Ly6g6c Gene Detail

Summary

• Symbol
  Ly6g6c
• Name
  lymphocyte antigen 6 family member G6C
• Synonyms
  1110003M04Rik, G6c, NG24

• Feature Type
  protein coding gene
• IDs
  MGI:2148930
  NCBI Gene: 68468
• Alliance
  genome feature page
• Transcription Start Sites
  21 TSS
• Candidate for QTL
  1 QTL

Location &
Maps

• Sequence Map
  Chr17:35286301-35289024 bp, + strand

  From NCBI annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 17, 18.59 cM
• Mapping Data
  3 experiments

Strain
Comparison

• SNPs within 2kb
  1 from dbSNP Build 142
• Strain Annotations
  19

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2148930	protein coding gene	Chr17:35284364-35289026 (+)
129S1/SvImJ	ENSMUSG00200050050	protein coding gene	Chr17:30988485-30993148 (+)
A/J	ENSMUSG00195039691	protein coding gene	Chr17:31888442-31893094 (+)
AKR/J	ENSMUSG00220050718	protein coding gene	Chr17:30917322-30921973 (+)
BALB/cJ	ENSMUSG00180035149	protein coding gene	Chr17:31258301-31262951 (+)
C3H/HeJ	ENSMUSG00175032524	protein coding gene	Chr17:30803437-30808086 (+)
C57BL/6NJ	ENSMUSG00215052453	protein coding gene	Chr17:30828696-30833357 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0021498	protein coding gene	Chr17:31806126-31810760 (+)
CAST/EiJ	ENSTCUG00005049470	protein coding gene	Chr17:31846133-31850785 (+)
CBA/J	ENSMUSG00210048772	protein coding gene	Chr17:30625531-30630180 (+)
DBA/2J	ENSMUSG00185045104	protein coding gene	Chr17:33277552-33282202 (+)
FVB/NJ	ENSMUSG00205038210	protein coding gene	Chr17:31145957-31150642 (+)
JF1/MsJ	ENSUMUG00000057169	protein coding gene	Chr17:32529981-32534610 (+)
LP/J	ENSMUSG00230054160	protein coding gene	Chr17:34386738-34391399 (+)
NOD/ShiLtJ	ENSMUSG00190030595	protein coding gene	Chr17:30747287-30751948 (+)
NZO/HlLtJ	ENSMUSG00225054314	protein coding gene	Chr17:36398949-36403570 (+)
PWK/PhJ	ENSLUMG00010038706	protein coding gene	Chr17:30365169-30369844 (+)
SPRET/EiJ	ENSMSPG00010034850	protein coding gene	Chr17:31549082-31553809 (+)
WSB/EiJ	ENSIUOG00005046170	protein coding gene	Chr17:31474468-31479127 (+)

Homology

• Human Ortholog
  LY6G6C, lymphocyte antigen 6 family member G6C

• Vertebrate Orthologs
  2

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  LY6G6C, lymphocyte antigen 6 family member G6C
  
• Synonyms
  C6orf24, G6c, NG24
• Links
  HGNC:13936

  NCBI Gene ID: 80740

  UniProt: O95867

  
  
• Chr Location
  6p21.33; chr6:31718648-31721746 (-)  GRCh38

---

• MGI Vertebrate Homology
  Ly6g6c stringent orthology
  1 human;1 mouse;1 rat
  
• HCOP
  vertebrate homology predictions: LY6G6C
• Gene Tree
  Ly6g6c
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  4 phenotype references
  

• All Mutations and Alleles
  5
• Gene trapped
  3
• Targeted
  2
• Incidental Mutations
  Mutagenetix , APF
• Find Mice (IMSR)
  8 strains or lines available

Gene Ontology
(GO)
Classifications

• All GO Annotations
  13
• GO References
  6

Expression

• Assay Results
  604
• Tissues
  7
• cDNA Data
  13
• Literature Summary
  1

Tissue x Stage Matrix

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas
• Other Vertebrate Links
  Xenbase ly6g6c

Sequences &
Gene Models

• All Sequences
  41
• RefSeq
  2
• UniProt
  4
• CCDS
  CCDS28677.1

• Ensembl
  ENSMUSG00000092586 (Evidence)
• NCBI Gene
  68468

Representative Sequences			Length	Strain/Species
genomic	68468	NCBI Gene Model | MGI Sequence Detail	2724	C57BL/6J
transcript	NM_023463	RefSeq | MGI Sequence Detail	960	C57BL/6
polypeptide	Q9Z1Q4	UniProt | EBI | MGI Sequence Detail	126	Not Applicable

Protein
Information

• UniProt
  4 Sequences
• Protein Ontology
  PR:000009992 lymphocyte antigen 6 complex locus protein G6c
  (term hierarchy)
• InterPro Domains
  IPR016054 Ly-6 antigen/uPA receptor-like
  IPR039237 Lymphocyte antigen 6 complex locus protein G6c
  IPR045860 Snake toxin-like superfamily
• GlyGen
  Q9Z1Q4 2 sites

Molecular
Reagents

• All nucleic 16

  Genomic 1

  cDNA 13

  Primer pair 2

  
  

  Microarray probesets 2

Other
Accession IDs

MGI:1915718, MGI:2146971

References

• Summaries
  All 31

  Developmental Gene Expression 1

  Gene Ontology 6

  Phenotypes 4
• Earliest
  J:60984 Ko MS, et al., Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development. Development. 2000 Apr;127(8):1737-49
• Latest
  J:270449 Loughner CL, et al., Organization, evolution and functions of the human and mouse Ly6/uPAR family genes. Hum Genomics. 2016 Apr 21;10:10

TSS for Ly6g6c:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr144200	Chr17:35285841-35285863 (+)	-449 bp
Tssr144201	Chr17:35285877-35285886 (+)	-419 bp
Tssr5100	Chr17:35286086-35286095 (+)	-210 bp
Tssr144202	Chr17:35286100-35286112 (+)	-195 bp
Tssr144203	Chr17:35286293-35286308 (+)	0 bp
Tssr144204	Chr17:35287670-35287688 (+)	1,378 bp
Tssr144205	Chr17:35287697-35287726 (+)	1,411 bp
Tssr144206	Chr17:35287798-35287807 (+)	1,502 bp
Tssr144207	Chr17:35287835-35287861 (+)	1,547 bp
Tssr144208	Chr17:35287880-35287898 (+)	1,588 bp
Tssr144209	Chr17:35288301-35288319 (+)	2,009 bp
Tssr144210	Chr17:35288348-35288362 (+)	2,054 bp
Tssr144211	Chr17:35288378-35288392 (+)	2,084 bp
Tssr144212	Chr17:35288413-35288418 (+)	2,115 bp
Tssr144213	Chr17:35288426-35288448 (+)	2,136 bp
Tssr144214	Chr17:35288453-35288481 (+)	2,166 bp
Tssr144215	Chr17:35288519-35288533 (+)	2,225 bp
Tssr144216	Chr17:35288557-35288566 (+)	2,261 bp
Tssr144217	Chr17:35288592-35288603 (+)	2,297 bp
Tssr144218	Chr17:35288666-35288698 (+)	2,381 bp
Tssr144219	Chr17:35288699-35288725 (+)	2,411 bp

Ly6g6c is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Cdcs5	Chr17, syntenic		J:109420	Microarray analysis was used to identify candidate genes for colitis susceptibility QTLs. Messenger RNA was analyzed for expression differences between colitis susceptible inbred strain C3H/HeJBir-Il10 and colitis resistant inbred strain C57BL/6J-Il10. Capn3 (67.2 cM) on mouse Chromosome 2 is upregulated 1.5- to 2-fold in C3H/HeJBir-Il10 animals. This candidate gene maps to the Cdcs3 (cytokine deficiency colitis susceptibility 3) interval centered near 65 cM. Gbp1 (67.4 cM) on mouse Chromosome 3 is upregulated over 15-fold in C3H/HeJBir-Il10 animals. This candidate gene is known to be polymorphic between C3H/HeJBir and C57BL/6J and exhibits expression differences in these parental wild type strains. Gbp1 maps to the Cdcs1 (cytokine deficiency colitis susceptibility 1) interval centered near 62 cM. Adh1 at 71.2 cM and Bglap2 at 42.6 cM also map to the same QTL interval. Adh1 is upregulated 1.5- to 2-fold, and Blgap2 is upregulated 2- to 5-fold, in C3H/HeJBir-Il10animals. Pla2g2a (68 cM) on mouse Chromosome 4 is upregulated over 15-fold in C3H/HeJBir-Il10 animals. This candidate gene is known to be polymorphic between C3H/HeJBir and C57BL/6J and exhibits expression differences in these parental wild typestrains. Pla2g2a maps to the Cdcs9 (cytokine deficiency colitis susceptibility 9) interval centered near 71 cM. Moreover, C57BL/6J animals are known to carry the frameshift mutation Pla2g2a resulting in multiple intestinal neoplasia. The human ortholog PLA2G2A maps near a irritable bowel disorder (IBD) susceptibility locus named IBD7. Gnb1 (79.4 cM) also maps to the Cdcs9 QTL interval and is upregulated 2- to 5-fold in C57BL/6J-Il10 animals. Errfi1 (formerly 1300002F13Rik) and Tceb3 also map to the Cdcs9 interval and are upregulated 1.5- to 2-fold in C57BL/6J-Il10 animals. Areg (51 cM) on mouse Chromosome 5 maps near the Cdcs10 QTL interval centered around 45 cM. This candidate gene is upregulated 1.5- to 2-fold in C57BL/6J-Il10 animals. Mtmr7 maps to mouse Chromosome 8 near the Cdcs4 interval centered around 21 cM. This candidate gene is upregulated over 15-fold in C57BL/6J-Il10 animals. Cd14 (31 cM) on mouse Chromosome 18 is upregulated 5- to 15-fold in C3H/HeJBir-Il10 animals. CD14 also exhibits expression differences in parental wild type strains C3H/HeJBir and C57BL/6J. This candidate gene maps to the Cdcs6 (cytokine deficiency colitis susceptibility 6) interval centered near 41 cM. The human ortholog CD14 maps near a human irritable bowel disorder (IBD) susceptibility locus named IBD5. Glo1 (16 cM) and Ly6g6c on mouse Chromosome 17 are upregulated 2- to 5-fold in C57BL/6J-Il10 animals. This candidate gene maps to the Cdcs5 (cytokine deficiency colitis susceptibility 5) interval centered near 19 cM. Hspa1a (18.9 cM) and Hspa1b (18.9 cM) also map to Cdcs5 and are upregulated 1.5- to 2-fold in C57BL/6J-Il10 animals.

*cM position of peak correlated region/marker