Msc (musculin) - Rat Genome Database

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Gene: Msc (musculin) Rattus norvegicus
Analyze
Symbol: Msc
Name: musculin
RGD ID: 1305496
Description: Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II; roof of mouth development; and skeletal muscle organ development. Predicted to act upstream of or within cellular response to leukemia inhibitory factor. Predicted to be located in nucleoplasm. Orthologous to human MSC (musculin); INTERACTS WITH (+)-schisandrin B; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC312897
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.254,547,335 - 4,553,206 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl54,547,405 - 4,553,203 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx56,681,276 - 6,682,621 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.058,320,164 - 8,321,509 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.058,014,163 - 8,015,508 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.053,954,902 - 3,956,974 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl53,955,227 - 3,956,572 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.053,931,016 - 3,936,807 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.453,703,215 - 3,704,560 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.153,703,146 - 3,704,560 (+)NCBI
Celera54,144,045 - 4,145,390 (+)NCBICelera
Cytogenetic Map5q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleoplasm  (IEA,ISO)
nucleus  (ISO)

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9892671   PMID:12493912   PMID:19796622   PMID:20439489  


Genomics

Comparative Map Data
Msc
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.254,547,335 - 4,553,206 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl54,547,405 - 4,553,203 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx56,681,276 - 6,682,621 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.058,320,164 - 8,321,509 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.058,014,163 - 8,015,508 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.053,954,902 - 3,956,974 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl53,955,227 - 3,956,572 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.053,931,016 - 3,936,807 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.453,703,215 - 3,704,560 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.153,703,146 - 3,704,560 (+)NCBI
Celera54,144,045 - 4,145,390 (+)NCBICelera
Cytogenetic Map5q11NCBI
MSC
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38871,841,560 - 71,844,412 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl871,841,560 - 71,844,412 (-)EnsemblGRCh38hg38GRCh38
GRCh37872,753,795 - 72,756,647 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36872,916,331 - 72,919,285 (-)NCBINCBI36Build 36hg18NCBI36
Build 34872,916,348 - 72,919,162NCBI
Celera868,753,235 - 68,756,193 (-)NCBICelera
Cytogenetic Map8q13.3NCBI
HuRef868,248,229 - 68,251,184 (-)NCBIHuRef
CHM1_1872,807,314 - 72,810,269 (-)NCBICHM1_1
T2T-CHM13v2.0872,276,765 - 72,279,617 (-)NCBIT2T-CHM13v2.0
Msc
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39114,823,570 - 14,826,216 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl114,823,570 - 14,826,216 (-)EnsemblGRCm39 Ensembl
GRCm38114,753,344 - 14,756,089 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl114,753,346 - 14,755,992 (-)EnsemblGRCm38mm10GRCm38
MGSCv37114,743,427 - 14,746,047 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36114,738,560 - 14,741,180 (-)NCBIMGSCv36mm8
Celera114,693,596 - 14,696,218 (-)NCBICelera
Cytogenetic Map1A3NCBI
cM Map14.5NCBI
Msc
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554448,064,867 - 8,067,408 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554448,064,867 - 8,067,381 (+)NCBIChiLan1.0ChiLan1.0
MSC
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1863,203,826 - 63,206,691 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0868,365,708 - 68,368,628 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1870,024,271 - 70,027,227 (-)NCBIpanpan1.1PanPan1.1panPan2
MSC
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12920,800,047 - 20,802,718 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2920,800,062 - 20,802,657 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2921,058,719 - 21,061,346 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02920,898,313 - 20,900,934 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2920,898,328 - 20,900,917 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12920,946,878 - 20,949,500 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02920,999,799 - 21,002,418 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02921,282,344 - 21,284,967 (-)NCBIUU_Cfam_GSD_1.0
Msc
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530358,486,807 - 58,490,213 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936648958,496 - 960,843 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936648958,396 - 961,777 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MSC
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl463,709,795 - 63,713,140 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1463,709,800 - 63,712,651 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2469,416,999 - 69,419,849 (+)NCBISscrofa10.2Sscrofa10.2susScr3
MSC
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1867,521,052 - 67,523,952 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl867,520,970 - 67,523,833 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603973,869,261 - 73,872,160 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Msc
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474419,269,944 - 19,273,768 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474419,268,734 - 19,272,611 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Msc
38 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:89
Count of miRNA genes:79
Interacting mature miRNAs:87
Transcripts:ENSRNOT00000009908
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
2312562Pur18Proteinuria QTL 182.60.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5213896532656739Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
631551Vetf1Vascular elastic tissue fragility QTL 150.0001aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)522822265904428Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
2313085Bss59Bone structure and strength QTL 592.90.0001long bone metaphysis morphology trait (VT:0000133)tibia midshaft total cross-sectional area (CMO:0001715)5384401826141981Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5384401847869213Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 7
Low 3 31 36 28 19 28 7 10 23 18 31 10 7
Below cutoff 8 19 13 13 1 1 39 10 3 1 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009908   ⟹   ENSRNOP00000009908
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl54,551,315 - 4,553,203 (+)Ensembl
Rnor_6.0 Ensembl53,955,227 - 3,956,572 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000094597   ⟹   ENSRNOP00000079652
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl54,547,405 - 4,553,203 (+)Ensembl
RefSeq Acc Id: NM_001191754   ⟹   NP_001178683
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.254,551,095 - 4,553,200 (+)NCBI
Rnor_6.053,955,227 - 3,956,572 (+)NCBI
Rnor_5.053,931,016 - 3,936,807 (+)NCBI
Celera54,144,045 - 4,145,390 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008763476   ⟹   XP_008761698
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.254,551,000 - 4,553,206 (+)NCBI
Rnor_6.053,954,902 - 3,956,974 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039109741   ⟹   XP_038965669
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.254,547,335 - 4,553,206 (+)NCBI
RefSeq Acc Id: XM_039109742   ⟹   XP_038965670
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.254,547,335 - 4,553,206 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001178683 (Get FASTA)   NCBI Sequence Viewer  
  XP_008761698 (Get FASTA)   NCBI Sequence Viewer  
  XP_038965669 (Get FASTA)   NCBI Sequence Viewer  
  XP_038965670 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000009908.4
  ENSRNOP00000079652
  ENSRNOP00000079652.1
Reference Protein Sequences
RefSeq Acc Id: NP_001178683   ⟸   NM_001191754
- UniProtKB: A0A8I5ZNI8 (UniProtKB/TrEMBL),   A6JFC6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008761698   ⟸   XM_008763476
- Peptide Label: isoform X1
- UniProtKB: D3ZWP1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009908   ⟸   ENSRNOT00000009908
RefSeq Acc Id: XP_038965669   ⟸   XM_039109741
- Peptide Label: isoform X1
- UniProtKB: D3ZWP1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038965670   ⟸   XM_039109742
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZNI8 (UniProtKB/TrEMBL),   A6JFC6 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000079652   ⟸   ENSRNOT00000094597
Protein Domains
bHLH

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZWP1-F1-model_v2 AlphaFold D3ZWP1 1-203 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305496 AgrOrtholog
BioCyc Gene G2FUF-42276 BioCyc
Ensembl Genes ENSRNOG00000007540 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009908.6 UniProtKB/TrEMBL
  ENSRNOT00000094597 ENTREZGENE
  ENSRNOT00000094597.1 UniProtKB/TrEMBL
Gene3D-CATH 4.10.280.10 UniProtKB/TrEMBL
InterPro HLH_DNA-bd UniProtKB/TrEMBL
  HLH_DNA-bd_sf UniProtKB/TrEMBL
KEGG Report rno:312897 UniProtKB/TrEMBL
NCBI Gene 312897 ENTREZGENE
PANTHER BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTOR, TWIST UniProtKB/TrEMBL
  MUSCULIN UniProtKB/TrEMBL
Pfam HLH UniProtKB/TrEMBL
PhenoGen Msc PhenoGen
PROSITE HLH UniProtKB/TrEMBL
RatGTEx ENSRNOG00000007540 RatGTEx
SMART HLH UniProtKB/TrEMBL
Superfamily-SCOP HLH_basic UniProtKB/TrEMBL
UniProt A0A8I5ZNI8 ENTREZGENE, UniProtKB/TrEMBL
  A6JFC6 ENTREZGENE, UniProtKB/TrEMBL
  D3ZWP1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Msc  musculin   Msc_predicted  musculin (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Msc_predicted  musculin (predicted)      Symbol and Name status set to approved 70820 APPROVED