Human Gene VPS72 (ENST00000368892.9_8) from GENCODE V47lift37
  Description: vacuolar protein sorting 72 homolog, transcript variant 2 (from RefSeq NM_005997.3)
Gencode Transcript: ENST00000368892.9_8
Gencode Gene: ENSG00000163159.15_10
Transcript (Including UTRs)
   Position: hg19 chr1:151,148,780-151,162,673 Size: 13,894 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr1:151,149,120-151,162,597 Size: 13,478 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:151,148,780-151,162,673)mRNA (may differ from genome)Protein (364 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: VPS72_HUMAN
DESCRIPTION: RecName: Full=Vacuolar protein sorting-associated protein 72 homolog; AltName: Full=Protein YL-1; AltName: Full=Transcription factor-like 1;
FUNCTION: Could be a DNA-binding transcriptional regulator. May be involved in chromatin modification and remodeling.
SUBUNIT: Component of the NuA4 histone acetyltransferase complex which contains the catalytic subunit KAT5/TIP60 and the subunits EP400, TRRAP/PAF400, BRD8/SMAP, EPC1, DMAP1/DNMAP1, RUVBL1/TIP49, RUVBL2, ING3, actin, ACTL6A/BAF53A, MORF4L1/MRG15, MORF4L2/MRGX, MRGBP, YEATS4/GAS41 and VPS72/YL1. Component of a NuA4-related complex which contains EP400, TRRAP/PAF400, SRCAP, BRD8/SMAP, EPC1, DMAP1/DNMAP1, RUVBL1/TIP49, RUVBL2, actin, ACTL6A/BAF53A, VPS72 and YEATS4/GAS41. Also part of a multiprotein complex which contains SRCAP and which binds to H2AFZ/H2AZ.
INTERACTION: Q9Y265:RUVBL1; NbExp=6; IntAct=EBI-399189, EBI-353675;
SUBCELLULAR LOCATION: Nucleus.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the VPS72/YL1 family.

-  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


-  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: 27.70 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 982.12 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 -26.9076-0.354 Picture PostScript Text
3' UTR -56.90340-0.167 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
IPR008895 - YL1
IPR013272 - YL1_C

Pfam Domains:
PF05764 - YL1 nuclear protein
PF08265 - YL1 nuclear protein C-terminal domain

ModBase Predicted Comparative 3D Structure on Q15906
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 orthologNo orthologNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0042393 histone binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0035019 somatic stem cell population maintenance
GO:0043486 histone exchange

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0016607 nuclear speck
GO:0032991 macromolecular complex


-  Descriptions from all associated GenBank mRNAs
  D43642 - Homo sapiens mRNA for YL-1 protein, complete cds.
LF383808 - JP 2014500723-A/191311: Polycomb-Associated Non-Coding RNAs.
AK225130 - Homo sapiens mRNA for transcription factor-like 1 variant, clone: CBL03629.
AK222939 - Homo sapiens mRNA for transcription factor-like 1 variant, clone: HRC10895.
BC003151 - Homo sapiens vacuolar protein sorting 72 homolog (S. cerevisiae), mRNA (cDNA clone MGC:4061 IMAGE:2958630), complete cds.
AK222935 - Homo sapiens mRNA for transcription factor-like 1 variant, clone: HRC10878.
JD428674 - Sequence 409698 from Patent EP1572962.
JD525616 - Sequence 506640 from Patent EP1572962.
JD290105 - Sequence 271129 from Patent EP1572962.
DQ892940 - Synthetic construct clone IMAGE:100005570; FLH191018.01X; RZPDo839G0676D vacuolar protein sorting 72 (S. cerevisiae) (VPS72) gene, encodes complete protein.
DQ896189 - Synthetic construct Homo sapiens clone IMAGE:100010649; FLH191014.01L; RZPDo839G0666D vacuolar protein sorting 72 (S. cerevisiae) (VPS72) gene, encodes complete protein.
BT019356 - Homo sapiens transcription factor-like 1 mRNA, complete cds.
BT019357 - Homo sapiens transcription factor-like 1 mRNA, complete cds.
AB464341 - Synthetic construct DNA, clone: pF1KB7632, Homo sapiens VPS72 gene for vacuolar protein sorting 72 homolog, without stop codon, in Flexi system.
AK297565 - Homo sapiens cDNA FLJ60050 complete cds, highly similar to Vacuolar protein sorting protein 72 homolog.
AK310045 - Homo sapiens cDNA, FLJ17087.
LF352477 - JP 2014500723-A/159980: Polycomb-Associated Non-Coding RNAs.
DQ655941 - Homo sapiens clone UGL1a11, mRNA sequence.
DQ656047 - Homo sapiens clone UGLsupplA, mRNA sequence.
LF352476 - JP 2014500723-A/159979: Polycomb-Associated Non-Coding RNAs.
LF352475 - JP 2014500723-A/159978: Polycomb-Associated Non-Coding RNAs.
LF352474 - JP 2014500723-A/159977: Polycomb-Associated Non-Coding RNAs.
LF352472 - JP 2014500723-A/159975: Polycomb-Associated Non-Coding RNAs.
LF352471 - JP 2014500723-A/159974: Polycomb-Associated Non-Coding RNAs.
MA619385 - JP 2018138019-A/191311: Polycomb-Associated Non-Coding RNAs.
MA588054 - JP 2018138019-A/159980: Polycomb-Associated Non-Coding RNAs.
MA588053 - JP 2018138019-A/159979: Polycomb-Associated Non-Coding RNAs.
MA588052 - JP 2018138019-A/159978: Polycomb-Associated Non-Coding RNAs.
MA588051 - JP 2018138019-A/159977: Polycomb-Associated Non-Coding RNAs.
MA588049 - JP 2018138019-A/159975: Polycomb-Associated Non-Coding RNAs.
MA588048 - JP 2018138019-A/159974: Polycomb-Associated Non-Coding RNAs.

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

Protein Q15906 (Reactome details) participates in the following event(s):

R-HSA-3321975 NuA4 complex acetylates histone H2A, HIST1H4
R-NUL-4551334 NuA4 complex actetylates H2A and H4
R-HSA-3214847 HATs acetylate histones
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-4839726 Chromatin organization

-  Other Names for This Gene
  Alternate Gene Symbols: A6NLK9, A6PW55, ENST00000368892.1, ENST00000368892.2, ENST00000368892.3, ENST00000368892.4, ENST00000368892.5, ENST00000368892.6, ENST00000368892.7, ENST00000368892.8, NM_005997, Q15906, Q53GJ2, Q5U0R4, TCFL1, uc318hdt.1, uc318hdt.2, VPS72_HUMAN, YL1
UCSC ID: ENST00000368892.9_8
RefSeq Accession: NM_005997.3
Protein: Q15906 (aka VPS72_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.