Smim23 (small integral membrane protein 23) - Rat Genome Database

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Gene: Smim23 (small integral membrane protein 23) Rattus norvegicus
Analyze
Symbol: Smim23
Name: small integral membrane protein 23
RGD ID: 1306625
Description: Orthologous to human SMIM23 (small integral membrane protein 23); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: hypothetical protein LOC360508; LOC360508; RGD1306625; uncharacterized protein LOC360508
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81017,907,716 - 17,911,350 (-)NCBIGRCr8
mRatBN7.21017,403,456 - 17,407,091 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1017,403,456 - 17,407,168 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1022,152,365 - 22,155,864 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01021,640,953 - 21,644,452 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01017,129,211 - 17,132,845 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01017,717,599 - 17,721,233 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1017,717,599 - 17,721,233 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01017,605,598 - 17,609,232 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41017,687,792 - 17,691,426 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11017,688,839 - 17,692,414 (-)NCBI
Celera1017,047,052 - 17,050,557 (-)NCBICelera
Cytogenetic Map10q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
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
Smim23
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81017,907,716 - 17,911,350 (-)NCBIGRCr8
mRatBN7.21017,403,456 - 17,407,091 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1017,403,456 - 17,407,168 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1022,152,365 - 22,155,864 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01021,640,953 - 21,644,452 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01017,129,211 - 17,132,845 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01017,717,599 - 17,721,233 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1017,717,599 - 17,721,233 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01017,605,598 - 17,609,232 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41017,687,792 - 17,691,426 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11017,688,839 - 17,692,414 (-)NCBI
Celera1017,047,052 - 17,050,557 (-)NCBICelera
Cytogenetic Map10q12NCBI
SMIM23
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385171,772,637 - 171,791,136 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5171,782,432 - 171,796,126 (+)EnsemblGRCh38hg38GRCh38
GRCh375171,212,821 - 171,218,140 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365171,145,481 - 171,166,221 (+)NCBINCBI36Build 36hg18NCBI36
Celera5167,162,218 - 167,266,076 (+)NCBICelera
Cytogenetic Map5q35.1NCBI
HuRef5166,309,194 - 166,314,503 (+)NCBIHuRef
CHM1_15170,645,301 - 170,650,600 (+)NCBICHM1_1
T2T-CHM13v2.05172,312,952 - 172,331,444 (+)NCBIT2T-CHM13v2.0
Smim23
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391132,770,376 - 32,774,594 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1132,768,529 - 32,774,605 (-)EnsemblGRCm39 Ensembl
GRCm381132,820,376 - 32,824,594 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1132,818,529 - 32,824,605 (-)EnsemblGRCm38mm10GRCm38
MGSCv371132,720,376 - 32,724,594 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361132,718,529 - 32,724,573 (-)NCBIMGSCv36mm8
Celera1135,239,451 - 35,243,685 (-)NCBICelera
Cytogenetic Map11A4NCBI
cM Map1119.11NCBI
Smim23
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540824,626,470 - 24,635,327 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540824,626,468 - 24,633,678 (+)NCBIChiLan1.0ChiLan1.0
SMIM23
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v24166,920,229 - 166,927,164 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan15165,059,779 - 165,066,703 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v05167,131,772 - 167,137,236 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.15174,048,837 - 174,054,098 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5174,048,837 - 174,057,589 (+)Ensemblpanpan1.1panPan2
SMIM23
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1440,427,841 - 40,434,357 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl440,428,036 - 40,434,359 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha440,376,734 - 40,383,249 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0440,803,162 - 40,809,683 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl440,803,357 - 40,809,588 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1440,618,344 - 40,624,858 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0440,808,669 - 40,815,178 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0441,318,857 - 41,325,364 (-)NCBIUU_Cfam_GSD_1.0
Smim23
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721394,676,110 - 94,683,159 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366093,398,891 - 3,405,769 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366093,398,891 - 3,405,769 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMIM23
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1652,404,004 - 52,412,792 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11652,404,463 - 52,412,731 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SMIM23
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12373,941,701 - 73,947,307 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660344,693,539 - 4,698,888 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Smim23
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473318,193,037 - 18,196,932 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473318,193,286 - 18,196,848 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Smim23
37 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:71
Count of miRNA genes:66
Interacting mature miRNAs:71
Transcripts:ENSRNOT00000031337
Prediction methods:Microtar, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
6893352Bw100Body weight QTL 1000.330.6body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101527595560275955Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10538701450387014Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101502851360430477Rat
6893350Bw99Body weight QTL 990.870.16body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10129497586Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
737823Alc12Alcohol consumption QTL 124.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)101724551319388279Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402719233348Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
1576304Schws7Schwannoma susceptibility QTL 70.0115nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)10476552719816042Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
7 6 6 35 34 30 16 12 16 5 67 34 22 6 27 14

Sequence


Ensembl Acc Id: ENSRNOT00000031337   ⟹   ENSRNOP00000038766
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1017,403,456 - 17,407,168 (-)Ensembl
Rnor_6.0 Ensembl1017,717,599 - 17,721,233 (-)Ensembl
RefSeq Acc Id: NM_001108271   ⟹   NP_001101741
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81017,907,716 - 17,911,350 (-)NCBI
mRatBN7.21017,403,456 - 17,407,091 (-)NCBI
Rnor_6.01017,717,599 - 17,721,233 (-)NCBI
Rnor_5.01017,605,598 - 17,609,232 (-)NCBI
RGSC_v3.41017,687,792 - 17,691,426 (-)RGD
Celera1017,047,052 - 17,050,557 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001101741 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM04064 (Get FASTA)   NCBI Sequence Viewer  
  EDM04065 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000038766.5
RefSeq Acc Id: NP_001101741   ⟸   NM_001108271
- UniProtKB: D4A0X0 (UniProtKB/TrEMBL),   A6HDG0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000038766   ⟸   ENSRNOT00000031337

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A0X0-F1-model_v2 AlphaFold D4A0X0 1-154 view protein structure

Transcriptome

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

Promoters
RGD ID:13697093
Promoter ID:EPDNEW_R7618
Type:initiation region
Name:Smim23_1
Description:small integral membrane protein 23
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_6.01017,721,239 - 17,721,299EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306625 AgrOrtholog
BioCyc Gene G2FUF-25617 BioCyc
Ensembl Genes ENSRNOG00000027196 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000031337.5 UniProtKB/TrEMBL
InterPro DUF4635 UniProtKB/TrEMBL
KEGG Report rno:360508 UniProtKB/TrEMBL
NCBI Gene 360508 ENTREZGENE
PANTHER PTHR37865 UniProtKB/TrEMBL
  SMALL INTEGRAL MEMBRANE PROTEIN 23 UniProtKB/TrEMBL
Pfam DUF4635 UniProtKB/TrEMBL
PhenoGen Smim23 PhenoGen
RatGTEx ENSRNOG00000027196 RatGTEx
UniProt A6HDG0 ENTREZGENE, UniProtKB/TrEMBL
  D4A0X0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-02-13 Smim23  small integral membrane protein 23  RGD1306625  LOC360508  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1306625  LOC360508   RGD1306625_predicted  LOC360508 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1306625_predicted  LOC360508 (predicted)  LOC360508_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC360508_predicted  LOC360508 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL