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TM6SF1 Gene

protein-coding   GIFtS: 45
GCID: GC15P083776

Transmembrane 6 Superfamily Member 1

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(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
Transmembrane 6 Superfamily Member 11 2

External Ids:    HGNC: 118601   Entrez Gene: 533462   Ensembl: ENSG000001364047   OMIM: 6065625   UniProtKB: Q9BZW53   

Export aliases for TM6SF1 gene to outside databases

Previous GC identifers: GC15P079702 GC15P076809 GC15P081354 GC15P081496 GC15P081567 GC15P060039


(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 TM6SF1 Gene:
TM6SF1 (transmembrane 6 superfamily member 1) is a protein-coding gene. An important paralog of this gene is TM6SF2.


(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 at NCBI GenBank:
NC_000015.9  NT_010194.18  NC_018926.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the TM6SF1 gene promoter:
         Nkx3-1   Nkx3-1 v4   AML1a   Pax-2a   Nkx3-1 v1   C/EBPalpha   c-Ets-1   Nkx3-1 v2   Pax-2b   Nkx3-1 v3   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTM6SF1 promoter sequence
   Search Chromatin IP Primers for TM6SF1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TM6SF1


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

Entrez Gene cytogenetic band: 15q24-q26   Ensembl cytogenetic band:  15q25.2   HGNC cytogenetic band: 15q24-q26

TM6SF1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TM6SF1 gene location

GeneLoc information about chromosome 15         GeneLoc Exon Structure

GeneLoc location for GC15P083776:  view genomic region     (about GC identifiers)

Start:
83,776,159 bp from pter      End:
83,813,606 bp from pter
Size:
37,448 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: TM6S1_HUMAN, Q9BZW5 (See protein sequence)
Recommended Name: Transmembrane 6 superfamily member 1  
Size: 370 amino acids; 41636 Da
Secondary accessions: A8K7T5 H3BU56 Q4U0U5
Alternative splicing: 2 isoforms:  Q9BZW5-1   Q9BZW5-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for TM6SF1: NX_Q9BZW5

Explore proteomics data for TM6SF1 at MOPED


See TM6SF1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts): 
NP_001138375.1  NP_075379.2  

ENSEMBL proteins: 
 ENSP00000317000   ENSP00000368700   ENSP00000368693   ENSP00000258909   ENSP00000457477  
 ENSP00000454275   ENSP00000454416   ENSP00000368696  

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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:
 IPR016964 Transmembrane_6/97

Graphical View of Domain Structure for InterPro Entry Q9BZW5

ProtoNet protein and cluster: Q9BZW5

UniProtKB/Swiss-Prot: TM6S1_HUMAN, Q9BZW5
Similarity: Belongs to the TM6SF family


Find genes that share domains with TM6SF1           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, 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--
     
Find genes that share ontologies with TM6SF1           About GenesLikeMe


Phenotypes:
     1 GenomeRNAi human phenotype for TM6SF1:
 Decreased viability with cispl 

Animal Models:
   genOway: Develop your customized and physiologically relevant rodent model for TM6SF1

miRNA
Products:
    
miRTarBase miRNAs that target TM6SF1:
hsa-mir-155-5p (MIRT001803), kshv-mir-k12-11-3p (MIRT002349)

Block miRNA regulation of human, mouse, rat TM6SF1 using miScript Target Protectors
1 qRT-PCR Assays for microRNA that regulate TM6SF1:
hsa-miR-590-3p
SwitchGear 3'UTR luciferase reporter plasmidTM6SF1 3' UTR sequence
Inhib. RNA
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Predesigned siRNA for gene silencing in human, mouse, rat TM6SF1

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Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TM6SF1


(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
TM6S1_HUMAN, Q9BZW5: Membrane; Multi-pass membrane protein (Potential)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
plasma membrane3
cytoskeleton1
endoplasmic reticulum1

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

GO IDQualified GO termEvidencePubMed IDs
GO:0016020membrane ----
GO:0016021integral component of membrane IEA--

Find genes that share ontologies with TM6SF1           About GenesLikeMe


(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 TM6SF1
Interactions:

    Search GeneGlobe Interaction Network for TM6SF1

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

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

Find genes that share ontologies with TM6SF1           About GenesLikeMe



(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 TM6SF1 (TM6S1)



(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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for TM6SF1 gene (2 alternative transcripts): 
NM_001144903.1  NM_023003.3  

Unigene Cluster for TM6SF1:

Transmembrane 6 superfamily member 1
Hs.513094  [show with all ESTs]
Unigene Representative Sequence: NM_023003
9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000322019(uc002bjp.3 uc010bmq.3) ENST00000379390(uc002bjq.3 uc010bmr.3)
ENST00000379384 ENST00000258909 ENST00000565774 ENST00000564988 ENST00000565982
ENST00000561551 ENST00000379386(uc002bjr.3)
miRNA
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1 qRT-PCR Assays for microRNA that regulate TM6SF1:
hsa-miR-590-3p
SwitchGear 3'UTR luciferase reporter plasmidTM6SF1 3' UTR sequence
Inhib. RNA
Products:
     
OriGene RNAi products in human, mouse, rat for TM6SF1
Predesigned siRNA for gene silencing in human, mouse, rat TM6SF1
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Primer
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OriGene qPCR primer pairs and template standards for TM6SF1
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  QuantiTect SYBR Green Assays in human, mouse, rat TM6SF1
  QuantiFast Probe-based Assays in human, mouse, rat TM6SF1

Additional mRNA sequence: 

AF255922.1 AK223246.1 AK292100.1 AK295568.1 BC032007.1 BC063487.1 DQ021909.1 

10 DOTS entries:

DT.446361  DT.97783410  DT.100746752  DT.99972920  DT.91721795  DT.121066672  DT.92420775  DT.95165333 
DT.95165335  DT.102822831 

Selected AceView cDNA sequences (see all 50):

AI215617 AI699582 BC032007 BC063487 Z40201 BP342067 F07097 AL711450 
BI021090 F03377 F09990 F04558 BG485442 AI863613 F04949 Z40771 
AL559396 AW467042 BG677723 BG570659 F07708 BI823388 BI600911 Z44242 

GeneLoc Exon Structure

4 Alternative Splicing Database (ASD) splice patterns (SP) for TM6SF1    About this scheme

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b
SP1:                          -                       -                                             
SP2:                          -                       -           -     -     -                     
SP3:                          -                       -     -     -     -     -                     
SP4:                                                                                                


ECgene alternative splicing isoforms for TM6SF1

(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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TM6SF1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TTCCTCCTTT
TM6SF1 Expression
About this image


TM6SF1 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
 
 Umbilical Cord (Extraembryonic Tissues)
         Wharton's jelly-derived stem cells
 
 Kidney (Urinary System)
         Renal Vesicle
 
 Blood (Hematopoietic System)
         Granulocytes Peripheral Blood
 
 Dermis (Integumentary System)
TM6SF1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

TM6SF1 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.513094

UniProtKB/Swiss-Prot: TM6S1_HUMAN, Q9BZW5
Tissue specificity: Enhanced expression in spleen, testis and peripheral blood leukocytes

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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TM6SF1

(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 TM6SF1 gene from Selected species (see all 12)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Tm6sf11 , 5 transmembrane 6 superfamily member 11, 5 89.64(n)1
94.32(a)1
  7 (45.71 cM)5
1077691  NM_145375.31  NP_663350.21 
 818590015 
chicken
(Gallus gallus)
Aves TM6SF11 transmembrane 6 superfamily member 1 77.3(n)
80.54(a)
  415462  NM_001277461.1  NP_001264390.1 
lizard
(Anolis carolinensis)
Reptilia TM6SF16
transmembrane 6 superfamily member 1
76(a)
1 ↔ 1
GL343836.1(124156-145668)
African clawed frog
(Xenopus laevis)
Amphibia Xl.24822 Xenopus laevis transcribed sequence with weak similarity more 76.68(n)    BJ068102.1 


ENSEMBL Gene Tree for TM6SF1 (if available)
TreeFam Gene Tree for TM6SF1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for TM6SF1 gene
TM6SF22  
1 SIMAP similar gene for TM6SF1 using alignment to 7 protein entries:     TM6S1_HUMAN (see all proteins):
TM6SF2

Find genes that share paralogs with TM6SF1           About GenesLikeMe



(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 TM6SF1 (see all 512)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 15 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1465731891,2
--83774342(+) GTGTTA/GATGGA 2 -- us2k10--------
rs284360271,2
C,F,H--83774399(+) GAGGAA/GGTGTC 2 -- us2k1 tfbs323Minor allele frequency- G:0.41NS EA NA WA CSA 2350
rs1412817611,2
--83774418(+) GGGAGC/GAAGTA 2 -- us2k10--------
rs1932508691,2
--83774482(+) GACAGA/GTGAGG 2 -- us2k10--------
rs563918271,2
C,F--83774555(+) CAGAGC/TTGGAG 2 -- us2k110Minor allele frequency- T:0.39WA NA CSA EA 370
rs776911321,2
F--83774623(+) GTGGCC/TCTGGA 2 -- us2k12Minor allele frequency- T:0.11NA 122
rs1422855191,2
--83774712(+) GCTCAC/GACCTG 2 -- us2k10--------
rs1512360391,2
C--83774783(+) CAGCTC/TGGGCA 2 -- us2k10--------
rs1406118351,2
--83774824(+) TGGTGC/TGAGAC 2 -- us2k10--------
rs1504807861,2
--83774875(+) CTTGGC/TGTGGG 2 -- us2k10--------

HapMap Linkage Disequilibrium report for TM6SF1 (83776159 - 83813606 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for TM6SF1: --
Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing TM6SF1
DNA2.0 Custom Variant and Variant Library Synthesis for TM6SF1

(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: 606562    OMIM disorders: --


Find genes that share disorders with TM6SF1           About GenesLikeMe


Export disorders for TM6SF1 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 TM6SF1 gene integrated from 10 sources:
(articles sorted by number of sources associating them with TM6SF1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Cloning of the novel gene TM6SF1 reveals conservation of clusters of paralogous genes between human chromosomes 15q24-q26 and 19p13.3- p12. (PubMed id 11124529)1, 2, 3 Carim-Todd L.... Sumoy L. (Cytogenet. Cell Genet. 2000)
  2. Analysis of the DNA sequence and duplication history of human chromosome 15. (PubMed id 16572171)2 Zody M.C....Nusbaum C. (Nature 2006)
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)
  4. 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)
  5. Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. (PubMed id 8125298)1 Maruyama K. and Sugano S. (Gene 1994)

(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: 53346 HGNC: 11860 AceView: TM6SF1 Ensembl:ENSG00000136404 euGenes: HUgn53346
ECgene: TM6SF1 H-InvDB: TM6SF1

(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 TM6SF1 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 TM6SF1 gene:
Search GeneIP for patents involving TM6SF1

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, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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 genOway)
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