LOC108663994 (ES cell cis-regulatory motif 1d) - 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: LOC108663994 (ES cell cis-regulatory motif 1d) Mus musculus
Analyze
Symbol: LOC108663994
Name: ES cell cis-regulatory motif 1d
RGD ID: 39129216
Description: This genomic element is located in the 5' regulatory region of the Gnl3 [guanine nucleotide binding protein-like 3 (nucleolar)] gene on chromosome 14, and it also overlaps the Pbrm1 (polybromo 1) gene. A subregion was predicted to be a cis-regulatory sequence based on the presence of a CGTGACG motif through Comparative MobyDick (CompMoby) analysis, which identified conserved overrepresented motifs in genes upregulated in pluripotent cells. It was validated as a functional enhancer in both undifferentiated and differentiated mouse embryonic stem (ES) cells when two copies were used in a reporter construct driven by a heterologous thymidine kinase (TK) promoter. 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: Rr366738
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391430,741,513 - 30,741,839 (+)NCBIGRCm39GRCm39mm39
GRCm381431,019,827 - 31,019,882 (+)NCBIGRCm38GRCm38mm10GRCm38
Cytogenetic Map14BNCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:17784790   PMID:31873292   PMID:31873293  


Genomics

Variants

.
Variants in LOC108663994
9 total Variants

QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
27226748Femd8_mfemur midshaft diameter 8, 10 week (mouse)141376927346737457Mouse
10043886Cia49_mcollagen induced arthritis QTL 49 (mouse)Not determined142999699463997133Mouse
1357527Epfpq1_mepididymal fat percentage QTL 1 (mouse)Not determined142106245071885801Mouse
14746973Manh76_mmandible shape 76 (mouse)142228721756287217Mouse
4142485Modor2_mmodifier of ocular retardation 2 (mouse)Not determined142492624858179769Mouse
1301372Sluc13_msusceptibility to lung cancer 13 (mouse)Not determined141882760452827726Mouse
13506929Recrq10_mrecombination rate in male meiosis QTL 10 (mouse)142792195761137449Mouse
1300909Ath13_matherosclerosis 13 (mouse)Not determined143033525064335381Mouse
1300998Cia17_mcollagen induced arthritis 17 (mouse)Not determined143033525064335381Mouse
1301991Wta3_mweight adult 3 (mouse)Not determined14388747337887650Mouse
4141864Mrdq4_mmodifier of retinal degeneration QTL 4 (mouse)Not determined992324548765082Mouse
1357589Kdnw2_mkidney weight 2 (mouse)Not determined1420887473121269804Mouse
27226752Femd4_mfemur midshaft diameter 4, 5 week (mouse)141376927347237457Mouse
27226774Tibl15_mtibia length 15, 10 week (mouse)143032195787937436Mouse
1300544Hypn_mhyperinsulinemia (mouse)Not determined141516061649160765Mouse
27226744Metcl6_mmetatarsal-calcaneal length 6, 5 week (mouse)143032195752937457Mouse
4141550Dbm3_mdiabetes modifier 3 (mouse)Not determined514347339143596Mouse
27226775Tibl7_mtibia length 7, 5 week (mouse)143032195748837457Mouse
1300779Dyscalc4_mdystrophic cardiac calcinosis 4 (mouse)Not determined141221287146213007Mouse


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NG_051565 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC154727 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles


Additional Information

Database Acc Id Source(s)
NCBI Gene LOC108663994 ENTREZGENE
PhenoGen LOC108663994 PhenoGen