Human Gene ABCA5 (uc002jig.2)
  Description: Homo sapiens ATP-binding cassette, sub-family A (ABC1), member 5 (ABCA5), transcript variant 2, mRNA.
RefSeq Summary (NM_172232): 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, but neither the substrate nor the function of this gene is known. Alternative splicing of this gene results in several transcript variants; however, not all variants have been fully described. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr17:67,240,576-67,323,323 Size: 82,748 Total Exon Count: 39 Strand: -
Coding Region
   Position: hg19 chr17:67,243,678-67,310,556 Size: 66,879 Coding Exon Count: 38 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:67,240,576-67,323,323)mRNA (may differ from genome)Protein (1642 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ABCA5_HUMAN
DESCRIPTION: RecName: Full=ATP-binding cassette sub-family A member 5;
FUNCTION: May play a role in the processing of autolysosomes (By similarity).
SUBCELLULAR LOCATION: Lysosome membrane; Multi-pass membrane protein. Late endosome membrane; Multi-pass membrane protein. Golgi apparatus membrane; Multi-pass membrane protein (By similarity).
TISSUE SPECIFICITY: Ubiquitously expressed. Highly expressed in testis, skeletal muscle, kidney, liver and placenta.
DEVELOPMENTAL STAGE: Expressed in fetal liver, kidney and brain.
PTM: N-glycosylated (By similarity).
SIMILARITY: Belongs to the ABC transporter superfamily. ABCA family.
SIMILARITY: Contains 2 ABC transporter domains.
SEQUENCE CAUTION: Sequence=BAB71700.1; Type=Erroneous initiation;
WEB RESOURCE: Name=ABCMdb; Note=Database for mutations in ABC proteins; URL="http://abcmutations.hegelab.org/proteinDetails?uniprot_id=Q8WWZ7";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ABCA5
CDC HuGE Published Literature: ABCA5
Positive Disease Associations: Lipoproteins, LDL , Parkinson Disease
Related Studies:
  1. Lipoproteins, LDL
    , , . [PubMed 0]
  2. Parkinson Disease
    , , . [PubMed 0]
  3. Parkinson Disease
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: ABCA5
Diseases sorted by gene-association score: hypertrichosis, congenital generalized, with or without gingival hyperplasia* (350)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 18.03 RPKM in Brain - Cerebellum
Total median expression: 345.02 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -64.20146-0.440 Picture PostScript Text
3' UTR -673.893102-0.217 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR003593 - AAA+_ATPase
IPR026082 - ABC_A
IPR003439 - ABC_transporter-like
IPR017871 - ABC_transporter_CS

Pfam Domains:
PF00005 - ABC transporter
PF12698 - ABC-2 family transporter protein

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases
53795 - PEP carboxykinase-like

ModBase Predicted Comparative 3D Structure on Q8WWZ7
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0005319 lipid transporter activity
GO:0005524 ATP binding
GO:0016887 ATPase activity
GO:0042626 ATPase activity, coupled to transmembrane movement of substances

Biological Process:
GO:0006869 lipid transport
GO:0010745 negative regulation of macrophage derived foam cell differentiation
GO:0030301 cholesterol transport
GO:0033344 cholesterol efflux
GO:0034375 high-density lipoprotein particle remodeling
GO:0043691 reverse cholesterol transport
GO:0055085 transmembrane transport

Cellular Component:
GO:0000139 Golgi membrane
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005768 endosome
GO:0005770 late endosome
GO:0005794 Golgi apparatus
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0031902 late endosome membrane
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  LP896083 - Sequence 947 from Patent EP3253886.
AY247065 - Homo sapiens ATP-binding cassette sub-family A member 10 (ABCA10) mRNA, complete cds.
AY028900 - Homo sapiens ATP-binding cassette A10 mRNA, complete cds.
BX647447 - Homo sapiens mRNA; cDNA DKFZp451F117 (from clone DKFZp451F117).
BC146819 - Homo sapiens cDNA clone IMAGE:8860425.
AB067475 - Homo sapiens mRNA for KIAA1888 protein, partial cds.
AY028897 - Homo sapiens ATP-binding cassette A5 mRNA, complete cds.
JD304268 - Sequence 285292 from Patent EP1572962.
AK094416 - Homo sapiens cDNA FLJ37097 fis, clone BRACE2018847, moderately similar to ATP-binding cassette, sub-family A member 8.
AK056533 - Homo sapiens cDNA FLJ31971 fis, clone NT2RP7008137, weakly similar to ATP-BINDING CASSETTE, SUB-FAMILY A, MEMBER 1.
JD349584 - Sequence 330608 from Patent EP1572962.
U66672 - Homo sapiens clone EST90625 mRNA sequence.
BX640746 - Homo sapiens mRNA; cDNA DKFZp686K07118 (from clone DKFZp686K07118).
AK058170 - Homo sapiens cDNA FLJ25441 fis, clone TST08455.
AJ275973 - Homo sapiens mRNA for ATP-binding cassette protein of the (ABCA subfamily).
JD424958 - Sequence 405982 from Patent EP1572962.
BC156256 - Synthetic construct Homo sapiens clone IMAGE:100061705, MGC:190078 ATP-binding cassette, sub-family A (ABC1), member 5 (ABCA5) mRNA, encodes complete protein.
AK122803 - Homo sapiens cDNA FLJ16381 fis, clone TLIVE2006359, weakly similar to Homo sapiens ATP-binding cassette, sub-family A (ABC1), member 8 (ABCA8).
AJ512612 - Homo sapiens mRNA for ABCA5 transporter (ABCA5 gene), V20+16 variant.
AK292592 - Homo sapiens cDNA FLJ77193 partial cds, highly similar to Homo sapiens mRNA for ATP-binding cassette protein of the (ABCA subfamily).
HV555708 - JP 2012000107-A/89: Diagnosis of tumor using novel small RNA as biomarker.
BC054480 - Homo sapiens ATP-binding cassette, sub-family A (ABC1), member 5, mRNA (cDNA clone IMAGE:6620671).
BC070126 - Homo sapiens ATP-binding cassette, sub-family A (ABC1), member 5, mRNA (cDNA clone IMAGE:4724012).
BX648540 - Homo sapiens mRNA; cDNA DKFZp779N2435 (from clone DKFZp779N2435).
BC029426 - Homo sapiens ATP-binding cassette, sub-family A (ABC1), member 5, mRNA (cDNA clone IMAGE:4723522), partial cds.
AK096664 - Homo sapiens cDNA FLJ39345 fis, clone PANCR1000091, weakly similar to ATP-binding cassette, sub-family A member 8.
JD192457 - Sequence 173481 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa02010 - ABC transporters

Reactome (by CSHL, EBI, and GO)

Protein Q8WWZ7 (Reactome details) participates in the following event(s):

R-HSA-8848053 ABCA5 transports CHOL from lysosomal lumen to cytosol
R-HSA-1369062 ABC transporters in lipid homeostasis
R-HSA-382556 ABC-family proteins mediated transport
R-HSA-382551 Transport of small molecules

-  Other Names for This Gene
  Alternate Gene Symbols: ABCA5_HUMAN, KIAA1888, NM_172232, NP_758424, Q8IVJ2, Q8WWZ7, Q96LJ1, Q96MS4, Q96PZ9, Q9NY14
UCSC ID: uc002jig.2
RefSeq Accession: NM_172232
Protein: Q8WWZ7 (aka ABCA5_HUMAN)
CCDS: CCDS11685.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_172232.2
exon count: 39CDS single in 3' UTR: no RNA size: 8177
ORF size: 4929CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 9697.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.