Smim24 (small integral membrane protein 24) - Rat Genome Database

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Gene: Smim24 (small integral membrane protein 24) Rattus norvegicus
Analyze
Symbol: Smim24
Name: small integral membrane protein 24
RGD ID: 2324237
Description: Orthologous to human SMIM24 (small integral membrane protein 24); INTERACTS WITH (+)-schisandrin B; aflatoxin B1; atrazine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC100366121; rCG29408-like
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
GRCr878,964,107 - 8,967,234 (-)NCBIGRCr8
mRatBN7.278,313,369 - 8,316,498 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx711,199,208 - 11,202,141 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0713,074,695 - 13,077,628 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0710,942,109 - 10,945,265 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0711,182,975 - 11,187,222 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl711,183,570 - 11,186,130 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0711,350,127 - 11,353,138 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera76,502,821 - 6,506,626 (-)NCBICelera
Cytogenetic Map7q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease 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
Additional References at PubMed
PMID:23376485  


Genomics

Comparative Map Data
Smim24
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr878,964,107 - 8,967,234 (-)NCBIGRCr8
mRatBN7.278,313,369 - 8,316,498 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx711,199,208 - 11,202,141 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0713,074,695 - 13,077,628 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0710,942,109 - 10,945,265 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0711,182,975 - 11,187,222 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl711,183,570 - 11,186,130 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0711,350,127 - 11,353,138 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera76,502,821 - 6,506,626 (-)NCBICelera
Cytogenetic Map7q11NCBI
SMIM24
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38193,473,986 - 3,480,525 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl193,473,986 - 3,480,525 (-)EnsemblGRCh38hg38GRCh38
GRCh37193,473,984 - 3,480,523 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36193,425,405 - 3,431,534 (-)NCBINCBI36Build 36hg18NCBI36
Celera193,411,216 - 3,417,351 (-)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef193,240,321 - 3,246,461 (-)NCBIHuRef
CHM1_1193,474,053 - 3,480,188 (-)NCBICHM1_1
T2T-CHM13v2.0193,452,142 - 3,458,692 (-)NCBIT2T-CHM13v2.0
Smim24
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391081,228,898 - 81,230,913 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1081,228,885 - 81,231,226 (+)EnsemblGRCm39 Ensembl
GRCm381081,393,064 - 81,395,079 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1081,393,051 - 81,395,392 (+)EnsemblGRCm38mm10GRCm38
MGSCv371080,855,809 - 80,857,824 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361080,796,180 - 80,798,627 (+)NCBIMGSCv36mm8
Celera1082,414,097 - 82,416,112 (+)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1039.72NCBI
Smim24
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554955,083,596 - 5,086,321 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554955,083,596 - 5,086,321 (+)NCBIChiLan1.0ChiLan1.0
SMIM24
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2207,864,238 - 7,879,573 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1197,102,939 - 7,111,191 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0192,501,013 - 2,507,693 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1193,451,893 - 3,457,211 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl193,451,893 - 3,457,208 (-)Ensemblpanpan1.1panPan2
SMIM24
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12055,910,182 - 55,914,168 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2055,910,240 - 55,913,985 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2055,634,661 - 55,638,657 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02056,569,185 - 56,573,169 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2056,569,252 - 56,572,986 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12055,625,089 - 55,629,084 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02056,108,544 - 56,112,546 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02056,307,264 - 56,311,248 (+)NCBIUU_Cfam_GSD_1.0
Smim24
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118215,859,582 - 215,863,225 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365881,971,904 - 1,973,846 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365881,971,558 - 1,976,191 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMIM24
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1275,178,848 - 75,182,271 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2275,722,137 - 75,725,259 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SMIM24
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.163,239,431 - 3,245,682 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660815,246,578 - 5,253,038 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Smim24
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248285,886,145 - 5,888,872 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248285,886,120 - 5,888,872 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Smim24
44 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:60
Count of miRNA genes:58
Interacting mature miRNAs:60
Transcripts:ENSRNOT00000075038
Prediction methods: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
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat

Markers in Region
RH130627  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.278,313,387 - 8,313,599 (+)MAPPERmRatBN7.2
Rnor_6.0711,182,996 - 11,183,207NCBIRnor6.0
Rnor_5.0711,350,149 - 11,350,360UniSTSRnor5.0
RGSC_v3.479,798,946 - 9,799,157UniSTSRGSC3.4
Celera76,502,842 - 6,503,053UniSTS


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 1
Medium 3 33 33 33 35 26 3
Low 36 19 8 18 8 2 5 65 14 8 2
Below cutoff 6 4 1 4 4 5 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000075038   ⟹   ENSRNOP00000066395
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl711,183,570 - 11,186,130 (-)Ensembl
RefSeq Acc Id: NM_001398619   ⟹   NP_001385548
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr878,964,107 - 8,967,234 (-)NCBI
mRatBN7.278,313,369 - 8,316,498 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001385548 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL89150 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000066395   ⟸   ENSRNOT00000075038
RefSeq Acc Id: NP_001385548   ⟸   NM_001398619
- Peptide Label: precursor
- UniProtKB: A6K880 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0RA54-F1-model_v2 AlphaFold M0RA54 1-118 view protein structure

Transcriptome

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

Promoters
RGD ID:13694981
Promoter ID:EPDNEW_R5496
Type:multiple initiation site
Name:Smim24_1
Description:small integral membrane protein 24
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_6.0711,186,172 - 11,186,232EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2324237 AgrOrtholog
BioCyc Gene G2FUF-35027 BioCyc
Ensembl Genes ENSRNOG00000048878 Ensembl
InterPro PDZK1IP1/SMIM24 UniProtKB/TrEMBL
KEGG Report rno:100366121 UniProtKB/TrEMBL
NCBI Gene 100366121 ENTREZGENE
PANTHER MEMBRANE-ASSOCIATED PROTEIN MAP17 UniProtKB/TrEMBL
  SMALL INTEGRAL MEMBRANE PROTEIN 24 UniProtKB/TrEMBL
Pfam MAP17 UniProtKB/TrEMBL
PhenoGen Smim24 PhenoGen
RatGTEx ENSRNOG00000048878 RatGTEx
UniProt A6K880 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-03-07 Smim24  small integral membrane protein 24  LOC100366121  rCG29408-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-06 LOC100366121  rCG29408-like      Symbol and Name status set to provisional 70820 PROVISIONAL