREZGENE, UniProtKB/TrEMBL
  G3V630 ENTREZGENE, UniProtKB/TrEMBL
  LY65C_RAT UniProtKB/Swiss-Prot
  Q6MG54 ENTREZGENE
  Q8CHN2 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