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SMCO4 Gene

protein-coding   GIFtS: 37
GCID: GC11M093212

Single-Pass Membrane Protein With Coiled-Coil Domains 4

(Previous name: chromosome 11 open reading frame 75)
(Previous symbol: C11orf75)
  See related disease
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 3

Aliases
Single-Pass Membrane Protein With Coiled-Coil Domains 41 2     Single-Pass Membrane And Coiled-Coil Domain-Containing Protein 42
C11orf751 2 3 5     UPF0443 Protein C11orf752
FN52 3 5     Protein FN53
Chromosome 11 Open Reading Frame 751     

External Ids:    HGNC: 248101   Entrez Gene: 569352   Ensembl: ENSG000001660027   OMIM: 6094775   UniProtKB: Q9NRQ53   
ORGUL members:         

Export aliases for SMCO4 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 SMCO4 Gene:
SMCO4 (single-pass membrane protein with coiled-coil domains 4) is a protein-coding gene. Diseases associated with SMCO4 include neurofibromatosis.


(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_000011.10  NC_018922.2  NT_033899.9  
Regulatory elements:
   Search for regulatory transcription factor binding sites for SMCO4
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSMCO4 promoter sequence
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SMCO4


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

Entrez Gene cytogenetic band: 11q21   Ensembl cytogenetic band:  11q21   HGNC cytogenetic band: 11q21

SMCO4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SMCO4 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11M093212:  view genomic region     (about GC identifiers)

Start:
93,211,638 bp from pter      End:
93,276,674 bp from pter
Size:
65,037 bases      Orientation:
minus 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, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SMCO4_HUMAN, Q9NRQ5 (See protein sequence)
Recommended Name: Single-pass membrane and coiled-coil domain-containing protein 4  
Size: 59 amino acids; 6738 Da

Explore the universe of human proteins at neXtProt for SMCO4: NX_Q9NRQ5

Explore proteomics data for SMCO4 at MOPED


See SMCO4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_064564.1  
ENSEMBL proteins: 
 ENSP00000431781   ENSP00000298966   ENSP00000433555   ENSP00000432581   ENSP00000435827  

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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:
 IPR027960 DUF4519

Graphical View of Domain Structure for InterPro Entry Q9NRQ5

ProtoNet protein and cluster: Q9NRQ5

UniProtKB/Swiss-Prot: SMCO4_HUMAN, Q9NRQ5
Similarity: Belongs to the SMCO4 family


SMCO4 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--
     
SMCO4 for ontologies           About GeneDecksing


Phenotypes:
     2 GenomeRNAi human phenotypes for SMCO4:
 Increased TP53 protein express  Increased gamma-H2AX phosphory 

Animal Models:
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hsa-mir-193b-3p (MIRT016301), hsa-mir-124-3p (MIRT004895)

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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
SMCO4_HUMAN, Q9NRQ5: 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--

SMCO4 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 SMCO4
Interactions:

    Search GeneGlobe Interaction Network for SMCO4

1 Interacting protein for SMCO4 (Q9NRQ53) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
BNIP3LO602383I2D: score=1 
About this table

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

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

SMCO4 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 SMCO4



(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 SMCO4 gene: 
NM_020179.2  

Unigene Cluster for SMCO4:

Single-pass membrane protein with coiled-coil domains 4
Hs.438064  [show with all ESTs]
Unigene Representative Sequence: BM911813
5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000525141 ENST00000298966(uc001pds.4) ENST00000527149 ENST00000529714
ENST00000526869
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Additional mRNA sequence: 

AF197137.1 BC031564.1 

8 DOTS entries:

DT.98131890  DT.92474815  DT.95273436  DT.95344395  DT.100656641  DT.120713915  DT.91755096  DT.100727163 

Selected AceView cDNA sequences (see all 67):

BG698163 BI091033 BG676605 CR624699 AA384878 AW512036 BQ049161 BM821929 
AA385921 T25513 AA530982 W95754 BC031564 CA395492 AI952281 CD370631 
BF846816 T36056 AA485088 AI815614 BU855610 AV752109 AW129242 BF849191 

GeneLoc Exon Structure

2 Alternative Splicing Database (ASD) splice patterns (SP) for SMCO4    About this scheme

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b · 4c
SP1:                                    
SP2:        -           -               


ECgene alternative splicing isoforms for SMCO4

(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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SMCO4 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
SMCO4 Expression
About this image

SMCO4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

SMCO4 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.438064
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SMCO4

(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 SMCO4 gene from Selected species (see all 10)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia BC0176125 cDNA sequence BC017612   --   9 (4.95 cM) 15505487 
chicken
(Gallus gallus)
Aves C11ORF756
Gallus gallus chromosome 1 open reading frame, hum...
95(a)
1 ↔ 1
1(185135723-185164284) ENSGALG00000026639
lizard
(Anolis carolinensis)
Reptilia SMCO46
single-pass membrane protein with coiled-coil doma...
95(a)
1 ↔ 1
3(196298668-196298861)
African clawed frog
(Xenopus laevis)
Amphibia AW634164.12   -- 83.73(n)    AW634164.1 
zebrafish
(Danio rerio)
Actinopterygii SMCO46
single-pass membrane protein with coiled-coil doma...
81(a)
1 ↔ 1
15(39764144-39771859) ENSDARG00000097824


ENSEMBL Gene Tree for SMCO4 (if available)
TreeFam Gene Tree for SMCO4 (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 SMCO4 (see all 1373)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 11 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1148907591,2
--93211351(+) ATACCG/AAGTTG 1 -- int11Minor allele frequency- A:0.01WA 118
rs2019901701,2
--93211446(+) TACCC-/TTTTTCT 1 -- int10--------
rs1421730961,2
C--93211475(+) ATTAT-/CGGTCA 1 -- int10--------
rs1909320671,2
--93211476(+) TTATCA/GGTCAA 1 -- int10--------
rs800237521,2
F--93211523(+) AGTGCT/CGGGGA 1 -- int11Minor allele frequency- C:0.03EA 120
rs1168788671,2
C,F--93211736(+) CCCTTT/CGGAGA 1 -- ut311Minor allele frequency- C:0.05EA 120
rs73651,2
C,F,A,H--93211764(+) AAAGAG/AGCATG 1 -- ut31 ese316Minor allele frequency- A:0.36MN NS EA NA WA CSA 1153
rs1813781091,2
--93211847(+) GTGGAA/GCTACT 1 -- ut310--------
rs585259711,2
C--93211880(+) ACACA-/CACA  
        
TGCGC
1 -- ut311Minor allele frequency- CACA:0.00NA 2
rs1129430701,2
C--93211880(+) AGAAG-/CACACA
        
CACAC
1 -- cds11Minor allele frequency- CACACA:0.50CSA 2

HapMap Linkage Disequilibrium report for SMCO4 (93211638 - 93276674 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for SMCO4: --
Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing SMCO4
DNA2.0 Custom Variant and Variant Library Synthesis for SMCO4

(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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OMIM gene information: 609477    OMIM disorders: --

1 disease for SMCO4:    
About MalaCards
neurofibromatosis


SMCO4 for disorders           About GeneDecksing


Export disorders for SMCO4 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 SMCO4 gene integrated from 10 sources:
(articles sorted by number of sources associating them with SMCO4)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Characterization of the Fugu rubripes NLK and FN5 genes flanking the NF1 (Neurofibromatosis type 1) gene in the 5' direction and mapping of the human counterparts. (PubMed id 10863097)1, 2, 3 Kehrer-Sawatzki H....Krone W. (Gene 2000)
  2. 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)
  3. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (Genomics 2007)
  4. Human chromosome 11 DNA sequence and analysis including novel gene identification. (PubMed id 16554811)2 Taylor T.D....Sakaki Y. (Nature 2006)
  5. 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: 56935 HGNC: 24810 AceView: FN5 Ensembl:ENSG00000166002 euGenes: HUgn56935
ECgene: SMCO4 H-InvDB: SMCO4

(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 SMCO4 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 SMCO4 gene:
Search GeneIP for patents involving SMCO4

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 ELISAs at Cloud-Clone Corp.
 Browse CLIAs at Cloud-Clone Corp.



 Browse ESI BIO Cell Lines and PureStem Progenitors for SMCO4
 Gene Synthesis
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 Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SMCO4
 SwitchGear 3'UTR luciferase reporter plasmids for SMCO4
 SwitchGear Promoter luciferase reporter plasmids for SMCO4
 Search ThermoFisher Antibodies for SMCO4
 Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SMCO4
 inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SMCO4
 inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for SMCO4
 LSBio Antibodies in human, mouse, rat for SMCO4
Customized transgenic rodents for:
 Humanization
 Biomarker expression
 Off-target effect monitoring
 Translational medicine
 Tissue-specific gene expresssion
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 Browse compounds at ApexBio
       
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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