Smim13 (small integral membrane protein 13) - Rat Genome Database

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Gene: Smim13 (small integral membrane protein 13) Rattus norvegicus
Analyze
Symbol: Smim13
Name: small integral membrane protein 13
RGD ID: 1591023
Description: Predicted to be located in membrane. Orthologous to human SMIM13 (small integral membrane protein 13); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; Cuprizon.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical protein LOC690806; LOC690806; rCG44158; RGD1566043; uncharacterized protein LOC690806; UPF0766 protein C6orf228 homolog
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81723,703,414 - 23,721,457 (-)NCBIGRCr8
mRatBN7.21723,497,662 - 23,515,705 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx1723,366,759 - 23,384,816 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01724,970,448 - 24,988,505 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01723,307,712 - 23,325,771 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01721,334,989 - 21,353,252 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1721,339,059 - 21,353,134 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01723,323,000 - 23,337,383 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41729,430,963 - 29,445,347 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1723,169,508 - 23,187,549 (-)NCBICelera
Cytogenetic Map17p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
membrane  (IEA)

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Smim13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81723,703,414 - 23,721,457 (-)NCBIGRCr8
mRatBN7.21723,497,662 - 23,515,705 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx1723,366,759 - 23,384,816 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01724,970,448 - 24,988,505 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01723,307,712 - 23,325,771 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01721,334,989 - 21,353,252 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1721,339,059 - 21,353,134 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01723,323,000 - 23,337,383 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41729,430,963 - 29,445,347 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1723,169,508 - 23,187,549 (-)NCBICelera
Cytogenetic Map17p12NCBI
SMIM13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38611,093,834 - 11,138,733 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl611,093,834 - 11,138,733 (+)EnsemblGRCh38hg38GRCh38
GRCh37611,094,067 - 11,138,966 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36611,242,617 - 11,246,957 (+)NCBINCBI36Build 36hg18NCBI36
Celera612,322,733 - 12,367,437 (+)NCBICelera
Cytogenetic Map6p24.2NCBI
HuRef611,025,782 - 11,070,397 (+)NCBIHuRef
CHM1_1611,096,365 - 11,141,415 (+)NCBICHM1_1
T2T-CHM13v2.0610,961,754 - 11,006,653 (+)NCBIT2T-CHM13v2.0
Smim13
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391341,403,320 - 41,430,053 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1341,403,320 - 41,430,053 (+)EnsemblGRCm39 Ensembl
GRCm381341,249,844 - 41,276,577 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1341,249,844 - 41,276,577 (+)EnsemblGRCm38mm10GRCm38
MGSCv371341,345,213 - 41,371,946 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361341,345,213 - 41,371,946 (+)NCBIMGSCv36mm8
Celera1342,331,977 - 42,358,679 (+)NCBICelera
Cytogenetic Map13A3.3NCBI
cM Map1320.41NCBI
Smim13
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554653,321,886 - 3,343,467 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554653,321,886 - 3,343,467 (-)NCBIChiLan1.0ChiLan1.0
SMIM13
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2525,741,001 - 25,785,445 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1621,730,474 - 21,775,474 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0610,932,158 - 10,976,874 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1611,208,331 - 11,252,281 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl611,208,331 - 11,252,269 (+)Ensemblpanpan1.1panPan2
SMIM13
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13510,783,392 - 10,811,914 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3510,732,363 - 10,760,956 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03510,885,428 - 10,909,960 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3510,885,462 - 10,910,365 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13510,716,109 - 10,744,704 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03510,764,472 - 10,793,092 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03512,086,122 - 12,114,646 (+)NCBIUU_Cfam_GSD_1.0
Smim13
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494613,632,561 - 13,642,249 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049365341,901,959 - 1,911,235 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMIM13
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl77,774,542 - 7,779,936 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.177,774,547 - 7,784,038 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.278,172,176 - 8,177,543 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SMIM13
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11761,007,013 - 61,049,871 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1761,011,107 - 61,049,381 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604411,125,782 - 11,169,049 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Smim13
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475614,883,126 - 14,902,371 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Smim13
88 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:28
Count of miRNA genes:27
Interacting mature miRNAs:28
Transcripts:ENSRNOT00000067898
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
2300002Iddm36Insulin dependent diabetes mellitus QTL 361.98blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)17999128640540197Rat
631499Stl1Serum triglyceride level QTL 13.6blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)17327139827389946Rat
2293664Bmd28Bone mineral density QTL 285.10.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)17435448727028127Rat
1354640Scl32Serum cholesterol level QTL 325.4blood HDL cholesterol amount (VT:0000184)blood high density lipoprotein cholesterol level (CMO:0000052)171578159260781592Rat
1300123Bp194Blood pressure QTL 1942.82arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)17211514934551001Rat
1582224Epfw4Epididymal fat weight QTL 43.50.0058epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)17920136523653323Rat
1582225Bw67Body weight QTL 676.20.0001body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582226Bw64Body weight QTL 644.20.0017body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
70157Niddm32Non-insulin dependent diabetes mellitus QTL 324.34blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)172245492450909196Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17429913069599340Rat
1354628Stl13Serum triglyceride level QTL 133.8blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)172129303960781592Rat
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17131701463Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17452803849528038Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17429913069599340Rat
61394Bp8Blood pressure QTL 82.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172308056759555013Rat
1582208Kidm32Kidney mass QTL 323.90.0018kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17920136523653323Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17429913069599340Rat
1354613Kidm14Kidney mass QTL 146.2kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)17429913035837242Rat
1331765Hrtrt15Heart rate QTL 154.094heart pumping trait (VT:2000009)heart rate (CMO:0000002)171533061355836425Rat
7394837Memor18Memory QTL 18exploratory behavior trait (VT:0010471)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)171864018263640182Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17452803849528038Rat
70184BpQTLcluster14Blood pressure QTL cluster 143.38arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)17131990913Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17886846253868462Rat
1582258Bw76Body weight QTL 764.60.0005body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17137830672Rat
1582199Insul5Insulin level QTL 53.40.0119blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)17920136523653323Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17429913060781592Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat
2293648Bmd31Bone mineral density QTL 314.50.0001femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)17435448727028127Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17160781592Rat
1354659Scl68Serum cholesterol level QTL 683.9blood VLDL cholesterol amount (VT:0005144)blood very low density lipoprotein cholesterol level (CMO:0000648)171578159260781592Rat
1582241Bw70Body weight QTL 704.60.0003body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat
1582245Bw73Body weight QTL 734.60.0004body mass (VT:0001259)body weight (CMO:0000012)17920136523653323Rat

Markers in Region
RH134225  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21723,501,407 - 23,501,620 (+)MAPPERmRatBN7.2
Rnor_6.01721,338,955 - 21,339,167NCBIRnor6.0
Rnor_6.01721,325,568 - 21,325,780NCBIRnor6.0
Rnor_5.01723,310,301 - 23,310,513UniSTSRnor5.0
Rnor_5.01723,323,086 - 23,323,298UniSTSRnor5.0
Celera1723,173,252 - 23,173,464UniSTS
RH 3.4 Map17278.1UniSTS
Cytogenetic Map17p12UniSTS
Cytogenetic Map17q12.1UniSTS
RH138588  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21723,502,099 - 23,502,242 (+)MAPPERmRatBN7.2
Rnor_6.01721,339,647 - 21,339,789NCBIRnor6.0
Rnor_5.01723,323,778 - 23,323,920UniSTSRnor5.0
RGSC_v3.41729,431,741 - 29,431,883UniSTSRGSC3.4
Celera1723,173,944 - 23,174,086UniSTS
RH 3.4 Map17279.0UniSTS
Cytogenetic Map17p12UniSTS


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 1 34 17 11 11 11 6 9 74 22 36 3 6
Low 2 9 40 30 8 30 2 2 13 5 8 2
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000067898   ⟹   ENSRNOP00000059626
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1721,339,059 - 21,353,134 (-)Ensembl
RefSeq Acc Id: NM_001135576   ⟹   NP_001129048
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81723,703,414 - 23,721,457 (-)NCBI
mRatBN7.21723,497,662 - 23,515,705 (-)NCBI
Rnor_6.01721,334,989 - 21,353,252 (-)NCBI
Rnor_5.01723,323,000 - 23,337,383 (-)NCBI
RGSC_v3.41729,430,963 - 29,445,347 (-)RGD
Celera1723,169,508 - 23,187,549 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001129048 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein D3ZR35 (Get FASTA)   NCBI Sequence Viewer  
  EDL98218 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00055010687
  ENSRNOP00060013043
  ENSRNOP00065009563
RefSeq Acc Id: NP_001129048   ⟸   NM_001135576
- UniProtKB: D3ZR35 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000059626   ⟸   ENSRNOT00000067898

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZR35-F1-model_v2 AlphaFold D3ZR35 1-88 view protein structure

Transcriptome

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

Promoters
RGD ID:13700373
Promoter ID:EPDNEW_R10897
Type:initiation region
Name:Smim13_1
Description:small integral membrane protein 13
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_6.01721,353,181 - 21,353,241EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1591023 AgrOrtholog
BioCyc Gene G2FUF-9737 BioCyc
Ensembl Genes ENSRNOG00000043288 Ensembl
  ENSRNOG00055007910 UniProtKB/Swiss-Prot
  ENSRNOG00060009892 UniProtKB/Swiss-Prot
  ENSRNOG00065008199 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00055013311 UniProtKB/Swiss-Prot
  ENSRNOT00060016693 UniProtKB/Swiss-Prot
  ENSRNOT00065012982 UniProtKB/Swiss-Prot
InterPro DUF4750 UniProtKB/Swiss-Prot
KEGG Report rno:690806 UniProtKB/Swiss-Prot
NCBI Gene 690806 ENTREZGENE
PANTHER PTHR36877 UniProtKB/Swiss-Prot
  SMALL INTEGRAL MEMBRANE PROTEIN 13 UniProtKB/Swiss-Prot
Pfam DUF4750 UniProtKB/Swiss-Prot
PhenoGen Smim13 PhenoGen
RatGTEx ENSRNOG00000043288 RatGTEx
  ENSRNOG00055007910 RatGTEx
  ENSRNOG00060009892 RatGTEx
  ENSRNOG00065008199 RatGTEx
UniProt D3ZR35 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-21 Smim13  small integral membrane protein 13  Smim13  small integral membrane protein 13  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC690806  hypothetical protein LOC690806      Symbol and Name status set to provisional 70820 PROVISIONAL