Smim29 (small integral membrane protein 29) - Rat Genome Database

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Gene: Smim29 (small integral membrane protein 29) Rattus norvegicus
Analyze
Symbol: Smim29
Name: small integral membrane protein 29
RGD ID: 1564450
Description: Predicted to be located in membrane. Orthologous to human SMIM29 (small integral membrane protein 29); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical LOC294291; hypothetical protein LOC294291; LOC294291; RGD1564450; RGD1564450; uncharacterized protein C6orf1 homolog; uncharacterized protein LOC294291
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2205,618,845 - 5,620,922 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl205,618,845 - 5,620,813 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx206,331,332 - 6,333,345 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0205,693,084 - 5,695,097 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0206,173,220 - 6,175,233 (-)NCBIRnor_WKY
Rnor_6.0207,140,241 - 7,142,316 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl207,140,245 - 7,142,213 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0209,342,411 - 9,344,670 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4205,773,534 - 5,775,502 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera207,181,798 - 7,183,766 (-)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
JMP syndrome  (ISO)

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
Additional References at PubMed
PMID:12477932  


Genomics

Comparative Map Data
Smim29
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2205,618,845 - 5,620,922 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl205,618,845 - 5,620,813 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx206,331,332 - 6,333,345 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0205,693,084 - 5,695,097 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0206,173,220 - 6,175,233 (-)NCBIRnor_WKY
Rnor_6.0207,140,241 - 7,142,316 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl207,140,245 - 7,142,213 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0209,342,411 - 9,344,670 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4205,773,534 - 5,775,502 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera207,181,798 - 7,183,766 (-)NCBICelera
Cytogenetic Map20p12NCBI
SMIM29
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38634,246,395 - 34,249,006 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl634,246,381 - 34,249,108 (-)EnsemblGRCh38hg38GRCh38
GRCh37634,214,172 - 34,216,783 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36634,322,135 - 34,324,882 (-)NCBINCBI36Build 36hg18NCBI36
Celera635,768,530 - 35,771,279 (-)NCBICelera
Cytogenetic Map6p21.31NCBI
HuRef633,936,822 - 33,939,571 (-)NCBIHuRef
CHM1_1634,216,746 - 34,219,495 (-)NCBICHM1_1
T2T-CHM13v2.0634,070,100 - 34,072,713 (-)NCBIT2T-CHM13v2.0
Smim29
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391727,782,743 - 27,784,710 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1727,782,547 - 27,784,730 (-)EnsemblGRCm39 Ensembl
GRCm381727,563,769 - 27,565,728 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1727,563,573 - 27,565,756 (-)EnsemblGRCm38mm10GRCm38
MGSCv371727,700,714 - 27,702,672 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361727,291,358 - 27,293,289 (-)NCBIMGSCv36mm8
Celera1728,115,873 - 28,117,831 (-)NCBICelera
Cytogenetic Map17A3.3NCBI
Smim29
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554372,486,918 - 2,489,003 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554372,486,918 - 2,489,003 (-)NCBIChiLan1.0ChiLan1.0
SMIM29
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1634,920,643 - 34,923,316 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl634,920,643 - 34,923,311 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0633,816,762 - 33,819,465 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SMIM29
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1123,538,756 - 3,541,344 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha123,554,313 - 3,556,924 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0123,874,885 - 3,877,494 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl123,874,890 - 3,877,928 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1123,537,240 - 3,539,849 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0123,618,753 - 3,621,225 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0123,717,099 - 3,719,708 (-)NCBIUU_Cfam_GSD_1.0
Smim29
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494639,164,551 - 39,165,847 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647624,793,223 - 24,795,661 (+)EnsemblSpeTri2.0
SpeTri2.0NW_00493647624,793,213 - 24,795,679 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC100156657
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl730,329,550 - 30,332,126 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1730,329,547 - 30,332,166 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2734,990,226 - 34,992,729 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SMIM29
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11737,845,160 - 37,847,944 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1737,846,855 - 37,847,851 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604434,161,143 - 34,163,841 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Smim29
16 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2036216499243559Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)20362164910078919Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
61474Eae1Experimental allergic encephalomyelitis QTL 13nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)2046066076691706Rat
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20460660717617956Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20460660717617956Rat

Markers in Region
RH128050  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X31,610,924 - 31,611,116 (+)MAPPERmRatBN7.2
mRatBN7.2205,618,454 - 5,618,649 (+)MAPPERmRatBN7.2
Rnor_6.0207,139,855 - 7,140,049NCBIRnor6.0
Rnor_6.0X33,348,165 - 33,348,356NCBIRnor6.0
Rnor_5.0209,342,210 - 9,342,404UniSTSRnor5.0
Rnor_5.0X33,695,628 - 33,695,819UniSTSRnor5.0
RGSC_v3.4X52,351,648 - 52,351,839UniSTSRGSC3.4
RGSC_v3.4205,773,144 - 5,773,338UniSTSRGSC3.4
Celera207,181,408 - 7,181,602UniSTS
CeleraX31,924,692 - 31,924,883UniSTS
RH 3.4 Map2076.95UniSTS
Cytogenetic Map20p12UniSTS
RH130079  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2205,618,876 - 5,619,070 (+)MAPPERmRatBN7.2
Rnor_6.0207,140,277 - 7,140,470NCBIRnor6.0
Rnor_5.0209,342,632 - 9,342,825UniSTSRnor5.0
RGSC_v3.4205,773,566 - 5,773,759UniSTSRGSC3.4
Celera207,181,830 - 7,182,023UniSTS
RH 3.4 Map2075.03UniSTS
Cytogenetic Map20p12UniSTS


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 2 8 19 66 8 12 8
Low 1 43 49 41 41 8 11 8 27 29 3 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000078918   ⟹   ENSRNOP00000072018
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl205,618,845 - 5,620,813 (-)Ensembl
Rnor_6.0 Ensembl207,140,245 - 7,142,213 (-)Ensembl
RefSeq Acc Id: NM_001106377   ⟹   NP_001099847
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2205,618,845 - 5,620,813 (-)NCBI
Rnor_6.0207,140,245 - 7,142,213 (-)NCBI
Rnor_5.0209,342,411 - 9,344,670 (-)NCBI
RGSC_v3.4205,773,534 - 5,775,502 (-)RGD
Celera207,181,798 - 7,183,766 (-)RGD
Sequence:
RefSeq Acc Id: XM_006256171   ⟹   XP_006256233
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2205,618,845 - 5,620,922 (-)NCBI
Rnor_6.0207,140,241 - 7,142,316 (-)NCBI
Rnor_5.0209,342,411 - 9,344,670 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017601591   ⟹   XP_017457080
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2205,618,845 - 5,620,856 (-)NCBI
Rnor_6.0207,140,241 - 7,142,213 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039098513   ⟹   XP_038954441
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2205,618,845 - 5,620,813 (-)NCBI
RefSeq Acc Id: XM_039098514   ⟹   XP_038954442
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2205,618,845 - 5,620,806 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001099847   ⟸   NM_001106377
- Sequence:
RefSeq Acc Id: XP_006256233   ⟸   XM_006256171
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017457080   ⟸   XM_017601591
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000072018   ⟸   ENSRNOT00000078918
RefSeq Acc Id: XP_038954441   ⟸   XM_039098513
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K1X2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038954442   ⟸   XM_039098514
- Peptide Label: isoform X2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K1X2-F1-model_v2 AlphaFold A0A0G2K1X2 1-114 view protein structure

Transcriptome

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

Promoters
RGD ID:13701448
Promoter ID:EPDNEW_R11971
Type:multiple initiation site
Name:Smim29_1
Description:small integral membrane protein 29
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_6.0207,142,261 - 7,142,321EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564450 AgrOrtholog
BioCyc Gene G2FUF-4465 BioCyc
Ensembl Genes ENSRNOG00000054374 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000072018 ENTREZGENE
  ENSRNOP00000072018.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000078918 ENTREZGENE
  ENSRNOT00000078918.2 UniProtKB/TrEMBL
InterPro SMIM29 UniProtKB/TrEMBL
NCBI Gene 294291 ENTREZGENE
PANTHER PTHR47730 UniProtKB/TrEMBL
  SMALL INTEGRAL MEMBRANE PROTEIN 29 UniProtKB/TrEMBL
PhenoGen Smim29 PhenoGen
UniProt A0A0G2K1X2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-04-20 Smim29  small integral membrane protein 29  RGD1564450  RGD1564450  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1564450  RGD1564450   RGD1564450_predicted  RGD1564450 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1564450_predicted  RGD1564450 (predicted)  LOC294291  hypothetical LOC294291  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC294291  hypothetical LOC294291      Symbol and Name status set to provisional 70820 PROVISIONAL