SMIM38 (small integral membrane protein 38) - Rat Genome Database

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Gene: SMIM38 (small integral membrane protein 38) Homo sapiens
Analyze
Symbol: SMIM38
Name: small integral membrane protein 38
RGD ID: 14394829
HGNC Page HGNC:54074
Description: Predicted to be located in membrane.
Type: protein-coding
RefSeq Status: VALIDATED
RGD Orthologs
Mouse
Rat
Bonobo
Dog
Squirrel
Green Monkey
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381169,155,573 - 69,162,440 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1169,155,478 - 69,162,440 (+)EnsemblGRCh38hg38GRCh38
GRCh371168,923,041 - 68,929,908 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map11q13.3NCBI
CHM1_11168,786,545 - 68,814,232 (+)NCBICHM1_1
T2T-CHM13v2.01169,167,904 - 69,174,769 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
membrane  (IEA)

References
Additional References at PubMed
PMID:16554811   PMID:31537640  


Genomics

Comparative Map Data
SMIM38
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381169,155,573 - 69,162,440 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1169,155,478 - 69,162,440 (+)EnsemblGRCh38hg38GRCh38
GRCh371168,923,041 - 68,929,908 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map11q13.3NCBI
CHM1_11168,786,545 - 68,814,232 (+)NCBICHM1_1
T2T-CHM13v2.01169,167,904 - 69,174,769 (+)NCBIT2T-CHM13v2.0
Smim38
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm397144,759,560 - 144,761,856 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl7144,759,562 - 144,761,856 (-)EnsemblGRCm39 Ensembl
GRCm387145,205,823 - 145,208,119 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl7145,205,825 - 145,208,119 (-)EnsemblGRCm38mm10GRCm38
MGSCv377152,391,723 - 152,394,024 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv367152,392,293 - 152,394,024 (-)NCBIMGSCv36mm8
Celera7144,973,820 - 144,976,121 (-)NCBICelera
Cytogenetic Map7F5NCBI
cM Map788.99NCBI
Smim38
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81209,795,854 - 209,801,269 (-)NCBIGRCr8
mRatBN7.21200,366,561 - 200,371,976 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx1208,742,278 - 208,747,693 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01215,828,593 - 215,834,008 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01208,502,815 - 208,508,230 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01218,369,204 - 218,374,619 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1218,369,204 - 218,374,619 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01225,236,071 - 225,241,739 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41205,652,988 - 205,658,404 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11205,806,440 - 205,811,857 (-)NCBI
Celera1197,921,301 - 197,926,716 (-)NCBICelera
Cytogenetic Map1q42NCBI
SMIM38
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2970,116,978 - 70,123,519 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11171,159,942 - 71,166,475 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01164,246,628 - 64,254,155 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SMIM38
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha1847,513,433 - 47,513,656 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01849,580,794 - 49,581,017 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.11849,026,834 - 49,027,057 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01848,613,243 - 48,613,466 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01849,359,749 - 49,359,972 (-)NCBIUU_Cfam_GSD_1.0
Smim38
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049474,832,344 - 4,836,429 (-)NCBIHiC_Itri_2
SMIM38
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Vero_WHO_p1.0NW_023666038102,697,812 - 102,700,476 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in SMIM38
2 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 11q13.2-13.4(chr11:68031693-71593495)x1 copy number loss See cases [RCV000142138] Chr11:68031693..71593495 [GRCh38]
Chr11:67799160..71304541 [GRCh37]
Chr11:67555736..70982189 [NCBI36]
Chr11:11q13.2-13.4		 likely pathogenic
GRCh38/hg38 11q13.2-13.3(chr11:67217264-69448598)x1 copy number loss See cases [RCV000135609] Chr11:67217264..69448598 [GRCh38]
Chr11:66984735..69263366 [GRCh37]
Chr11:66741311..68972547 [NCBI36]
Chr11:11q13.2-13.3		 likely pathogenic
GRCh38/hg38 11q13.2-13.3(chr11:68205963-69580475)x3 copy number gain See cases [RCV000137992] Chr11:68205963..69580475 [GRCh38]
Chr11:67973430..69395243 [GRCh37]
Chr11:67730006..69104424 [NCBI36]
Chr11:11q13.2-13.3		 likely benign

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

circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 229
Low 10 6 6 140 6 30 15 31
Below cutoff 9 13 13 1 13 3 1 2 3

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000641280
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1169,155,910 - 69,159,740 (+)Ensembl
RefSeq Acc Id: ENST00000641568   ⟹   ENSP00000493332
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1169,155,478 - 69,159,752 (+)Ensembl
RefSeq Acc Id: ENST00000686237   ⟹   ENSP00000509996
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1169,155,935 - 69,162,440 (+)Ensembl
RefSeq Acc Id: ENST00000686937   ⟹   ENSP00000509659
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1169,155,935 - 69,162,440 (+)Ensembl
RefSeq Acc Id: NM_001369201   ⟹   NP_001356130
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381169,155,935 - 69,162,440 (+)NCBI
T2T-CHM13v2.01169,168,266 - 69,174,769 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001394169   ⟹   NP_001381098
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381169,155,573 - 69,162,440 (+)NCBI
T2T-CHM13v2.01169,167,904 - 69,174,769 (+)NCBI
Sequence:
RefSeq Acc Id: NR_161183
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381169,155,935 - 69,162,440 (+)NCBI
T2T-CHM13v2.01169,168,266 - 69,174,769 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001356130 (Get FASTA)   NCBI Sequence Viewer  
  NP_001381098 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein A0A286YFK9 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000493332
  ENSP00000493332.1
  ENSP00000509659.1
  ENSP00000509996
  ENSP00000509996.1
Reference Protein Sequences
RefSeq Acc Id: NP_001356130   ⟸   NM_001369201
- UniProtKB: A0A286YFK9 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: ENSP00000493332   ⟸   ENST00000641568
RefSeq Acc Id: NP_001381098   ⟸   NM_001394169
- UniProtKB: A0A286YFK9 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: ENSP00000509996   ⟸   ENST00000686237
RefSeq Acc Id: ENSP00000509659   ⟸   ENST00000686937

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A286YFK9-F1-model_v2 AlphaFold A0A286YFK9 1-51 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:54074 AgrOrtholog
COSMIC SMIM38 COSMIC
Ensembl Genes ENSG00000284713 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000641568 ENTREZGENE
  ENST00000641568.1 UniProtKB/Swiss-Prot
  ENST00000686237 ENTREZGENE
  ENST00000686237.1 UniProtKB/Swiss-Prot
  ENST00000686937.1 UniProtKB/Swiss-Prot
GTEx ENSG00000284713 GTEx
HGNC ID HGNC:54074 ENTREZGENE
Human Proteome Map SMIM38 Human Proteome Map
NCBI Gene SMIM38 ENTREZGENE
PharmGKB PA166181651 PharmGKB
UniProt A0A286YFK9 ENTREZGENE, UniProtKB/Swiss-Prot