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SMIM11 Gene

protein-coding   GIFtS: 36
GCID: GC21P035748

Small Integral Membrane Protein 11

(Previous names: chromosome 21 open reading frame 51, family with sequence...)
(Previous symbols: C21orf51, FAM165B)
  See related diseases
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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Aliases
Small Integral Membrane Protein 111 2
C21orf511 2 3
FAM165B1 2 3
Family With Sequence Similarity 165, Member B1 2
Chromosome 21 Open Reading Frame 511
Protein FAM165B2

External Ids:    HGNC: 12931   Entrez Gene: 540652   Ensembl: ENSG000002056707   UniProtKB: P585113   

Export aliases for SMIM11 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 SMIM11 Gene:
SMIM11 (small integral membrane protein 11) is a protein-coding gene. Diseases associated with SMIM11 include down syndrome, and cerebritis.


(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_000021.9  NC_018932.2  NT_011512.12  
Regulatory elements:
   Search for regulatory transcription factor binding sites for SMIM11
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSMIM11 promoter sequence
   Search Chromatin IP Primers for SMIM11

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SMIM11


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

Entrez Gene cytogenetic band: 21q22.12   Ensembl cytogenetic band:  21q22.11   HGNC cytogenetic band: 21q22.12

SMIM11 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SMIM11 gene location

GeneLoc information about chromosome 21         GeneLoc Exon Structure

GeneLoc location for GC21P035748:  view genomic region     (about GC identifiers)

Start:
35,747,749 bp from pter      End:
35,780,164 bp from pter
Size:
32,416 bases      Orientation:
plus strand

(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, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: SIM11_HUMAN, P58511 (See protein sequence)
Recommended Name: Small integral membrane protein 11  
Size: 58 amino acids; 6886 Da

Explore the universe of human proteins at neXtProt for SMIM11: NX_P58511

Explore proteomics data for SMIM11 at MOPED


See SMIM11 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_478062.1  
ENSEMBL proteins: 
 ENSP00000382231   ENSP00000382238   ENSP00000382234  

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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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1 InterPro protein domain:
 IPR028023 FAM165

Graphical View of Domain Structure for InterPro Entry P58511

ProtoNet protein and cluster: P58511

UniProtKB/Swiss-Prot: SIM11_HUMAN, P58511
Similarity: Belongs to the SMIM11 family


SMIM11 for domains           About GeneDecksing


(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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     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003674molecular_function ND--
     
SMIM11 for ontologies           About GeneDecksing


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
SIM11_HUMAN, P58511: Membrane; Single-pass membrane protein (Potential)

Gene Ontology (GO): 2 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005575cellular_component ND--
GO:0016021integral component of membrane IEA--

SMIM11 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 SMIM11
Interactions:

    Search GeneGlobe Interaction Network for SMIM11

STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

2 Interacting proteins for SMIM11 (P585113 ENSP000003822314) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
TMBIM4Q9HC243, ENSP000003509654I2D: score=1 STRING: ENSP00000350965
ELAVL1ENSP000003852694STRING: ENSP00000385269
About this table

Gene Ontology (GO): 1 biological process term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0008150biological_process ND--

SMIM11 for ontologies           About GeneDecksing



(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 SMIM11 (SIM11)



(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,
Conferences by KenesGroup, 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 SMIM11 gene: 
NM_058182.4  

Unigene Cluster for SMIM11:

Small integral membrane protein 11
Hs.656195  [show with all ESTs]
Unigene Representative Sequence: BC064410
7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000481710(uc002ytv.2 uc002ytw.2) ENST00000399292(uc002ytu.4)
ENST00000399299 ENST00000489469 ENST00000495363 ENST00000474455 ENST00000399295

miRNA
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Additional mRNA sequence: 

AK057880.1 AY033902.1 AY081143.1 BC015596.2 BC045820.1 BC064410.1 

9 DOTS entries:

DT.307424  DT.410133  DT.99992103  DT.91650577  DT.100747165  DT.121141775  DT.201911  DT.91801777 
DT.97819293 

Selected AceView cDNA sequences (see all 106):

BF447618 AI085659 NM_058182 AI492954 AY033902 BM454999 AI418967 BE463990 
BF057737 T94470 BC064410 AY081144 BC015596 CR615562 AI623244 AI355385 
BM788901 AA306264 BI752276 AA909214 BX108079 AW129104 AI433697 BI857966 

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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SMIM11 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
SMIM11 Expression
About this image


SMIM11 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 4) fully expand
 
 Brain (Nervous System)    fully expand to see all 6 entries
         Cerebral Cortex
 
 Neural Tube (Nervous System)    fully expand to see all 2 entries
         Telencephalon
 
 Gut Tube (Gastrointestinal Tract)
         Foregut
 
 Thyroid (Endocrine System)
SMIM11 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

SMIM11 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.656195

UniProtKB/Swiss-Prot: SIM11_HUMAN, P58511
Tissue specificity: Expressed in heart, spleen, liver, stomach, muscle, lung, testis, skin, PBL and bone marrow

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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SMIM11

(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 chordates.

Orthologs for SMIM11 gene from Selected species (see all 6)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Smim115 family with sequence similarity 165, member B   --   16 (53.55 cM) 92301286 
lizard
(Anolis carolinensis)
Reptilia SMIM116
small integral membrane protein 11
74(a)
1 ↔ 1
3(142513875-142514036)


ENSEMBL Gene Tree for SMIM11 (if available)
TreeFam Gene Tree for SMIM11 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for SMIM11 gene
1 SIMAP similar gene for SMIM11 using alignment to 1 protein entry:     SIM11_HUMAN:
SMIM11P1

SMIM11 for paralogs           About GeneDecksing



(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 SMIM11 (see all 340)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 21 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs110882801,2
C,F,A,H--35745783(+) CTAACT/GTACTG 1 -- us2k125Minor allele frequency- G:0.12NS EA NA WA CSA 2582
rs1472620871,2
--35745825(+) TCTAGA/TTAGGA 1 -- us2k10--------
rs1999790491,2
--35745883(+) TATGC-/ATTTCCAC 1 -- us2k10--------
rs1408368741,2
--35745906(+) CTGCTC/TAAGCC 1 -- us2k10--------
rs733557881,2
C,F--35745994(+) GTCAAT/ACCTTA 1 -- us2k16Minor allele frequency- A:0.17WA CSA EA 246
rs1497062691,2
--35746056(+) AAAATC/TGAGGT 1 -- us2k10--------
rs792446981,2
F--35746057(+) AAATCG/AAGGTT 1 -- us2k11Minor allele frequency- A:0.03NA 120
rs1158623261,2
C,F--35746072(+) TGGCCG/AGGTGC 1 -- us2k11Minor allele frequency- A:0.04WA 118
rs1817741441,2
C--35746218(+) GGTGGG/TGGGTG 1 -- us2k10--------
rs1864321831,2
--35746328(+) CTTGGC/TGACTG 1 -- us2k10--------

HapMap Linkage Disequilibrium report for SMIM11 (35747749 - 35780164 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for SMIM11: --
Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing SMIM11
DNA2.0 Custom Variant and Variant Library Synthesis for SMIM11

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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3 diseases for SMIM11:    
About MalaCards
down syndrome    cerebritis    thyroiditis


SMIM11 for disorders           About GeneDecksing


Export disorders for SMIM11 gene to outside databases

(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 SMIM11 gene, integrated from 10 sources (see all 11):
(articles sorted by number of sources associating them with SMIM11)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  2. Annotation of human chromosome 21 for relevance to Down syndrome: gene structure and expression analysis. (PubMed id 12036298)1, 2 Gardiner K.... Davisson M. (Genomics 2002)
  3. From PREDs and open reading frames to cDNA isolation: revisiting the human chromosome 21 transcription map. (PubMed id 11707072)1, 2 Reymond A....Antonarakis S.E. (Genomics 2001)
  4. The DNA sequence of human chromosome 21. (PubMed id 10830953)1, 2 Hattori M.... Yaspo M.-L. (Nature 2000)
  5. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
  6. Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (J. Biol. Chem. 2011)
  7. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (Mol. Med. 2010)
  8. Ubiquitin-mediated proteolysis of HuR by heat shock. (PubMed id 19322201)1 Abdelmohsen K....Gorospe M. (EMBO J. 2009)
  9. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
  10. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

(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: 54065 HGNC: 1293 AceView: C21orf51 Ensembl:ENSG00000205670 euGenes: HUgn54065
ECgene: SMIM11 H-InvDB: SMIM11

(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 SMIM11 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 SMIM11 gene:
Search GeneIP for patents involving SMIM11

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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 Browse ESI BIO Cell Lines and PureStem Progenitors for SMIM11
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 Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SMIM11
 inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SMIM11
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Customized transgenic rodents for:
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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