Alpha-re (alpha-globin locus regulatory region) - Rat Genome Database

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Gene: Alpha-re (alpha-globin locus regulatory region) Mus musculus
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Symbol: Alpha-re
Name: alpha-globin locus regulatory region
RGD ID: 39129403
Description: This genomic region represents the regulatory region that exists upstream of the mouse alpha-globin gene cluster. It is orthologous to the human alpha-globin locus control region (LCR), which regulates developmental stage- and erythroid lineage-specific expression of the embryonic and adult alpha-globin genes. This region overlaps the Nprl3 (nitrogen permease regulator-like 3) gene, which is transcribed in the opposite orientation compared to the downstream alpha-globin genes, and it also overlaps the 3' end of the Mpg (N-methylpurine-DNA glycosylase) gene. Like the human ortholog, this mouse region is characterized by several DNase I hypersensitive sites (HSs), including the conserved erythroid-specific sites HS-8, HS-21, HS-26 and HS-31. Mouse HS-26 is orthologous to human HS-40, which is the major regulatory element in human. However, unlike human HS-40, mouse HS-26 has relatively weak enhancer activity and does not have LCR activity, suggesting that additional cis-acting elements are necessary for complete developmental regulation of the alpha-globin genes in mice. Five enhancer-like elements, R1, R2, R3, Rm and R4, which correlate with the HSs and/or ATAC-seq accessible sites, are located in this region. Together they constitute a super-enhancer, where each constituent enhancer acts in an additive manner to regulate developmental expression of the alpha-globin genes. Similar to the human counterpart, this mouse upstream regulatory region forms an active chromatin hub based on observed looping interactions with the active alpha-globin genes. [provided by RefSeq, May 2017]
Type: biological-region
RefSeq Status: REVIEWED
Previously known as: alpha-MRE
RGD Orthologs
Human
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391132,181,303 - 32,220,102 (+)NCBIGRCm39GRCm39mm39
GRCm381132,231,303 - 32,270,102 (+)NCBIGRCm38GRCm38mm10GRCm38
Cytogenetic Map11A4NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References
Additional References at PubMed
PMID:7606006   PMID:8088839   PMID:8318735   PMID:8383794   PMID:8575760   PMID:8838797   PMID:8980258   PMID:8995756   PMID:9887104   PMID:11157800   PMID:11593024   PMID:12393394  
PMID:15060003   PMID:15215894   PMID:15998734   PMID:16617330   PMID:16626283   PMID:16782894   PMID:17130149   PMID:17218265   PMID:17380126   PMID:17493269   PMID:18282505   PMID:19696073  
PMID:19696202   PMID:22056776   PMID:23209182   PMID:23716600   PMID:24885809   PMID:25330308   PMID:25411453   PMID:27376235  


Genomics

Comparative Map Data
Alpha-re
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391132,181,303 - 32,220,102 (+)NCBIGRCm39GRCm39mm39
GRCm381132,231,303 - 32,270,102 (+)NCBIGRCm38GRCm38mm10GRCm38
Cytogenetic Map11A4NCBI
HBA-LCR
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381687,808 - 152,854 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3716137,807 - 202,853 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map16p13.3NCBI
T2T-CHM13v2.01681,410 - 146,425 (+)NCBIT2T-CHM13v2.0

Variants

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Variants in Alpha-re
1582 total Variants

QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10044008Hbnr15_mHeligmosomoides bakeri nematode resistance 15 (mouse)Not determined1122705234227232Mouse
1300599Cocrb11_mcocaine related behavior 11 (mouse)Not determined11267035536671472Mouse
27095904Scvln12_msacral vertebrae length 2, 10 week (mouse)11325000034495048Mouse
27095909Scvln6_msacral vertebrae length 2, 5 week (mouse)11325000044090827Mouse
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
27226741Metcl5_mmetatarsal-calcaneal length 5, 5 week (mouse)11465000046290827Mouse
27226735Metcl16_mmetatarsal-calcaneal length 16, 16 week (mouse)11525000035090827Mouse
1357518Tgyl1_mtriglyceride level 1 (mouse)Not determined11688027733916219Mouse
1300905Scc6_mcolon tumor susceptibility 6 (mouse)Not determined11688027789019734Mouse
1300990Bits3_mbitterness sensitivity 3 (mouse)Not determined11837212142372260Mouse
27226738Metcl11_mmetatarsal-calcaneal length 11, 10 week (mouse)11885000061390826Mouse
1302171Pgia28_mproteoglycan induced arthritis 28 (mouse)Not determined11890609742906218Mouse
4141047Nilac1_mnicotine induced locomotor activity 1 (mouse)Not determined11901178043011942Mouse
13524844Ppiq9_mprepulse inhibition QTL 9 (mouse)11904999735077325Mouse
13463472Mcvq15_mmean corpuscular volume QTL 15 (mouse)111095123244951464Mouse
13463479Mchq19_mmean corpuscular hemoglobin QTL 19 (mouse)111095123244951464Mouse
26884401Huml4_mhumerus length 4, 10 week (mouse)111155000068490826Mouse
27226762Feml21_mfemur length 21, 16 week (mouse)111175000065990826Mouse
10412216Eae44_mexperimental allergic encephalomyelitis susceptibility 44 (mouse)Not determined111226863739950840Mouse
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
12801459Leuf1_mleukocyte filtration 1 (mouse)111857861652578716Mouse
12801460Intim2_mintima modifier 2 (mouse)111857861652578716Mouse
12801457Intmrm2_mintima/media ratio modifier 2 (mouse)111857861652578716Mouse
1300938Bulb3_mbulb size 3 (mouse)Not determined111857861652578716Mouse
4141894Nidd6k_mNidd6 on KK-A (mouse)Not determined1912420496897826Mouse
1300579Thypr1_mthymocyte proliferative response 1 (mouse)Not determined111928257753282715Mouse
14746971Manh70_mmandible shape 70 (mouse)111990589053905890Mouse
4141398Tgq22_mtriglyceride QTL 22 (mouse)Not determined2116340655163406Mouse
10412246Dfs2_mdental fluorosis suseptibility 2 (mouse)Not determined112180736495881231Mouse
1300607Tnbs2_mtri-nitrobenzene sulfonic acid susceptible 2 (mouse)Not determined112489805235126680Mouse
10044006Hbnr13_mHeligmosomoides bakeri nematode resistance 13 (mouse)Not determined112577262659772741Mouse
1301814Bbaa7_mB.burgdorferi-associated arthritis 7 (mouse)Not determined112601178044264695Mouse
12910801Pwbwq14_mpost-weaning body weight QTL 14 (mouse)112719805750636094Mouse
12910804Pwbwq16_mpost-weaning body weight QTL 16 (mouse)112719805750636094Mouse
12910806Pwbwq15_mpost-weaning body weight QTL 15 (mouse)112719805750636094Mouse
12910817Pwgrq20_mpost-weaning growth rate QTL 20 (mouse)112719805750636094Mouse
12910818Ogrq5_moverall growth rate QTL 5 (mouse)112719805750636094Mouse
1357844Si5lq5_mserum IGFBP-5 level QTL 5 (mouse)Not determined112816587362165976Mouse
13524848Ppiq7_mprepulse inhibition QTL 7 (mouse)112856914762569147Mouse
1301426Desp2_mdespair 2 (mouse)Not determined112870858162708700Mouse
25394552Skmw69_mskeletal muscle weight 69, TA (mouse)112969902932329535Mouse
11522752Cocia18_mcocaine-induced activity, QTL 18 (mouse)113100820965008209Mouse
25394550Skmw71_mskeletal muscle weight 71, gastroc (mouse)113127543232745567Mouse
25394551Skmw70_mskeletal muscle weight 70, EDL (mouse)113132273732594975Mouse
25394558Skmw72_mskeletal muscle weight 72, soleus (mouse)113132943032785551Mouse
11059563Lmr31_mleishmaniasis resistance 31 (mouse)113210057766100694Mouse


Expression


Sequence



Additional Information

Database Acc Id Source(s)
NCBI Gene Alpha-re ENTREZGENE
PhenoGen Alpha-re PhenoGen