LOC128925778 (CapStarr-seq enhancer MGSCv37_chr7:117129931-117130114) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: LOC128925778 (CapStarr-seq enhancer MGSCv37_chr7:117129931-117130114) Mus musculus
Analyze
Symbol: LOC128925778
Name: CapStarr-seq enhancer MGSCv37_chr7:117129931-117130114
RGD ID: 163677781
Description: This locus includes a subregion that was identified as a candidate cis-regulatory module (CRM) in developing mouse thymocytes based on a combination of DNase I hypersensitivity and transcription factor binding. That CRM was validated as an active enhancer by high-throughput CapStarr-seq reporter assays showing weak activity in NIH3T3 fibroblasts. This locus also includes a B cell regulatory element that was identified by FAIRE-seq (formaldehyde-assisted isolation of regulatory elements sequencing), and which was validated as an enhancer by STARR-seq (self-transcribing active regulatory region sequencing) in lipopolysaccharide-activated mouse splenic B cells. [provided by RefSeq, Oct 2023]
Type: biological-region
RefSeq Status: REVIEWED
Previously known as: Rr368400
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm397109,585,429 - 109,585,807 (+)NCBIGRCm39GRCm39mm39
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:25872643   PMID:31873292   PMID:31873293  


Genomics

Variants

.
Variants in LOC128925778
8 total Variants

QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
25314307Mlh1fc2_mMLH1 foci count 2 (mouse)76502999133501729Mouse
12792978Fbmd3_mfemoral bone mineral density 3, females only (mouse)77050288142367832Mouse
10412199Sst2_msusceptibility to tuberculosis 2 (mouse)Not determined718728794119485380Mouse
1301158Eae4_msusceptibility to experimental allergic encephalomyelitis 4 (mouse)Not determined719147398141919804Mouse
1301082Bbaa16_mB.burgdorferi-associated arthritis 16 (mouse)Not determined736280015116416877Mouse
10043926Bw1n_mbody weight 1 in NSY (mouse)Not determined745161966118693530Mouse
13208555Lgth10_mbody length 10 (mouse)751649748125599172Mouse
27226751Femd5_mfemur midshaft diameter 5, 10 week (mouse)753249748143153737Mouse
25823170Hrsq7_mhost response to SARS QTL 7, log titer (mouse)754819589116822815Mouse
27226778Femd11_mfemur midshaft diameter 11, 16 week (mouse)756949748134001729Mouse
26884408Bzwq13_mbi-zygomatic width QTL 13, 16 week (mouse)761749748121399223Mouse
27095916Scvln15_msacral vertebrae length 2, 16 week (mouse)761749748123699223Mouse
26884440Sklq4_mskull length QTL 4, 5 week (mouse)765249748126499172Mouse
27226715Metcl3_mmetatarsal-calcaneal length 3, 5 week (mouse)767849748119499223Mouse
26884444Sklq8_mskull length QTL 8, 10 week (mouse)767849748124199223Mouse
26884451Sklq14_mskull length QTL 14, 16 week (mouse)767849748124999172Mouse
27095907Scvln4_msacral vertebrae length 2, 5 week (mouse)769949748120499223Mouse
27095910Pglq13_mpelvic girdle length QTL 13, 16 week (mouse)773049748125699172Mouse
27095933Ulnl3_mulna length 3, 5 week (mouse)773149748143153737Mouse
27226745Metcl9_mmetatarsal-calcaneal length 9, 10 week (mouse)774849748122199223Mouse
27226781Tibl3_mtibia length 3, 5 week (mouse)774849748122199223Mouse
14746989Manh62_mmandible shape 62 (mouse)775742528109742528Mouse
26884398Humsd6_mhumerus midshaft diameter 6, 16 week (mouse)778649748136901729Mouse
10412110Cctq1_mcentral corneal thickness QTL 1 (mouse)Not determined780551681114551791Mouse
4142500Morq1_mmodifier of Rs1 QTL 1 (mouse)Not determined80551681114551791Mouse
27095930Ulnl10_mulna length 10, 16 week (mouse)780849748126699172Mouse
27095923Pglq3_mpelvic girdle length QTL 3, 5 week (mouse)781249748124199223Mouse
27095903Scvln10_msacral vertebrae length 2, 10 week (mouse)781449748126499172Mouse
27226765Tibl18_mtibia length 18, 16 week (mouse)781849748126499172Mouse
27226763Feml20_mfemur length 20, 16 week (mouse)785049208124199223Mouse
1301997Cia7_mcollagen induced arthritis QTL 7 (mouse)Not determined785365595112533819Mouse
1301647Elpt_melevated leptin (mouse)Not determined786500186120500329Mouse
1301188Heal6_mwound healing/regeneration 6 (mouse)Not determined787043932121044066Mouse
1302062Stheal6_msoft tissue heal 6 (mouse)Not determined787043932121044066Mouse
13463473Hbbcq4_mhemoglobin concentration QTL 4 (mouse)787043932121044066Mouse
1301781Capsq3_mcapsaicin sensitivity related QTL 3 (mouse)Not determined787143137119485380Mouse
27226769Tibl12_mtibia length 12, 10 week (mouse)787249208126499172Mouse
27226790Feml15_mfemur length 15, 10 week (mouse)787249208126499172Mouse
1357664Nba3_mNew Zealand Black autoimmunity 3 (mouse)Not determined791482996125483156Mouse
1301937Skull10_mskull morphology 10 (mouse)Not determined791482996125483156Mouse
1300528Ssial3_msusceptibility to sialadenitis 3 (mouse)Not determined793391848127392041Mouse
1301478Eae26_msusceptibility to experimental allergic encephalomyelitis 26 (mouse)Not determined798164922132165010Mouse
13524850Asrq7_macoustic startle response 7 (mouse)798394974132394974Mouse
10412104Tons2_mtongue size 2 (mouse)Not determined799837716133837716Mouse
11039524Tbbr3_mTrypanosoma brucei brucei response 3 (mouse)7100750722134750843Mouse
1301447Fembm3_mfemoral bone morphometry 3 (mouse)Not determined7100993261134993342Mouse
1357460Vtbt4_mvertebral trabecular bone trait 4 (mouse)Not determined7101693381135693530Mouse
1301105Cfld4_mcystic fibrosis lung disease 4 (mouse)Not determined7101693381135693530Mouse
1300721Cfbw3_mcystic fibrosis body weight 3 (mouse)Not determined7101693381135693530Mouse
4142312Nilac4_mnicotine induced locomotor activity 4 (mouse)Not determined7102485219136485380Mouse
5491192Mobq1_mmultigenic obesity QTL 1 (mouse)Not determined7105250663139250811Mouse
13524852Asrq7a_macoustic startle response 7a (mouse)7105350008139350008Mouse
25394573Skmw62_mskeletal muscle weight 62, gastroc (mouse)7106893715110612309Mouse
13524524Bodwtq6_mbody wweight QTL 6 (mouse)7107245693113055693Mouse
4141056Lskcn2_mLSK cell number 2 (mouse)Not determined108482996118693530Mouse
35673311Ari6_mantibody response to influenza 6, day 15, IgG2b (mouse)7108699207115099235Mouse
25394557Skmw64_mskeletal muscle weight 64, soleus (mouse)7108715780114592736Mouse
25394559Skmw63_mskeletal muscle weight 63, TA (mouse)7108791458110612309Mouse
25394556Skmw65_mskeletal muscle weight 65, EDL (mouse)7109059337110612309Mouse


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NG_153698 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC140235 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles


Additional Information

Database Acc Id Source(s)
NCBI Gene LOC128925778 ENTREZGENE
PhenoGen LOC128925778 PhenoGen