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ABCA6 Gene

protein-coding   GIFtS: 53

GC17M064586
ATP-binding cassette, sub-family A (ABC1), member 6
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
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Aliases
EST155051 1, 2
FLJ43498 2
Descriptions
ABC transporter ABCA6 2
ATP-binding cassette A6 2
ATP-binding cassette, sub-family A (ABC1), member 6 2
ATP-binding cassette, sub-family A, member 6 2
External Ids
HGNC: 361
Entrez Gene: 234602
UniProtKB: Q8N1393
Ensembl: ENSG000001542627
Search outside databases for aliases for ABCA6 gene

Previous GC identifers: GC17M066873 GC17M070035 GC17M067539 GC17M067671

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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EntrezGene summary for ABCA6:
The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding
cassette (ABC) transporters. ABC proteins transport various molecules across extra- and
intracellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP,
MRP, ALD, OABP, GCN20, and White). This encoded protein is a member of the ABC1 subfamily. Members
of the ABC1 subfamily comprise the only major ABC subfamily found exclusively in multicellular
eukaryotes. This gene is clustered among 4 other ABC1 family members on 17q24 and may play a role
in macrophage lipid homeostasis. [provided by RefSeq]

UniProtKB/Swiss-Prot: ABCA6_HUMAN, Q8N139
Function: Probable transporter which may play a role in macrophage lipid homeostasis

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the ABCA6 gene  

Entrez Gene cytogenetic band: 17q24.3   Ensembl cytogenetic band:  17q24.3   HGNC cytogenetic band: 17q21

ABCA6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17M064586:     (about GC identifiers)

Start:
64,586,442 bp from pter
End:
64,649,610 bp from pter
Size:
63,169 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000017.9  NT_010641.15  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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UniProtKB/Swiss-Prot: ABCA6_HUMAN, Q8N139 (See protein sequence)
Recommended Name: ATP-binding cassette sub-family A member 6  
Size: 1617 amino acids; 184286 Da
Subcellular location: Membrane; Multi-pass membrane protein (Potential)
Developmental stage: Expressed in fetal kidney, lung and liver
Sequence caution: Sequence=AAM77557.1; Type=Frameshift; Positions=998, 1000; Sequence=AAM77558.1;
Type=Frameshift; Positions=998, 1000;
Secondary accessions: Q6NSH9 Q8N856 Q8WWZ6
Alternative splicing: 3 isoforms:  Q8N139-1   Q8N139-2   Q8N139-3   

REFSEQ proteins: NP_525023.2  

ENSEMBL proteins: 
ENSP00000284425 


Human Recombinant Proteins 
Browse Drug Discovery Central at Invitrogen for human recombinant proteins
Browse Purified and Recombinant Proteins at Millipore
Browse Human Recombinant Proteins at Sigma-Aldrich  
Browse R&D Systems for human recombinant proteins
Browse recombinant and purified proteins available from Enzo Life Sciences
Recombinant Proteins from Abcam (ABCA6)
Human Recombinant Proteins from Abnova (ABCA6)
                Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

2 Gene Ontology (GO) cellular component terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0016020 membrane IEA--
GO:0016021 integral to membrane IEA--
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Antibodies for ABCA6: 
Browse Antibodies Central at Invitrogen
Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
Sigma-Aldrich Antibodies for ABCA6
Browse R&D Systems for Antibodies
Antibodies from Abcam (ABCA6), each with their AbpromiseSM
Monoclonal and Polyclonal Antibodies from Abnova (ABCA6)
Novus Biologicals Antibodies for ABCA6

Assays for ABCA6: 
Browse Invitrogen for biochemical assays
Browse Kits and Assays available from Millipore
Browse R&D Systems for biochemical assays
Browse biochemical assays available from Enzo Life Sciences

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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3 InterPro domains/families:
 IPR003593 ATPase_AAA+_core
 IPR003439 ABC_transporter-like
 IPR017871 ABC_transporter_CS


   GeneDecks  ABCA6 for the domains selected above  
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Graphical View of Domain Structure for InterPro Entry Q8N139

ProtoNet protein and cluster: Q8N139

UniProtKB/Swiss-Prot: ABCA6_HUMAN, Q8N139
Similarity: Belongs to the ABC transporter family. ABCA subfamily
Similarity: Contains 2 ABC transporter domains

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (ABCA6)
Browse for Gene Knock-down Tools from Millipore
Abnova Chimera RNAi Products for Gene knock-down (ABCA6)
               OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_172346

              Applied Biosystems Silencer® siRNAs for ABCA6

              Sigma-Aldrich siRNA and siRNA Panels for ABCA6  
                     Sigma-Aldrich shRNA for ABCA6  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Clones:Invitrogen Clones for ABCA6
Browse Clones for the Expression of Recombinant Proteins Available from Millipore
              OriGene GFP tagged cDNA clone in CMV expression vector: NM_080284
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_080284
                                 untagged cDNA clone in CMV expression vector: NM_080284 

Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
              OriGene genome-wide validated SYBR primer pairs: NM_080284

UniProtKB/Swiss-Prot: ABCA6_HUMAN, Q8N139
Function: Probable transporter which may play a role in macrophage lipid homeostasis
Induction: Up-regulated during monocyte differentiation into macrophages. Down-regulated by
cholesterol loading of macrophages

Genatlas biochemistry entry for ABCA6:
ATP binding cassette superfamily A,member 6

3 Gene Ontology (GO) molecular function terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0000166 nucleotide binding IEA--
GO:0005524 ATP binding IEA--
GO:0016887 ATPase activity IEA--
About this table

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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1 Kegg Pathway  (Kegg details for ABCA6):
 hsa02010 ABC transporters

   GeneDecks  ABCA6 for the pathways selected above  
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 Gene Network CentralTM Interacting Genes and Proteins Network for  ABCA6 

1 Gene Ontology (GO) biological process term (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0006810 transport IEA--
About this table
(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Browse drugs & compounds from Enzo Life Sciences
Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for ABCA6

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section

Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (ABCA6)
Browse for Gene Knock-down Tools from Millipore
Abnova Chimera RNAi Products for Gene knock-down (ABCA6)
               OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_172346

              Sigma-Aldrich siRNA and siRNA Panels for ABCA6  
                     Sigma-Aldrich shRNA for ABCA6  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Applied Biosystems Silencer® siRNAs: 

NM_080284  

REFSEQ mRNAs for ABCA6 gene: 

NM_080284.2   

Applied Biosystems TaqMan ® Gene Expression Assays: 

NM_080284  

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_080284
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_080284
                                 untagged cDNA clone in CMV expression vector: NM_080284 

Additional cDNA sequence: 

AF373290.1 AK097296.1 AK125487.1 AK308431.1 AY028898.1 BC029852.1 BC070125.1 BC125231.1 
BC125232.1 BX647672.1 CR593055.1 

9 DOTS entries:

DT.92414827  DT.92041769  DT.102835331  DT.95159621  DT.101981440  DT.100779501  DT.75181599  DT.91715365 
DT.91735387 

24/78 AceView cDNA sequences (see all 78 ):

CB163196 BX342947 AK125487 AY028898 CD516271 CR593055 BQ722528 AF373290 
BF589727 NM_080284 NM_172346 BC029852 AI695358 AV763271 BX106954 BQ008043 
BQ185780 BX342946 AW576555 AI476130 AK097296 CD104808 AA703500 AA099357 

highest scoring ESTs for ABCA6:

AI651024 AY028898 BC029852 BI489985 BI767934 BG538229 AA101906 CD000686 CF596886 DA361238 

Unigene Cluster for ABCA6:

ATP-binding cassette, sub-family A (ABC1), member 6
Hs.709514  [show with all ESTs]
Unigene Representative Sequence: BX647672


GeneLoc Exon Structure

1 Ensembl transcript including schematic representation:
ENST00000284425  
(Experimental results according to 1GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
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ABCA6 expression in normal and diseased human tissues

 Applied Biosystems TaqMan ® Gene Expression Assays for ABCA6

1 / 2 / 3

4 probe-sets matching ABCA6 gene


Affymetrix
probe-set
Array  GeneAnnot data GeneNote data GeneTide data
# genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
35389_s_at2, 3 U95-A 1 1.00 1.00 0.99 1.01 U66680 0.60 0.83 0.73 1
35390_at2, 3 U95-A 1 1.00 1.00 0.99 1.00 AI651024 0.80 0.88 0.84 1

217504_at2, 3 U133-A 1 1.00 1.00 -- -- AA099357 0.60 0.83 0.73 1

217504_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
GeneDecks  ABCA6 for binary patterns associated with the probe-sets selected above  
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Data from (Publications) and GNF BioGPS
    About these images
About these images

CGAP SAGE TAG: CTGTGGTCTG

SOURCE GeneReport for Unigene cluster: Hs.709514

Expression variation in blood from EXPOLDB for ABCA6

UniProtKB/Swiss-Prot: ABCA6_HUMAN, Q8N139
Tissue specificity: Widely expressed with higher expression in liver

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section


Orthologs for ABCA6 gene from 5 species
Organism Gene Locus Description Human
Similarity
NCBI accessions
dog
(Canis familiaris)
ABCA61   -- ATP-binding cassette, sub-family A (ABC1), member 6 82.5(n)
75.33(a)
480456  XM_845829.1  XP_850922.1 
chimpanzee
(Pan troglodytes)
ABCA61   -- ATP-binding cassette, sub-family A (ABC1), member 6 98.47(n)
97.95(a)
742817  XM_001146278.1  XP_001146278.1 
cow
(Bos taurus)
ABCA61   -- ATP-binding cassette, sub-family A (ABC1), member 6 78.76(n)
72.56(a)
537351  XM_617513.3  XP_617513.3 
mouse
(Mus musculus)
Abca61, 5 115
ATP-binding cassette, sub-family A (ABC1), member 61, 5 76.48(n)1
67.97(a)1
761841  NM_147218.11  NP_671751.11 
 AA9859775  AF4983615  (see all 13)
rice
(Oryza sativa)
Os.186952   -- Oryza sativa (japonica cultivar-group) cDNA cloneJ more 71.6(n)  AK122145.1 
About this table        Species with no ortholog for ABCA6

ENSEMBL Gene Tree for ABCA6
(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section

Paralogs for ABCA6 gene
ABCA102  ABCA92  ABCA52  ABCA82  

(According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
About This Section


10/264 NCBI SNPs in ABCA6 are shown (see all 264 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 110)
ABGenomic DataTranscription DataAllele Frequencies
SNP IDValidChr 17 posSequenceRecsAA
Chg
TypeMoreRecsAllele
freq
PopTotal
sample
More
------------
rs23021341,2
A,C,F,H,O64593425(+) CACCAT/CTGGGT 1 S/N mis1 ese311Minor allele frequency- C:0.37EU EA WA NA 1066
rs37444891,2
A,C,F,H64649733(-) ACCACG/AGAACA 1 -- ng3112Minor allele frequency- A:0.45EA NA EU WA 2384
rs99166931,2
A,C,F,H64650158(+) AATACA/TTATGA 1 -- ng31 tfbs34Minor allele frequency- T:0.43EU EA WA 412
rs124539141,2
A,C,F,H64650473(+) AACTAC/AAGCCA 1 -- ng318Minor allele frequency- A:0.44EU EA WA 836
rs23022901,2
A,C,F,H64586667(-) AAACTC/TATGTT 1 -- ut31 ese35Minor allele frequency- T:0.49MN EU EA WA 600
rs72125061,2
A,C,F,H64613313(+) GCATAT/CATTAT 1 I/M mis1 ese311Minor allele frequency- C:0.23EU EA WA NA 980
rs49688391,2
A,C,F,H64637435(+) TGTAAC/TGAATA 1 V/I mis112Minor allele frequency- N:0.00EA NA EU WA 1054
rs92825541,2
C,F,H64621428(-) AAGATA/TACCTT 1 N/Y mis116Minor allele frequency- T:0.10MN CSAM EA EU WA NA 1386
rs92825531,2
C,F,H64619957(-) TCTATG/CTTTTT 1 I/M mis117Minor allele frequency- C:0.21MN CSAM EA EU WA NA 1598
rs19903351,2
C,F,H64586292(-) ACCAAC/GTACAA 1 -- ng518Minor allele frequency- G:0.39EA NA EU WA 584
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HapMap Linkage Disequilibrium images for ABCA6 (up to first 250kb)

(in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
About This Section

OMIM: 612504

Human Genome Epidemiology Navigator: ABCA6 (2 documents)

(Possibly Related Articles in Doctor's Guide)
About This Section

  --

(in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
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10/11 PubMed articles for ABCA6 gene (see all 11 ):
(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, and/or H-InvDB)
About This Section

Entrez Gene: 23460 HGNC: 36 AceView: ABCA6 Ensembl:ENSG00000154262 euGenes: HUgn23460
ECgene: ABCA6 H-InvDB: ABCA6
(According to HUGE)
About This Section

  --
(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
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  --
(Available from WIS Yeda, Salk, Tufts)
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  --
(Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
Enzo Life Sciences, and/or Tocris Bioscience)
About This Section



Products for ABCA6:
 TaqMan ® Gene Expression Assays
 TaqMan ® Genotyping Assays
  Free SNP selection tool



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 Millipore Target Screening & Profiling Services


 Predesigned and custom siRNAs for ABCA6 Antibodies for ABCA6
 Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
 Lentivirus-delivered shRNAs for ABCA6 Browse small molecules at Sigma-Aldrich
 "Your Favorite Gene" Pathwaysfeedback


  
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 Search www.enzolifesicences.com for proteins, assays, substrates, inhibitors & antibodies
 Antibodies for ABCA6

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