Human Gene RP11-803J6.1 (uc002vkc.2)
  Description: Homo sapiens ATP-binding cassette, sub-family B (MDR/TAP), member 6 (RP11-803J6.1), nuclear gene encoding mitochondrial protein, mRNA.
RefSeq Summary (NM_005689): This gene encodes a member of the ATP-binding cassette (ABC) transporter superfamily. ABC proteins transport various molecules across extra- and intra-cellular membranes. This protein is a member of the heavy metal importer subfamily and plays a role in porphyrin transport. This gene is the molecular basis of the Langereis (Lan) blood group antigen and mutations in this gene underlie familial pseudohyperkalemia and dyschromatosis universalis hereditaria. [provided by RefSeq, Mar 2017].
Transcript (Including UTRs)
   Position: hg19 chr2:220,074,488-220,085,174 Size: 10,687 Total Exon Count: 19 Strand: -
Coding Region
   Position: hg19 chr2:220,074,660-220,083,395 Size: 8,736 Coding Exon Count: 19 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:220,074,488-220,085,174)mRNA (may differ from genome)Protein (842 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHPRDLynxMGIneXtProtOMIM
PubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ABCB6_HUMAN
DESCRIPTION: RecName: Full=ATP-binding cassette sub-family B member 6, mitochondrial; AltName: Full=Mitochondrial ABC transporter 3; Short=Mt-ABC transporter 3; AltName: Full=P-glycoprotein-related protein; AltName: Full=Ubiquitously-expressed mammalian ABC half transporter;
FUNCTION: Binds heme and porphyrins and functions in their ATP- dependent uptake into the mitochondria. Plays a crucial role in heme synthesis.
SUBUNIT: Homodimer.
SUBCELLULAR LOCATION: Cell membrane. Mitochondrion outer membrane; Multi-pass membrane protein. Endoplasmic reticulum. Golgi apparatus.
TISSUE SPECIFICITY: Widely expressed. High expression is detected in the retinal epithelium.
DEVELOPMENTAL STAGE: Highly expressed in fetal liver.
INDUCTION: Up-regulated by cellular porphyrins (at protein level).
POLYMORPHISM: Genetic variations in ABCB6 define the Langereis blood group system (LAN) [MIM:111600]. Individuals with Lan(-) blood group lack the Lan antigen on their red blood cells. These individuals may have anti-Lan antibodies in their serum, which can cause transfusion reactions or hemolytic disease of the fetus or newborn. The Lan(-) blood group is only clinically significant in transfusion settings or during pregnancy; otherwise Lan(-) individuals have no clinical features.
DISEASE: Defects in ABCB6 are the cause of microphthalmia, isolated, with coloboma, type 7 (MCOPCB7) [MIM:614497]. A disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues. Ocular abnormalities like opacities of the cornea and lens, scaring of the retina and choroid, cataract and other abnormalities like cataract may also be present. Ocular colobomas are a set of malformations resulting from abnormal morphogenesis of the optic cup and stalk, and the fusion of the fetal fissure (optic fissure).
MISCELLANEOUS: Depletion of Abcb6 by RNAi abrogates heme biosynthesis. Overexpression enhances porphyrin biosynthesis.
SIMILARITY: Belongs to the ABC transporter superfamily. ABCB family. Heavy Metal importer (TC 3.A.1.210) subfamily.
SIMILARITY: Contains 1 ABC transmembrane type-1 domain.
SIMILARITY: Contains 1 ABC transporter domain.
SEQUENCE CAUTION: Sequence=AAG33617.1; Type=Erroneous initiation; Sequence=AAG33618.1; Type=Erroneous initiation; Sequence=AAH43423.1; Type=Miscellaneous discrepancy; Note=Intron retention; Sequence=BAD18782.1; Type=Erroneous termination; Positions=168; Note=Translated as Trp; Sequence=BAD92291.1; Type=Miscellaneous discrepancy; Note=Chimeric cDNA;
WEB RESOURCE: Name=ABCMdb; Note=Database for mutations in ABC proteins; URL="http://abcmutations.hegelab.org/proteinDetails?uniprot_id=Q9NP58";

-  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


+  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: 50.08 RPKM in Testis
Total median expression: 846.19 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 -792.331779-0.445 Picture PostScript Text
3' UTR -48.30172-0.281 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
IPR003439 - ABC_transporter-like
IPR017871 - ABC_transporter_CS
IPR017940 - ABC_transporter_type1
IPR001140 - ABC_transptr_TM_dom
IPR011527 - ABC_transptrTM_dom_typ1

Pfam Domains:
PF00005 - ABC transporter
PF00664 - ABC transporter transmembrane region
PF16185 - Mitochondrial ABC-transporter N-terminal five TM region

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases
53795 - PEP carboxykinase-like
90123 - Multidrug resistance ABC transporter MsbA, N-terminal domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3NH6 - X-ray MuPIT 3NH9 - X-ray MuPIT 3NHA - X-ray MuPIT 3NHB - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9NP58
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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 orthologGenome BrowserGenome BrowserGenome BrowserNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsemblFlyBase  
 Protein SequenceProtein SequenceProtein Sequence  
 AlignmentAlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0005524 ATP binding
GO:0015232 heme transporter activity
GO:0015439 heme-transporting ATPase activity
GO:0015562 efflux transmembrane transporter activity
GO:0016887 ATPase activity
GO:0020037 heme binding
GO:0042626 ATPase activity, coupled to transmembrane movement of substances

Biological Process:
GO:0006779 porphyrin-containing compound biosynthetic process
GO:0006879 cellular iron ion homeostasis
GO:0007420 brain development
GO:0015886 heme transport
GO:0043588 skin development
GO:0055085 transmembrane transport

Cellular Component:
GO:0000139 Golgi membrane
GO:0005654 nucleoplasm
GO:0005739 mitochondrion
GO:0005740 mitochondrial envelope
GO:0005741 mitochondrial outer membrane
GO:0005768 endosome
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0031307 integral component of mitochondrial outer membrane
GO:0043190 ATP-binding cassette (ABC) transporter complex
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  U66673 - Homo sapiens clone EST45597 mRNA sequence.
BC043423 - Homo sapiens ATP-binding cassette, sub-family B (MDR/TAP), member 6, mRNA (cDNA clone IMAGE:5288180), complete cds.
AF070598 - Homo sapiens clone 24410 ABC transporter mRNA, partial cds.
AK026067 - Homo sapiens cDNA: FLJ22414 fis, clone HRC08477, highly similar to AF070598 Homo sapiens clone 24410 ABC transporter mRNA.
AK172812 - Homo sapiens cDNA FLJ23973 fis, clone HEP18305, highly similar to ATP-binding cassette, sub-family B, member 6, mitochondrial precursor.
AK057026 - Homo sapiens cDNA FLJ32464 fis, clone SKNMC1000251, highly similar to Homo sapiens MT-ABC transporter (MTABC) mRNA.
AF308472 - Homo sapiens ATP-binding cassette half-transporter (PRP) mRNA, complete cds.
BC000559 - Homo sapiens ATP-binding cassette, sub-family B (MDR/TAP), member 6, mRNA (cDNA clone MGC:3021 IMAGE:3162881), complete cds.
AB209054 - Homo sapiens mRNA for ATP-binding cassette, sub-family B, member 6 variant protein.
AJ289233 - Homo sapiens mRNA for ABC transporter umat (ABCB6 gene).
JD326550 - Sequence 307574 from Patent EP1572962.
JD312888 - Sequence 293912 from Patent EP1572962.
AF076775 - Homo sapiens MT-ABC transporter (MTABC) mRNA, complete cds.
KJ904642 - Synthetic construct Homo sapiens clone ccsbBroadEn_14036 ABCB6 gene, encodes complete protein.
DQ891876 - Synthetic construct clone IMAGE:100004506; FLH180836.01X; RZPDo839G07134D ATP-binding cassette, sub-family B (MDR/TAP), member 6 (ABCB6) gene, encodes complete protein.
DQ895063 - Synthetic construct Homo sapiens clone IMAGE:100009523; FLH180832.01L; RZPDo839G07133D ATP-binding cassette, sub-family B (MDR/TAP), member 6 (ABCB6) gene, encodes complete protein.
AK303230 - Homo sapiens cDNA FLJ61508 complete cds, moderately similar to ATP-binding cassette sub-family B member 6, mitochondrial precursor.
CU674272 - Synthetic construct Homo sapiens gateway clone IMAGE:100020508 5' read ABCB6 mRNA.
LP896216 - Sequence 1080 from Patent EP3253886.
JD019642 - Sequence 666 from Patent EP1572962.
JD035454 - Sequence 16478 from Patent EP1572962.
DQ573157 - Homo sapiens piRNA piR-41269, complete sequence.
JD077864 - Sequence 58888 from Patent EP1572962.
JD217108 - Sequence 198132 from Patent EP1572962.
BC021202 - Homo sapiens ATG9 autophagy related 9 homolog A (S. cerevisiae), mRNA (cDNA clone IMAGE:4100336), partial cds.
BC001098 - Homo sapiens ATG9 autophagy related 9 homolog A (S. cerevisiae), mRNA (cDNA clone IMAGE:3508043), partial cds.
AL833865 - Homo sapiens mRNA; cDNA DKFZp434P0426 (from clone DKFZp434P0426).
AK025822 - Homo sapiens cDNA: FLJ22169 fis, clone HRC00632.
BC001206 - Homo sapiens ATG9 autophagy related 9 homolog A (S. cerevisiae), mRNA (cDNA clone IMAGE:3502018), containing frame-shift errors.
BX538192 - Homo sapiens mRNA; cDNA DKFZp686J01204 (from clone DKFZp686J01204); complete cds.
BX537984 - Homo sapiens mRNA; cDNA DKFZp686G18201 (from clone DKFZp686G18201); complete cds.
BC065534 - Homo sapiens ATG9 autophagy related 9 homolog A (S. cerevisiae), mRNA (cDNA clone MGC:70685 IMAGE:5787445), complete cds.
BX538198 - Homo sapiens mRNA; cDNA DKFZp686O20208 (from clone DKFZp686O20208); complete cds.
LF205251 - JP 2014500723-A/12754: Polycomb-Associated Non-Coding RNAs.
AK027448 - Homo sapiens cDNA FLJ14542 fis, clone NT2RM2001504.
AK021732 - Homo sapiens cDNA FLJ11670 fis, clone HEMBA1004725.
AK056595 - Homo sapiens cDNA FLJ32033 fis, clone NTONG2000265, highly similar to Autophagy-related protein 9A.
JD054831 - Sequence 35855 from Patent EP1572962.
JD316777 - Sequence 297801 from Patent EP1572962.
JD261379 - Sequence 242403 from Patent EP1572962.
JD266379 - Sequence 247403 from Patent EP1572962.
JD278056 - Sequence 259080 from Patent EP1572962.
JD177122 - Sequence 158146 from Patent EP1572962.
LF318623 - JP 2014500723-A/126126: Polycomb-Associated Non-Coding RNAs.
JD375846 - Sequence 356870 from Patent EP1572962.
JD282648 - Sequence 263672 from Patent EP1572962.
AK289755 - Homo sapiens cDNA FLJ77748 complete cds.
AK302521 - Homo sapiens cDNA FLJ55634 complete cds, highly similar to Autophagy-related protein 9A.
JD394278 - Sequence 375302 from Patent EP1572962.
JD098272 - Sequence 79296 from Patent EP1572962.
JD058435 - Sequence 39459 from Patent EP1572962.
JD215272 - Sequence 196296 from Patent EP1572962.
JD134950 - Sequence 115974 from Patent EP1572962.
JD192651 - Sequence 173675 from Patent EP1572962.
JD271086 - Sequence 252110 from Patent EP1572962.
JD136827 - Sequence 117851 from Patent EP1572962.
MA440828 - JP 2018138019-A/12754: Polycomb-Associated Non-Coding RNAs.
MA554200 - JP 2018138019-A/126126: Polycomb-Associated Non-Coding RNAs.

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

Reactome (by CSHL, EBI, and GO)

Protein Q9NP58 (Reactome details) participates in the following event(s):

R-HSA-1369065 ABCB6 transports porphyrin from cytosol to mitchondrial matrix
R-HSA-1369007 Mitochondrial ABC transporters
R-HSA-382556 ABC-family proteins mediated transport
R-HSA-382551 Transport of small molecules

-  Other Names for This Gene
  Alternate Gene Symbols: ABCB6, ABCB6_HUMAN, MTABC3, NM_005689, NP_005680, O75542, PRP, Q49A66, Q59GQ5, Q6ZME6, Q96ME8, Q9HAQ6, Q9HAQ7, Q9NP58, UMAT
UCSC ID: uc002vkc.2
RefSeq Accession: NM_005689
Protein: Q9NP58 (aka ABCB6_HUMAN or ABC6_HUMAN)
CCDS: CCDS2436.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_005689.2
exon count: 19CDS single in 3' UTR: no RNA size: 3021
ORF size: 2529CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4337.00frame shift in genome: no % Coverage: 99.90
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.