Smpx (small muscle protein, X-linked) - Rat Genome Database

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Gene: Smpx (small muscle protein, X-linked) Rattus norvegicus
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Symbol: Smpx
Name: small muscle protein, X-linked
RGD ID: 69233
Description: Predicted to be located in contractile fiber and nucleus. Predicted to be active in M band; costamere; and muscle tendon junction. Human ortholog(s) of this gene implicated in X-linked deafness 4. Orthologous to human SMPX (small muscle protein X-linked); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; aconitine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: small muscular protein; stretch-responsive skeletal muscle protein
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
GRCr8X41,049,354 - 41,107,323 (-)NCBIGRCr8
mRatBN7.2X37,233,209 - 37,292,266 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX37,234,294 - 37,276,708 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX38,423,422 - 38,481,226 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X41,890,629 - 41,948,431 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X39,575,342 - 39,633,141 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X40,029,200 - 40,086,870 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX40,030,248 - 40,086,870 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X40,340,762 - 40,397,380 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X58,521,059 - 58,581,070 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1X58,574,529 - 58,634,539 (-)NCBI
CeleraX37,866,028 - 37,923,593 (-)NCBICelera
Cytogenetic MapXq21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
contractile fiber  (ISO)
costamere  (IBA,IEA,ISO)
cytoplasm  (ISO)
M band  (IBA,IEA,ISO)
muscle tendon junction  (IBA,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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
6. Identification, mapping, and genomic structure of a novel X-chromosomal human gene (SMPX) encoding a small muscular protein. Patzak D, etal., Hum Genet 1999 Nov;105(5):506-12.
7. GOA pipeline RGD automated data pipeline
8. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
10. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
Additional References at PubMed
PMID:11381084   PMID:11401441  


Genomics

Comparative Map Data
Smpx
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X41,049,354 - 41,107,323 (-)NCBIGRCr8
mRatBN7.2X37,233,209 - 37,292,266 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX37,234,294 - 37,276,708 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX38,423,422 - 38,481,226 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X41,890,629 - 41,948,431 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X39,575,342 - 39,633,141 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X40,029,200 - 40,086,870 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX40,030,248 - 40,086,870 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X40,340,762 - 40,397,380 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X58,521,059 - 58,581,070 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1X58,574,529 - 58,634,539 (-)NCBI
CeleraX37,866,028 - 37,923,593 (-)NCBICelera
Cytogenetic MapXq21NCBI
SMPX
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X21,705,978 - 21,758,116 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX21,705,978 - 21,758,116 (-)EnsemblGRCh38hg38GRCh38
GRCh37X21,724,096 - 21,776,234 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X21,634,012 - 21,686,151 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X21,483,747 - 21,535,887NCBI
CeleraX25,845,385 - 25,897,515 (-)NCBICelera
Cytogenetic MapXp22.12NCBI
HuRefX19,465,725 - 19,517,905 (-)NCBIHuRef
CHM1_1X21,754,516 - 21,806,704 (-)NCBICHM1_1
T2T-CHM13v2.0X21,289,285 - 21,341,420 (-)NCBIT2T-CHM13v2.0
Smpx
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X156,481,969 - 156,535,587 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX156,481,906 - 156,535,587 (+)EnsemblGRCm39 Ensembl
GRCm38X157,698,973 - 157,752,591 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX157,698,910 - 157,752,591 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X154,137,050 - 154,190,521 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X153,043,223 - 153,096,694 (+)NCBIMGSCv36mm8
CeleraX140,952,572 - 141,005,978 (+)NCBICelera
Cytogenetic MapXF4NCBI
cM MapX72.67NCBI
Smpx
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555092,067,351 - 2,093,732 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555092,043,854 - 2,185,294 (-)NCBIChiLan1.0ChiLan1.0
SMPX
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X23,514,798 - 23,567,082 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X23,518,188 - 23,570,472 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X14,336,846 - 14,389,125 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X21,719,905 - 21,744,977 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX21,719,905 - 21,744,977 (-)Ensemblpanpan1.1panPan2
SMPX
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X17,520,564 - 17,578,453 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX17,520,644 - 17,573,614 (-)EnsemblCanFam3.1canFam3CanFam3.1
ROS_Cfam_1.0X17,480,026 - 17,537,925 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX17,480,106 - 17,533,083 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X17,514,285 - 17,572,159 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X17,535,989 - 17,593,898 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X17,596,164 - 17,654,098 (-)NCBIUU_Cfam_GSD_1.0
Smpx
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X10,498,541 - 10,554,663 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366242,603,171 - 2,659,364 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366242,603,210 - 2,659,368 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMPX
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX17,889,030 - 17,938,293 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X17,889,030 - 17,938,206 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Pig CytomapXp24NCBI
SMPX
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X20,170,996 - 20,234,693 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX20,172,347 - 20,227,028 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605622,040,729 - 22,068,492 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Smpx
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248296,655,549 - 6,679,832 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248296,633,027 - 6,679,508 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Smpx
140 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:260
Count of miRNA genes:181
Interacting mature miRNAs:207
Transcripts:ENSRNOT00000010027
Prediction methods:Microtar, Miranda, Pita, 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
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X143491017Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X292789847927898Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7440600049406000Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X449454949494549Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
71116Niddm16Non-insulin dependent diabetes mellitus QTL 167.81blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X1529780260297802Rat
1598873Memor2Memory QTL 22.5exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)X2099094741052531Rat
2290375Gluco34Glucose level QTL 342.75blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X2099094741203591Rat


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 43 8 11 22 22 8 8
Low 2 30 15 9 15 27 13 19 3
Below cutoff 1 10 9 8 9 14

Sequence


RefSeq Acc Id: ENSRNOT00000010027   ⟹   ENSRNOP00000010027
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX37,234,294 - 37,276,708 (-)Ensembl
Rnor_6.0 EnsemblX40,030,248 - 40,086,870 (-)Ensembl
RefSeq Acc Id: NM_053395   ⟹   NP_445847
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X41,049,354 - 41,107,137 (-)NCBI
mRatBN7.2X37,234,292 - 37,292,080 (-)NCBI
Rnor_6.0X40,030,256 - 40,086,870 (-)NCBI
Rnor_5.0X40,340,762 - 40,397,380 (-)NCBI
RGSC_v3.4X58,521,059 - 58,581,070 (-)RGD
CeleraX37,866,028 - 37,923,593 (-)RGD
Sequence:
RefSeq Acc Id: XM_006256945   ⟹   XP_006257007
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X41,049,354 - 41,104,023 (-)NCBI
mRatBN7.2X37,234,288 - 37,288,686 (-)NCBI
Rnor_6.0X40,029,200 - 40,083,475 (-)NCBI
Rnor_5.0X40,340,762 - 40,397,380 (-)NCBI
Sequence:
RefSeq Acc Id: XR_005498074
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X41,049,354 - 41,107,323 (-)NCBI
mRatBN7.2X37,233,209 - 37,292,266 (-)NCBI
RefSeq Acc Id: NP_445847   ⟸   NM_053395
- UniProtKB: Q925F0 (UniProtKB/Swiss-Prot),   A6IPP6 (UniProtKB/TrEMBL),   A0A8L2Q474 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257007   ⟸   XM_006256945
- Peptide Label: isoform X1
- UniProtKB: Q925F0 (UniProtKB/Swiss-Prot),   A6IPP6 (UniProtKB/TrEMBL),   A0A8L2Q474 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000010027   ⟸   ENSRNOT00000010027

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q925F0-F1-model_v2 AlphaFold Q925F0 1-85 view protein structure

Transcriptome

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

Promoters
RGD ID:13701814
Promoter ID:EPDNEW_R12338
Type:initiation region
Name:Smpx_1
Description:small muscle protein, X-linked
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X40,086,884 - 40,086,944EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69233 AgrOrtholog
BioCyc Gene G2FUF-2468 BioCyc
Ensembl Genes ENSRNOG00000007495 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00055014714 UniProtKB/Swiss-Prot
  ENSRNOG00060019324 UniProtKB/Swiss-Prot
  ENSRNOG00065013085 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000010027.5 UniProtKB/TrEMBL
  ENSRNOT00055025223 UniProtKB/Swiss-Prot
  ENSRNOT00060033442 UniProtKB/Swiss-Prot
  ENSRNOT00065021454 UniProtKB/Swiss-Prot
InterPro Chisel UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:84416 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 84416 ENTREZGENE
PANTHER PTHR17416 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SMALL MUSCULAR PROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Chisel UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Smpx PhenoGen
RatGTEx ENSRNOG00000007495 RatGTEx
  ENSRNOG00055014714 RatGTEx
  ENSRNOG00060019324 RatGTEx
  ENSRNOG00065013085 RatGTEx
TIGR TC204506
UniProt A0A8L2Q474 ENTREZGENE, UniProtKB/TrEMBL
  A6IPP6 ENTREZGENE, UniProtKB/TrEMBL
  A6IPP7_RAT UniProtKB/TrEMBL
  Q925F0 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Smpx  small muscle protein, X-linked      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference