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SMIM17 Gene

protein-coding   GIFtS: 23
GCID: GC19P057154

Small Integral Membrane Protein 17

  Search for SMIM17
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 4

Aliases
Small Integral Membrane Protein 171 2

External Ids:    HGNC: 271141   Entrez Gene: 1476702   Ensembl: ENSG000002681827   UniProtKB: P0DL123   
ORGUL members:    fRNAdb10:FR154164      
H-InvDB12:HIT000020054    
NCBI13:AK095199    
NONCODE14:n383563    

Export aliases for SMIM17 gene to outside databases


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for SMIM17 Gene:
SMIM17 (small integral membrane protein 17) is a protein-coding gene.

fRNAdb sequence ontology for SMIM17:
ncRNA - An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000019.10  NT_011109.17  NC_018930.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for SMIM17
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for SMIM17

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SMIM17


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19q13.43   Ensembl cytogenetic band:  19q13.43   HGNC cytogenetic band: 19q13.43

SMIM17 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SMIM17 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P057154:  view genomic region     (about GC identifiers)

Start:
57,154,513 bp from pter      End:
57,168,614 bp from pter
Size:
14,102 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for SMIM17

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SIM17_HUMAN, P0DL12 (See protein sequence)
Recommended Name: Small integral membrane protein 17  
Size: 118 amino acids; 13332 Da

Explore the universe of human proteins at neXtProt for SMIM17: NX_P0DL12

REFSEQ proteins: NP_001180557.1  
ENSEMBL proteins: 
 ENSP00000471126   ENSP00000472019  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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ProtoNet protein and cluster: P0DL12


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Animal Models:
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
SIM17_HUMAN, P0DL12: Membrane; Single-pass membrane protein (Potential)

Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0016021integral component of membrane IEA--

SMIM17 for ontologies           About GeneDecksing


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SMIM17
Interactions:

    Search GeneGlobe Interaction Network for SMIM17

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for SMIM17 (SIM17)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for SMIM17 gene: 
NM_001193628.1  

Unigene Cluster for SMIM17:

Small integral membrane protein 17
Hs.336588  [show with all ESTs]
Unigene Representative Sequence: NM_001193628
2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000598409 ENST00000600547
miRNA
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Additional mRNA sequence: AK095199.1 

2 DOTS entries:

DT.99999679  DT.91687178 

10 AceView cDNA sequences:

AL539783 AA332991 AK095199 BX424362 BI604137 BI753827 BG910569 BG716415 
BX452251 AL568046 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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SMIM17 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
SMIM17 Expression
About this image

SMIM17 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.336588
    Custom PCR Arrays for SMIM17
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In Situ
Assay Products:
 

 
Search Advanced Cell Diagnostics for RNAscope RNA in situ hybridization assays for SMIM17

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of human and mouse.

Orthologs for SMIM17 gene from Selected species (see all 4)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Smim175
Gm165321
predicted gene, 165321, 5 86.54(n)1
89.91(a)1
  7 (3.71 cM)5
1000424501  NM_001134752.11  NP_001128224.11 
 63987155 


ENSEMBL Gene Tree for SMIM17 (if available)
TreeFam Gene Tree for SMIM17 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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  --

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for SMIM17 (see all 394)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 19 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs81114571,2
C,F--57152565(+) CACCTG/CGTCTC 1 -- us2k11Minor allele frequency- C:0.03WA 118
rs1166188371,2
C,F--57152600(+) AGGAGG/ATGATG 1 -- us2k11Minor allele frequency- A:0.04WA 118
rs1168279741,2
C,F--57152693(+) TCATCT/GTCTAA 1 -- us2k11Minor allele frequency- G:0.03WA 118
rs1850926281,2
--57152701(+) TAAACA/CTAGAA 1 -- us2k10--------
rs1904269751,2
--57152702(+) AAACAG/TAGAAA 1 -- us2k10--------
rs602637581,2
C,F--57152752(+) AAACTC/TGTAGG 1 -- us2k13Minor allele frequency- T:0.12WA 122
rs1458620931,2
--57152802(+) CCTTTC/GTACAA 1 -- us2k10--------
rs1820095481,2
C--57152877(+) TTGGGC/TTGTTG 1 -- us2k10--------
rs726291551,2
C,F--57152954(+) TTTTTG/TTTTTT 1 -- us2k12Minor allele frequency- T:0.04NA EA 240
rs2010449481,2
--57152954(+) TTTTT-/GTTTTT 1 -- us2k10--------

HapMap Linkage Disequilibrium report for SMIM17 (57154513 - 57168614 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for SMIM17: --
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing SMIM17
DNA2.0 Custom Variant and Variant Library Synthesis for SMIM17

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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  --

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for SMIM17 gene integrated from 10 sources:
(articles sorted by number of sources associating them with SMIM17)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  2. Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. (PubMed id 21145461)1 Bennett E.J....Harper J.W. (Cell 2010)
  3. The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)2 Grimwood J.... Lucas S.M. (Nature 2004)
  4. (PubMed id 17451645)10 
  5. (PubMed id 15103394)10 
  6. (PubMed id 18089548)10 

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 147670 HGNC: 27114 AceView: LOC147670 Ensembl:ENSG00000268182 euGenes: HUgn147670
ECgene: SMIM17 H-InvDB: SMIM17

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for SMIM17 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for SMIM17 gene:
Search GeneIP for patents involving SMIM17

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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