Th2-lcr (Th2 cytokine locus control region) - Rat Genome Database

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Gene: Th2-lcr (Th2 cytokine locus control region) Mus musculus
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Symbol: Th2-lcr
Name: Th2 cytokine locus control region
RGD ID: 39130439
Description: This genomic region represents a locus control region (LCR) that can confer copy number-dependent, position-independent expression on the T helper type 2 (Th2) cytokine locus in transgenic assays. It regulates coordinated expression of the interleukin 4 (Il4), interleukin 13 (Il13) and interleukin 5 (Il5) genes during differentiation of naive CD4+ T cells along the Th2 pathway. The LCR overlaps the 3' end of the Rad50 gene, which is located between the Il13 and Il5 genes. The LCR is characterized by four DNase I hypersensitive sites (RHS4-RHS7), which bind transcription factors necessary for induction of the Il4, Il5 and Il13 genes. The promoters of these genes first undergo looping interactions with each other to form a pre-poised hub, and later in differentiation the LCR participates in the hub, resulting in a poised structure for rapid transcription activation. In addition to participating in long-range intrachromosomal interactions, this Th2 LCR on chromosome 11 can also form interchromosomal interactions with the Th1 interferon gamma (Ifng) promoter on chromosome 10, and also with the interleukin 17A (Il17a) locus on chromosome 1. Deletion of this LCR results in various lung and airway defects in a mouse model of allergic asthma, suggesting that it functions in the pathogenesis of that disease. [provided by RefSeq, Aug 2015]
Type: biological-region
RefSeq Status: REVIEWED
Previously known as: Rr366633
RGD Orthologs
Human
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391153,538,416 - 53,563,179 (+)NCBIGRCm39GRCm39mm39
GRCm381153,647,589 - 53,672,352 (+)NCBIGRCm38GRCm38mm10GRCm38
Cytogenetic Map11A5-B1NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:12871646   PMID:15507491   PMID:15589174   PMID:15608641   PMID:15880101   PMID:15947163   PMID:16199489   PMID:16309780   PMID:16472999   PMID:16551261   PMID:16617008   PMID:16618596  
PMID:17312108   PMID:17940027   PMID:18479352   PMID:18485687   PMID:18502111   PMID:18554247   PMID:18647314   PMID:19124743   PMID:19151746   PMID:20038639   PMID:20192806   PMID:20483988  
PMID:20636338   PMID:21632975   PMID:21703230   PMID:21867929   PMID:22771806   PMID:23248301   PMID:23569250   PMID:23668241   PMID:24245687   PMID:24613343   PMID:24839135   PMID:25764217  
PMID:25903499  


Genomics

Comparative Map Data
Th2-lcr
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391153,538,416 - 53,563,179 (+)NCBIGRCm39GRCm39mm39
GRCm381153,647,589 - 53,672,352 (+)NCBIGRCm38GRCm38mm10GRCm38
Cytogenetic Map11A5-B1NCBI
TH2-LCR
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385132,629,263 - 132,642,195 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh375131,964,955 - 131,977,887 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map5q31NCBI
T2T-CHM13v2.05133,149,065 - 133,161,997 (+)NCBIT2T-CHM13v2.0

Variants

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Variants in Th2-lcr
725 total Variants

QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
27226798Scvln18_msacral vertebrae length 2, 16 week (mouse)11325000060690826Mouse
26884446Sklq10_mskull length QTL 10, 10 week (mouse)11325000062890826Mouse
26884453Sklq16_mskull length QTL 16, 16 week (mouse)11325000072690826Mouse
13208559Wght10_mweight 10 (mouse)11395000088890826Mouse
13208558Lgth12_mbody length 12 (mouse)11395000094890826Mouse
1300905Scc6_mcolon tumor susceptibility 6 (mouse)Not determined11688027789019734Mouse
27226738Metcl11_mmetatarsal-calcaneal length 11, 10 week (mouse)11885000061390826Mouse
26884401Huml4_mhumerus length 4, 10 week (mouse)111155000068490826Mouse
27226762Feml21_mfemur length 21, 16 week (mouse)111175000065990826Mouse
1357640Orq2_movulation rate QTL 2 (mouse)Not determined111226863768500330Mouse
4141127W3q4_mweight 3 weeks QTL 4 (mouse)Not determined1226863768500330Mouse
4141470Egq4_mearly growth QTL 4 (mouse)Not determined1226863768500330Mouse
4142109W10q2_mweight 10 weeks QTL 2 (mouse)Not determined1226863768500330Mouse
4141582Lgaq1_mlate growth adjusted QTL 1 (mouse)Not determined1226863768500330Mouse
4142308W6q3_mweight 6 weeks QTL 3 (mouse)Not determined111226863768500330Mouse
4142216Lgq1_mlate growth QTL 1 (mouse)Not determined1226863768500330Mouse
4141966Tailq1_mtail length QTL 1 (mouse)Not determined1226863768500330Mouse
1357851Scfq3_msubcutaneous fat pad weight QTL 3 (mouse)Not determined111226863768500330Mouse
1357720Kidpq1_mkidney weight percentage QTL 1 (mouse)Not determined111226863768500330Mouse
1357437Epfq4_mepididymal fat pad weight QTL 4 (mouse)Not determined111226863768500330Mouse
1559002Lmrq4_mLeishmania major resistance QTL 4 (mouse)Not determined111226863769684947Mouse
39128214Lwq20_mliver weight QTL 20 (mouse)1112268637118022724Mouse
1558945Orgwq8_morgan weight QTL 8 (mouse)Not determined111705617567078411Mouse
10053687Eae6_msusceptibility to experimental allergic encephalomyelitis 6 (mouse)Not determined111778196668500330Mouse
4141894Nidd6k_mNidd6 on KK-A (mouse)Not determined1912420496897826Mouse
14746971Manh70_mmandible shape 70 (mouse)111990589053905890Mouse
4141398Tgq22_mtriglyceride QTL 22 (mouse)Not determined2116340655163406Mouse
10412246Dfs2_mdental fluorosis suseptibility 2 (mouse)Not determined112180736495881231Mouse
10044006Hbnr13_mHeligmosomoides bakeri nematode resistance 13 (mouse)Not determined112577262659772741Mouse
1357844Si5lq5_mserum IGFBP-5 level QTL 5 (mouse)Not determined112816587362165976Mouse
13524848Ppiq7_mprepulse inhibition QTL 7 (mouse)112856914762569147Mouse
1301426Desp2_mdespair 2 (mouse)Not determined112870858162708700Mouse
11522752Cocia18_mcocaine-induced activity, QTL 18 (mouse)113100820965008209Mouse
11059563Lmr31_mleishmaniasis resistance 31 (mouse)113210057766100694Mouse
1357782Char8_mP. chabaudi malaria resistance QTL 8 (mouse)Not determined113557861669684987Mouse
13208569Bmiq10_mbody mass index QTL 10 (mouse)113589082784890826Mouse
1301328Mol4_mmodifier of LPS-response 4 (mouse)Not determined113628257783481356Mouse
1301788Lbw8_mlupus NZB x NZW 8 (mouse)Not determined113650328770509492Mouse
1301896Tria1_mT-cell receptor induced activation 1 (mouse)Not determined113661356570613855Mouse
4141853Skmw17_mskeletal muscle weight 17 (mouse)Not determined113708094171081064Mouse
4142475Ity2a_mimmunity to S. typhimurium 2a (mouse)Not determined113776858060402716Mouse
10766457Nwa3_mNew Zealand White autoimmunity 3 (mouse)113801611572016209Mouse
10053675Eae44b_mexperimental allergic encephalomyelitis susceptibility 44b (mouse)Not determined113995072854094448Mouse
11532698Sluc36a_msusceptibility to lung cancer 36a (mouse)114225661776256730Mouse
11532699Sluc36b_msusceptibility to lung cancer 36b (mouse)114225661776256730Mouse
1300713Vmbic10_mventral midbrain iron content 10 (mouse)Not determined114277262654081064Mouse
4142300Ctrq3_mC. trachomatis resistance QTL 3 (mouse)Not determined114463003876854757Mouse
4141367Inf1_macute ozone induced inflammation (mouse)Not determined44630038113058009Mouse
1302021Nidd1n_mnon-insulin-dependent diabetes mellitus 1 in NSY (mouse)Not determined114516587379978324Mouse
1357878Mastr_mmodifier of astrocytoma (mouse)Not determined114570858189818733Mouse
1300765Bbaa4_mB.burgdorferi-associated arthritis 4 (mouse)Not determined114618516780185262Mouse
1301988Bmd11_mbone mineral density 11 (mouse)Not determined114631940780319522Mouse
1301830Ssta4_msusceptibility to Salmonella typhimurium antigens 4 (mouse)Not determined115007819184078411Mouse
4141770Tcpm1_mT-cell phenotype modifier 1 (mouse)Not determined5145247953615930Mouse
13524840Ppiq9a_mprepulse inhibition QTL 9a (mouse)115249438586494385Mouse
1300774Pgia7_mproteoglycan induced arthritis 7 (mouse)Not determined115339058887390737Mouse


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NG_042300 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AL645741 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles


Additional Information

Database Acc Id Source(s)
NCBI Gene Th2-lcr ENTREZGENE
PhenoGen Th2-lcr PhenoGen