Human Gene PDCD6IP (ENST00000307296.8_10) from GENCODE V47lift37
  Description: programmed cell death 6 interacting protein, transcript variant 1 (from RefSeq NM_013374.6)
Gencode Transcript: ENST00000307296.8_10
Gencode Gene: ENSG00000170248.15_14
Transcript (Including UTRs)
   Position: hg19 chr3:33,840,122-33,911,195 Size: 71,074 Total Exon Count: 18 Strand: +
Coding Region
   Position: hg19 chr3:33,840,221-33,908,017 Size: 67,797 Coding Exon Count: 18 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:33,840,122-33,911,195)mRNA (may differ from genome)Protein (868 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
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WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PDC6I_HUMAN
DESCRIPTION: RecName: Full=Programmed cell death 6-interacting protein; Short=PDCD6-interacting protein; AltName: Full=ALG-2-interacting protein 1; AltName: Full=Hp95;
FUNCTION: Class E VPS protein involved in concentration and sorting of cargo proteins of the multivesicular body (MVB) for incorporation into intralumenal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome. Binds to the phospholipid lysobisphosphatidic acid (LBPA) which is abundant in MVBs internal membranes. The MVB pathway appears to require the sequential function of ESCRT-O, -I,-II and -III complexes. The ESCRT machinery also functions in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis and enveloped virus budding (HIV-1 and other lentiviruses). Appears to be an adapter for a subset of ESCRT-III proteins, such as CHMP4, to function at distinct membranes. Required for completion of cytokinesis. Involved in HIV-1 virus budding. Can replace TSG101 it its role of supporting HIV-1 release; this function implies the interaction with CHMP4B. May play a role in the regulation of both apoptosis and cell proliferation.
SUBUNIT: Interacts with SH3KBP1. Interacts with PDCD6 and TSG101 in a calcium-dependent manner. Interacts with and SGSM3. Self- associates. Interacts with CHMP4A; the interaction is direct. Interacts with CHMP4B; the interaction is direct. Interacts with CHMP4C; the interaction is direct. Interacts with HIV-1 p6. Interacts with EIAV p9; the interaction has been shown in vitro. Interacts with CEP55; the interaction is direct; CEP55 binds PDCD6IP in a 2:1 stoechiometry. May interact with PDGFRB. Interacts with SH3GL1 and SH3GL2. Interacts with murine leukemia virus Gag polyprotein (via LYPX(n)L motif). Interacts with murine leukemia virus Gag polyprotein (via LYPX(n)L motif).
INTERACTION: P03347:gag (xeno); NbExp=2; IntAct=EBI-310624, EBI-1220741; P69730:gag (xeno); NbExp=2; IntAct=EBI-310624, EBI-1220941; O75340:PDCD6; NbExp=5; IntAct=EBI-310624, EBI-352915;
SUBCELLULAR LOCATION: Cytoplasm, cytosol. Melanosome. Cytoplasm, cytoskeleton, centrosome. Note=Identified by mass spectrometry in melanosome fractions from stage I to stage IV. Colocalized with CEP55 in the midbody during cytokinesis. Colocalized with CEP55 at centrosomes of non-dividing cells.
PTM: May be phosphorylated on tyrosine residues by activated PDGFRB.
SIMILARITY: Contains 1 BRO1 domain.
SEQUENCE CAUTION: Sequence=BAA92092.1; Type=Erroneous initiation;

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: PDCD6IP
Diseases sorted by gene-association score: adult neuronal ceroid lipofuscinosis (9), hiv-1 (4)

-  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: 34.26 RPKM in Nerve - Tibial
Total median expression: 1049.23 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 -38.7099-0.391 Picture PostScript Text
3' UTR -726.203178-0.229 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
IPR025304 - ALIX_V_dom
IPR004328 - BRO1_dom

Pfam Domains:
PF03097 - BRO1-like domain
PF13949 - ALIX V-shaped domain binding to HIV

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2OEV - X-ray MuPIT 2OEW - X-ray MuPIT 2OEX - X-ray MuPIT 2OJQ - X-ray MuPIT 2R02 - X-ray MuPIT 2R03 - X-ray MuPIT 2R05 - X-ray MuPIT 2XS1 - X-ray MuPIT 2XS8 - X-ray MuPIT 2ZNE - X-ray MuPIT 3C3O - X-ray MuPIT 3C3Q - X-ray MuPIT 3C3R - X-ray MuPIT 3E1R - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q8WUM4
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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 orthologNo orthologNo orthologNo orthologNo orthologGenome Browser
Gene DetailsGene Details Gene Details Gene Details
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 RGDEnsembl  SGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0031871 proteinase activated receptor binding
GO:0042803 protein homodimerization activity
GO:0046983 protein dimerization activity
GO:0048306 calcium-dependent protein binding

Biological Process:
GO:0000281 mitotic cytokinesis
GO:0000915 actomyosin contractile ring assembly
GO:0000920 cell separation after cytokinesis
GO:0006915 apoptotic process
GO:0007049 cell cycle
GO:0010824 regulation of centrosome duplication
GO:0015031 protein transport
GO:0016032 viral process
GO:0019058 viral life cycle
GO:0036258 multivesicular body assembly
GO:0039702 viral budding via host ESCRT complex
GO:0045199 maintenance of epithelial cell apical/basal polarity
GO:0046755 viral budding
GO:0051260 protein homooligomerization
GO:0051301 cell division
GO:0070830 bicellular tight junction assembly
GO:0090559 regulation of membrane permeability
GO:0090611 ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway
GO:1903543 positive regulation of exosomal secretion
GO:1903551 regulation of extracellular exosome assembly
GO:1903553 positive regulation of extracellular exosome assembly
GO:0006997 nucleus organization
GO:0007080 mitotic metaphase plate congression
GO:1901673 regulation of mitotic spindle assembly

Cellular Component:
GO:0001772 immunological synapse
GO:0005576 extracellular region
GO:0005737 cytoplasm
GO:0005815 microtubule organizing center
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005923 bicellular tight junction
GO:0005925 focal adhesion
GO:0016020 membrane
GO:0030054 cell junction
GO:0042470 melanosome
GO:0042641 actomyosin
GO:0043209 myelin sheath
GO:0070062 extracellular exosome
GO:0070971 endoplasmic reticulum exit site
GO:0090543 Flemming body
GO:1903561 extracellular vesicle


-  Descriptions from all associated GenBank mRNAs
  KJ892896 - Synthetic construct Homo sapiens clone ccsbBroadEn_02290 PDCD6IP gene, encodes complete protein.
KJ898138 - Synthetic construct Homo sapiens clone ccsbBroadEn_07532 PDCD6IP gene, encodes complete protein.
BC068454 - Homo sapiens programmed cell death 6 interacting protein, mRNA (cDNA clone MGC:87040 IMAGE:4830724), complete cds.
AF349951 - Homo sapiens HP95 mRNA, complete cds.
AF151793 - Homo sapiens ALG-2 interacting protein 1 (AIP1) mRNA, complete cds.
BC020066 - Homo sapiens programmed cell death 6 interacting protein, mRNA (cDNA clone MGC:17003 IMAGE:4340998), complete cds.
AF250394 - Homo sapiens dopamine receptor interacting protein 4 (DRIP4) mRNA, complete cds.
GQ131806 - Homo sapiens programmed cell death 6 interacting protein (PDCD6IP) mRNA, complete cds, alternatively spliced.
CU686637 - Synthetic construct Homo sapiens gateway clone IMAGE:100022852 5' read PDCD6IP mRNA.
CU676494 - Synthetic construct Homo sapiens gateway clone IMAGE:100017503 5' read PDCD6IP mRNA.
AB384596 - Synthetic construct DNA, clone: pF1KA1375, Homo sapiens PDCD6IP gene for programmed cell death 6-interacting protein, complete cds, without stop codon, in Flexi system.
BT007367 - Homo sapiens programmed cell death 6 interacting protein mRNA, complete cds.
AK295042 - Homo sapiens cDNA FLJ55458 complete cds, highly similar to Programmed cell death 6-interacting protein.
AK002122 - Homo sapiens cDNA FLJ11260 fis, clone PLACE1009060, weakly similar to BRO1 PROTEIN.
AK298727 - Homo sapiens cDNA FLJ56126 complete cds, highly similar to Programmed cell death 6-interacting protein.
AB037796 - Homo sapiens mRNA for KIAA1375 protein, partial cds.
JD222287 - Sequence 203311 from Patent EP1572962.
JD081462 - Sequence 62486 from Patent EP1572962.
JD048343 - Sequence 29367 from Patent EP1572962.
JD096554 - Sequence 77578 from Patent EP1572962.
JD157869 - Sequence 138893 from Patent EP1572962.
JD509994 - Sequence 491018 from Patent EP1572962.
JD350427 - Sequence 331451 from Patent EP1572962.
JD087566 - Sequence 68590 from Patent EP1572962.
JD134200 - Sequence 115224 from Patent EP1572962.
JD313734 - Sequence 294758 from Patent EP1572962.
DL491346 - Novel nucleic acids.
DL491344 - Novel nucleic acids.
JD068891 - Sequence 49915 from Patent EP1572962.
JD291198 - Sequence 272222 from Patent EP1572962.
JD302898 - Sequence 283922 from Patent EP1572962.
JD139517 - Sequence 120541 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q8WUM4 (Reactome details) participates in the following event(s):

R-HSA-3159232 Recruitment Of HIV Virion Budding Machinery
R-HSA-162588 Budding and maturation of HIV virion
R-HSA-162599 Late Phase of HIV Life Cycle
R-HSA-162587 HIV Life Cycle
R-HSA-162906 HIV Infection
R-HSA-5663205 Infectious disease
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: AIP1, ALIX, C5MQH7, E9PFU1, ENST00000307296.1, ENST00000307296.2, ENST00000307296.3, ENST00000307296.4, ENST00000307296.5, ENST00000307296.6, ENST00000307296.7, KIAA1375, NM_013374, PDC6I_HUMAN, Q6NUS1, Q8WUM4, Q9BX86, Q9NUN0, Q9P2H2, Q9UKL5, uc317oao.1, uc317oao.2
UCSC ID: ENST00000307296.8_10
RefSeq Accession: NM_013374.6
Protein: Q8WUM4 (aka PDC6I_HUMAN or PD6I_HUMAN)

-  Gene Model Information
  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.