Human Gene TAP1 (uc003ocg.3) Description and Page Index
  Description: Homo sapiens transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) (TAP1), mRNA.
RefSeq Summary (NM_000593): 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 intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the MDR/TAP subfamily. Members of the MDR/TAP subfamily are involved in multidrug resistance. The protein encoded by this gene is involved in the pumping of degraded cytosolic peptides across the endoplasmic reticulum into the membrane-bound compartment where class I molecules assemble. Mutations in this gene may be associated with ankylosing spondylitis, insulin-dependent diabetes mellitus, and celiac disease. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2014].
Transcript (Including UTRs)
   Position: hg19 chr6:32,812,986-32,821,748 Size: 8,763 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg19 chr6:32,813,356-32,821,593 Size: 8,238 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:32,812,986-32,821,748)mRNA (may differ from genome)Protein (808 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
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H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: TAP1_HUMAN
DESCRIPTION: RecName: Full=Antigen peptide transporter 1; Short=APT1; AltName: Full=ATP-binding cassette sub-family B member 2; AltName: Full=Peptide supply factor 1; AltName: Full=Peptide transporter PSF1; Short=PSF-1; AltName: Full=Peptide transporter TAP1; AltName: Full=Peptide transporter involved in antigen processing 1; AltName: Full=Really interesting new gene 4 protein;
FUNCTION: Involved in the transport of antigens from the cytoplasm to the endoplasmic reticulum for association with MHC class I molecules. Also acts as a molecular scaffold for the final stage of MHC class I folding, namely the binding of peptide. Nascent MHC class I molecules associate with TAP via tapasin. Inhibited by the covalent attachment of herpes simplex virus ICP47 protein, which blocks the peptide-binding site of TAP. Inhibited by human cytomegalovirus US6 glycoprotein, which binds to the lumenal side of the TAP complex and inhibits peptide translocation by specifically blocking ATP-binding to TAP1 and prevents the conformational rearrangement of TAP induced by peptide binding. Inhibited by human adenovirus E3-19K glycoprotein, which binds the TAP complex and acts as a tapasin inhibitor, preventing MHC class I/TAP association. Expression of TAP1 is down-regulated by human Epstein-Barr virus vIL-10 protein, thereby affecting the transport of peptides into the endoplasmic reticulum and subsequent peptide loading by MHC class I molecules.
SUBUNIT: Heterodimer of TAP1 and TAP2. Interacts with Epstein-Barr virus BNLF2a. Interacts with PSMB5 and PSMB8.
INTERACTION: P27797:CALR; NbExp=2; IntAct=EBI-747259, EBI-1049597; P07237:P4HB; NbExp=4; IntAct=EBI-747259, EBI-395883; P30101:PDIA3; NbExp=4; IntAct=EBI-747259, EBI-979862; Q03519:TAP2; NbExp=6; IntAct=EBI-747259, EBI-780781; O15533:TAPBP; NbExp=7; IntAct=EBI-747259, EBI-874801;
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Multi-pass membrane protein. Note=The transmembrane segments seem to form a pore in the membrane.
INDUCTION: By IFNG/IFN-gamma.
DOMAIN: The peptide-binding site is shared between the cytoplasmic loops of TAP1 and TAP2.
POLYMORPHISM: There are five common alleles; TAP1*01:01 (PSF1A), TAP1*02:01 (PSF1B), TAP1*03:01 (PSF1C), TAP1*01:04 and TAP1*x. The sequence of TAP1*01:01 is shown here.
DISEASE: Defects in TAP1 are a cause of bare lymphocyte syndrome type 1 (BLS1) [MIM:604571]; also called HLA class I deficiency. BLS1 is a class I antigen deficiency that is not accompanied by particular pathologic manifestations during the first years of life. Systemic infections have not been described. Chronic bacterial infections, often beginning in the first decade of life, are restricted to the respiratory tract.
SIMILARITY: Belongs to the ABC transporter superfamily. ABCB family. MHC peptide exporter (TC 3.A.1.209) subfamily.
SIMILARITY: Contains 1 ABC transmembrane type-1 domain.
SIMILARITY: Contains 1 ABC transporter domain.
CAUTION: It is uncertain whether Met-1 or Met-61 is the initiator.
SEQUENCE CAUTION: Sequence=CAA47025.1; Type=Erroneous initiation; Sequence=CAA60785.1; Type=Erroneous initiation;
WEB RESOURCE: Name=TAP1base; Note=TAP1 mutation db; URL="http://bioinf.uta.fi/TAP1base/";
WEB RESOURCE: Name=ABCMdb; Note=Database for mutations in ABC proteins; URL="http://abcmutations.hegelab.org/proteinDetails?uniprot_id=Q03518";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TAP1
CDC HuGE Published Literature: TAP1
Positive Disease Associations: asthma , cervical cancer , cystic fibrosis , Diabetes Mellitus, Type 1 , glaucoma, primary open-angle , Graves' disease , inflammatory urogenital disease , psoriasis , recurrent respiratory papillomatosis , Reiter's syndrome , urinary calculus
Related Studies:
  1. asthma
    Hang, L. W. et al. 2003, TAP1 gene AccI polymorphism is associated with atopic bronchial asthma., Journal of clinical laboratory analysis. 2003 ;17(2):57-60. [PubMed 12640628]
    The results show that the AccI polymorphism may be an indicator for atopic bronchial asthma.
  2. cervical cancer
    Gostout BS 2003, , Gynecologic oncology. 2003 Mar;88(3):326-32. [PubMed 12648582]
    We demonstrated a significant association between immune response genes and the risk of cervical cancer. Our data create a compelling argument for a gene or a cluster of genes in the HLA region of chromosome 6 that regulates host immune responses to human papillomavirus infection in a manner that results in inherited susceptibility or resistance to the transforming properties of oncogenic papillomaviruses.
  3. cystic fibrosis
    Ozbas-Gerceker, F. et al. 2002, Analysis of the modifying effects of TAP 1/2 genes on cystic fibrosis phenotype., The Turkish journal of pediatrics. 2002 Apr-Jun;44(2):91-7. [PubMed 12026214]
    We demonstrated that TAP genes might have modifying effects on the CF phenotype.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: TAP1
Diseases sorted by gene-association score: bare lymphocyte syndrome, type i* (654), immunodeficiency by defective expression of hla class 1* (433), herpes simplex (13), orbital melanoma (12), spondylitis (12), hereditary choroidal atrophy (8), cleft soft palate (7), choroidal sclerosis (7), partial central choroid dystrophy (7), branchiootorenal syndrome (5), idiopathic bronchiectasis (5)
* = 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: 118.93 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 900.97 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 -47.90155-0.309 Picture PostScript Text
3' UTR -99.70370-0.269 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
IPR013305 - ABC_B2
IPR003439 - ABC_transporter-like
IPR017871 - ABC_transporter_CS
IPR017940 - ABC_transporter_type1
IPR001140 - ABC_transptr_TM_dom
IPR011527 - ABC_transptrTM_dom_typ1
IPR005293 - Ag_transporter2

Pfam Domains:
PF00005 - ABC transporter
PF00664 - ABC transporter transmembrane 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

1JJ7
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q03518
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-  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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0015433 peptide antigen-transporting ATPase activity
GO:0016887 ATPase activity
GO:0023029 MHC class Ib protein binding
GO:0042287 MHC protein binding
GO:0042288 MHC class I protein binding
GO:0042605 peptide antigen binding
GO:0042626 ATPase activity, coupled to transmembrane movement of substances
GO:0042803 protein homodimerization activity
GO:0043531 ADP binding
GO:0046978 TAP1 binding
GO:0046979 TAP2 binding
GO:1904680 peptide transmembrane transporter activity

Biological Process:
GO:0002250 adaptive immune response
GO:0002376 immune system process
GO:0002474 antigen processing and presentation of peptide antigen via MHC class I
GO:0002479 antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent
GO:0006952 defense response
GO:0015031 protein transport
GO:0015833 peptide transport
GO:0016032 viral process
GO:0019885 antigen processing and presentation of endogenous peptide antigen via MHC class I
GO:0046967 cytosol to ER transport
GO:0055085 transmembrane transport
GO:1990668 vesicle fusion with endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membrane

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005815 microtubule organizing center
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030176 integral component of endoplasmic reticulum membrane
GO:0030670 phagocytic vesicle membrane
GO:0033116 endoplasmic reticulum-Golgi intermediate compartment membrane
GO:0042825 TAP complex


-  Descriptions from all associated GenBank mRNAs
  LF210795 - JP 2014500723-A/18298: Polycomb-Associated Non-Coding RNAs.
AK093980 - Homo sapiens cDNA FLJ36661 fis, clone UTERU2002736.
AX748392 - Sequence 1917 from Patent EP1308459.
BC001587 - Homo sapiens cDNA clone IMAGE:2966578, **** WARNING: chimeric clone ****.
BC001849 - Homo sapiens cDNA clone IMAGE:2966578, **** WARNING: chimeric clone ****.
BC014081 - Homo sapiens transporter 1, ATP-binding cassette, sub-family B (MDR/TAP), mRNA (cDNA clone MGC:20334 IMAGE:4304716), complete cds.
LQ882898 - Sequence 47 from Patent WO2018160841.
BX648013 - Homo sapiens mRNA; cDNA DKFZp686L1859 (from clone DKFZp686L1859).
AK130176 - Homo sapiens cDNA FLJ26666 fis, clone MPG02817, highly similar to ANTIGEN PEPTIDE TRANSPORTER 1.
AK123494 - Homo sapiens cDNA FLJ41500 fis, clone BRTHA2006974, highly similar to ANTIGEN PEPTIDE TRANSPORTER 1.
AK302340 - Homo sapiens cDNA FLJ53627 complete cds, highly similar to Antigen peptide transporter 1.
X57522 - H.sapiens RING4 cDNA.
JD308536 - Sequence 289560 from Patent EP1572962.
LF341243 - JP 2014500723-A/148746: Polycomb-Associated Non-Coding RNAs.
JD160208 - Sequence 141232 from Patent EP1572962.
AH007356 - Homo sapiens Unknown (TAP1) mRNA, TAP1-A allele, complete cds.
AH007357 - Homo sapiens Unknown (TAP1) mRNA, TAP1-C allele, complete cds.
JD257599 - Sequence 238623 from Patent EP1572962.
JD317734 - Sequence 298758 from Patent EP1572962.
JD164761 - Sequence 145785 from Patent EP1572962.
JD537834 - Sequence 518858 from Patent EP1572962.
JD414063 - Sequence 395087 from Patent EP1572962.
AY523970 - Homo sapiens TAP1 (TAP1) mRNA, TAP1*02 variant allele, complete cds.
AY523971 - Homo sapiens TAP1 (TAP1) mRNA, TAP1*020101 allele, complete cds.
KJ892250 - Synthetic construct Homo sapiens clone ccsbBroadEn_01644 TAP1 gene, encodes complete protein.
AB012644 - Homo sapiens TAP1*0102N mRNA for TAP1N, complete cds.
L21204 - Homo sapiens peptide transporter (TAP1) mRNA, complete cds.
L21205 - Homo sapiens peptide transporter (TAP1) mRNA, complete cds.
L21206 - Homo sapiens peptide transporter (TAP1) mRNA, complete cds.
L21207 - Homo sapiens peptide transporter (TAP1) mRNA, complete cds.
L21208 - Homo sapiens peptide transporter (TAP1) mRNA, complete cds.
AK313762 - Homo sapiens cDNA, FLJ94363, highly similar to Homo sapiens transporter 1, ATP-binding cassette, sub-family B(MDR/TAP) (TAP1), mRNA.
DQ896350 - Synthetic construct Homo sapiens clone IMAGE:100010810; FLH193530.01L; RZPDo839H0368D transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) (TAP1) gene, encodes complete protein.
EU176425 - Synthetic construct Homo sapiens clone IMAGE:100006629; FLH264105.01X; RZPDo839E05257D transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) (TAP1) gene, encodes complete protein.
AB528393 - Synthetic construct DNA, clone: pF1KB5751, Homo sapiens TAP1 gene for Antigen peptide transporter 1, without stop codon, in Flexi system.
KU178346 - Homo sapiens transporter 1 ATP-binding cassette sub-family B isoform 1 (TAP1) mRNA, partial cds, alternatively spliced.
KU178347 - Homo sapiens transporter 1 ATP-binding cassette sub-family B isoform 2 (TAP1) mRNA, partial cds, alternatively spliced.
S70266 - TAP1 (TAP1-B) {ATP binding region} [human, Caucasoids, mRNA Partial, 100 nt].
X57521 - H.sapiens partial mRNA Y3 for peptide supply factor gene (PSF).
LF341242 - JP 2014500723-A/148745: Polycomb-Associated Non-Coding RNAs.
LF341241 - JP 2014500723-A/148744: Polycomb-Associated Non-Coding RNAs.
LF212706 - JP 2014500723-A/20209: Polycomb-Associated Non-Coding RNAs.
JD494091 - Sequence 475115 from Patent EP1572962.
JD473710 - Sequence 454734 from Patent EP1572962.
LQ927262 - Sequence 39 from Patent WO2018191660.
MA446372 - JP 2018138019-A/18298: Polycomb-Associated Non-Coding RNAs.
MA576820 - JP 2018138019-A/148746: Polycomb-Associated Non-Coding RNAs.
MA576819 - JP 2018138019-A/148745: Polycomb-Associated Non-Coding RNAs.
MA576818 - JP 2018138019-A/148744: Polycomb-Associated Non-Coding RNAs.
MA448283 - JP 2018138019-A/20209: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa02010 - ABC transporters
hsa04612 - Antigen processing and presentation
hsa05340 - Primary immunodeficiency

Reactome (by CSHL, EBI, and GO)

Protein Q03518 (Reactome details) participates in the following event(s):

R-HSA-983142 Formation of peptide loading complex (PLC)
R-HSA-8863914 Transport of SEC22B, TAP and PLC from ER to ERGIC
R-HSA-983161 Dissociation of the Antigenic peptide:MHC:B2M peptide loading complex
R-HSA-8951595 CALR, TAP, TAPBP dissociate from SEC22B:STX4
R-HSA-8863858 SEC22B, CALR, STX4, TAP and TAPBP bind
R-HSA-8951499 Loading of antigenic peptides on to class I MHC
R-HSA-983144 Transport of Antigen peptide in to ER
R-HSA-1236949 Translocation of antigenic peptides back to phagosomes via TAP
R-HSA-983170 Antigen Presentation: Folding, assembly and peptide loading of class I MHC
R-HSA-1236974 ER-Phagosome pathway
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-1236975 Antigen processing-Cross presentation
R-HSA-1280218 Adaptive Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: ABCB2, NM_000593, NP_000584, PSF1, Q03518, Q16149, Q96CP4, RING4, TAP1_HUMAN, Y3
UCSC ID: uc003ocg.3
RefSeq Accession: NM_000593
Protein: Q03518 (aka TAP1_HUMAN)
CCDS: CCDS4758.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_000593.5
exon count: 11CDS single in 3' UTR: no RNA size: 2974
ORF size: 2427CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5006.00frame shift in genome: no % Coverage: 99.26
has start codon: yes stop codon in genome: no # of Alignments: 8
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.