Hmgb3-ps (Hmgb3 retrotransposed pseudogene) - Rat Genome Database

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Gene: Hmgb3-ps (Hmgb3 retrotransposed pseudogene) Mus musculus
Analyze
Symbol: Hmgb3-ps
Name: Hmgb3 retrotransposed pseudogene
RGD ID: 5147080
MGI Page MGI
Description:
Type: pseudo (Ensembl: processed_pseudogene)
RefSeq Status: INFERRED
Previously known as: Gm16543
Related Functional Gene: Hmgb3  
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391412,606,119 - 12,606,695 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1412,606,071 - 12,606,671 (-)EnsemblGRCm39 Ensembl
GRCm38149,863,078 - 9,863,654 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl149,863,102 - 9,863,702 (+)EnsemblGRCm38mm10GRCm38
MGSCv371410,695,616 - 10,696,181 (+)NCBIGRCm37MGSCv37mm9NCBIm37
Celera145,469,880 - 5,470,445 (+)NCBICelera
Cytogenetic Map14A1NCBI
cM Map145.77NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Genomics

Variants

.
Variants in Hmgb3-ps
34 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:68
Count of miRNA genes:67
Interacting mature miRNAs:67
Transcripts:ENSMUST00000162465
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10412071Ssen3_msuseptibility to Sendai virus 3 (mouse)Not determined14126987934Mouse
11532711Sluc40_msusceptibility to lung cancer 40 (mouse)14127379943Mouse
13824988Phsq1_mpercent hyperactivated sperm QTL 1 (mouse)14305000119469772Mouse
1301991Wta3_mweight adult 3 (mouse)Not determined14388747337887650Mouse
4141550Dbm3_mdiabetes modifier 3 (mouse)Not determined514347339143596Mouse
4141265Appd2_mAPP associated premature death 2 (mouse)Not determined14594555230114862Mouse
4141864Mrdq4_mmodifier of retinal degeneration QTL 4 (mouse)Not determined992324548765082Mouse
1300779Dyscalc4_mdystrophic cardiac calcinosis 4 (mouse)Not determined141221287146213007Mouse

Markers in Region
PMC18303P1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38149,861,912 - 9,862,277UniSTSGRCm38
MGSCv371410,694,426 - 10,694,791UniSTSGRCm37
Celera145,468,690 - 5,469,055UniSTS
Cytogenetic Map14A2UniSTS
cM Map141.75UniSTS


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NG_019959 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC154570 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSMUST00000162465
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1412,606,071 - 12,606,671 (-)Ensembl
GRCm38.p6 Ensembl149,863,102 - 9,863,702 (+)Ensembl

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSMUSG00000089795 Ensembl, ENTREZGENE
MGD MGI:4414963 ENTREZGENE
NCBI Gene 100417024 ENTREZGENE
PhenoGen Hmgb3-ps PhenoGen


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-11-05 Hmgb3-ps  Hmgb3 retrotransposed pseudogene  Gm16543  predicted gene 16543  Symbol and/or name change 5135510 APPROVED