Flicr Gene Detail

Summary

• Symbol
  Flicr
• Name
  Foxp3 regulating long intergenic noncoding RNA
• Synonyms
  4930524L23Rik, Ppp1r3fos

• Feature Type
  lncRNA gene
• IDs
  MGI:1925435
  NCBI Gene: 78185
• Alliance
  gene page
• Transcription Start Sites
  10 TSS

Location &
Maps

• Sequence Map
  ChrX:7439839-7447255 bp, + strand

  From NCBI annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome X, 3.41 cM, cytoband A1.1
• Mapping Data
  2 experiments

Strain
Comparison

• SNPs within 2kb
  157 from dbSNP Build 142
• Strain Annotations
  18

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1925435	lncRNA gene	ChrX:7439839-7447266 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0004714	antisense lncRNA gene	ChrX:2183683-2191103 (+)
A/J	MGP_AJ_G0004692	antisense lncRNA gene	ChrX:2145080-2153678 (+)
AKR/J	MGP_AKRJ_G0004675	antisense lncRNA gene	ChrX:2248603-2256013 (+)
BALB/cJ	MGP_BALBcJ_G0004676	antisense lncRNA gene	ChrX:2165405-2172865 (+)
C3H/HeJ	MGP_C3HHeJ_G0004624	antisense lncRNA gene	ChrX:2218464-2227081 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0004825	antisense lncRNA gene	ChrX:2260650-2269509 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0004266	antisense lncRNA gene	ChrX:1714970-1722336 (+)
CAST/EiJ	MGP_CASTEiJ_G0004581	antisense lncRNA gene	ChrX:2120771-2128192 (+)
CBA/J	MGP_CBAJ_G0004619	antisense lncRNA gene	ChrX:2374434-2381866 (+)
DBA/2J	MGP_DBA2J_G0004634	antisense lncRNA gene	ChrX:2167132-2174546 (+)
FVB/NJ	MGP_FVBNJ_G0004652	antisense lncRNA gene	ChrX:2131541-2139276 (+)
LP/J	MGP_LPJ_G0004716	antisense lncRNA gene	ChrX:2187548-2194965 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0004638	antisense lncRNA gene	ChrX:2340392-2347871 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0004825	antisense lncRNA gene	ChrX:2167428-2174839 (+)
PWK/PhJ	MGP_PWKPhJ_G0004533	antisense lncRNA gene	ChrX:2099337-2106757 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0004470	antisense lncRNA gene	ChrX:2139125-2146531 (+)
WSB/EiJ	MGP_WSBEiJ_G0004624	antisense lncRNA gene	ChrX:2171013-2178427 (+)

Homology

• Gene Tree
  Flicr
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  2 phenotypes from 1 allele in 1 genetic background
  3 phenotype references
  

• All Mutations and Alleles
  4
• Endonuclease-mediated
  2
• Gene trapped
  2
• Find Mice (IMSR)
  1 strains or lines available

Homozygous knockout mice of this negative regulator of Foxp3 show decreased susceptibility to autoimmune diabetes and reduced severity of insulitis.

Expression

• Assay Results
  706
• cDNA Data
  4

Tissue x Stage Matrix

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas

Sequences &
Gene Models

• All Sequences
  32
• RefSeq
  1
• UniProt
  2

• Ensembl
  ENSMUSG00000039545 (Evidence)
• NCBI Gene
  78185

Representative Sequences			Length	Strain/Species
genomic	78185	NCBI Gene Model | MGI Sequence Detail	7417	C57BL/6J
transcript	NR_029473	RefSeq | MGI Sequence Detail	3456	C57BL/6
polypeptide	Q8BNV6	UniProt | EBI | MGI Sequence Detail	130	Not Applicable

Protein
Information

• UniProt
  2 Sequences

Molecular
Reagents

• All nucleic 5

  cDNA 5

  
  

  Microarray probesets 1

Other
Accession IDs

MGI:5901917

References

• Summaries
  All 14

  Phenotypes 3
• Earliest
  J:65060 Kawai J, et al., Functional annotation of a full-length mouse cDNA collection. Nature. 2001 Feb 8;409(6821):685-90
• Latest
  J:241346 Zemmour D, et al., Flicr, a long noncoding RNA, modulates Foxp3 expression and autoimmunity. Proc Natl Acad Sci U S A. 2017 Apr 25;114(17):E3472-E3480

TSS for Flicr:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr160373	ChrX:7438778-7438793 (+)	-1,053 bp
Tssr160374	ChrX:7438851-7438862 (+)	-982 bp
Tssr160375	ChrX:7438878-7438889 (+)	-955 bp
Tssr160376	ChrX:7438905-7438910 (+)	-931 bp
Tssr160377	ChrX:7438912-7438928 (+)	-919 bp
Tssr160378	ChrX:7438938-7438962 (+)	-889 bp
Tssr160379	ChrX:7438976-7438989 (+)	-856 bp
Tssr160380	ChrX:7439035-7439048 (+)	-797 bp
Tssr160381	ChrX:7439444-7439486 (+)	-374 bp
Tssr160382	ChrX:7443735-7443760 (+)	3,909 bp