Human Gene PSMD4 (ENST00000368884.8_10) from GENCODE V47lift37
  Description: proteasome 26S subunit ubiquitin receptor, non-ATPase 4, transcript variant 2 (from RefSeq NM_002810.4)
Gencode Transcript: ENST00000368884.8_10
Gencode Gene: ENSG00000159352.16_14
Transcript (Including UTRs)
   Position: hg19 chr1:151,227,210-151,239,955 Size: 12,746 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr1:151,227,259-151,239,819 Size: 12,561 Coding Exon Count: 10 

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 (chr1:151,227,210-151,239,955)mRNA (may differ from genome)Protein (377 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
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-  Comments and Description Text from UniProtKB
  ID: PSMD4_HUMAN
DESCRIPTION: RecName: Full=26S proteasome non-ATPase regulatory subunit 4; AltName: Full=26S proteasome regulatory subunit RPN10; AltName: Full=26S proteasome regulatory subunit S5A; AltName: Full=Antisecretory factor 1; Short=AF; Short=ASF; AltName: Full=Multiubiquitin chain-binding protein;
FUNCTION: Binds and presumably selects ubiquitin-conjugates for destruction. Displays selectivity for longer polyubiquitin chains. Modulates intestinal fluid secretion.
SUBUNIT: The 26S proteasome is composed of a core protease, known as the 20S proteasome, capped at one or both ends by the 19S regulatory complex (RC). The RC is composed of at least 18 different subunits in two subcomplexes, the base and the lid, which form the portions proximal and distal to the 20S proteolytic core, respectively. Directly interacts with NUB1. Interacts with SQSTM1. Interacts with UBQLN4. Interacts with UBE3A.
INTERACTION: P24610:Pax3 (xeno); NbExp=3; IntAct=EBI-359318, EBI-1208116; P54725:RAD23A; NbExp=2; IntAct=EBI-359318, EBI-746453; P54727:RAD23B; NbExp=5; IntAct=EBI-359318, EBI-954531; Q9P0W5:SCHIP1; NbExp=2; IntAct=EBI-359318, EBI-1397509;
DOMAIN: The 2 UIM motifs are involved in the binding to a multi- ubiquitin chain in a cooperative way.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the proteasome subunit S5A family.
SIMILARITY: Contains 2 UIM (ubiquitin-interacting motif) repeats.
SIMILARITY: Contains 1 VWFA domain.

-  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: PSMD4
Diseases sorted by gene-association score: angelman syndrome (3)

-  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: 106.78 RPKM in Testis
Total median expression: 2979.32 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 -15.4049-0.314 Picture PostScript Text
3' UTR -34.80136-0.256 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
IPR003903 - Ubiquitin-int_motif
IPR002035 - VWF_A

Pfam Domains:
PF00092 - von Willebrand factor type A domain
PF02809 - Ubiquitin interaction motif
PF04056 - Ssl1-like
PF13519 - von Willebrand factor type A domain

SCOP Domains:
75217 - alpha/beta knot
53300 - vWA-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1P9C - NMR MuPIT 1P9D - NMR MuPIT 1UEL - NMR MuPIT 1YX4 - NMR MuPIT 1YX5 - NMR MuPIT 1YX6 - NMR MuPIT 2KDE - NMR MuPIT 2KDF - NMR MuPIT


ModBase Predicted Comparative 3D Structure on P55036
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 orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0031593 polyubiquitin binding
GO:0042802 identical protein binding

Biological Process:
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0016579 protein deubiquitination
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0043248 proteasome assembly
GO:0043687 post-translational protein modification

Cellular Component:
GO:0000502 proteasome complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005829 cytosol
GO:0008540 proteasome regulatory particle, base subcomplex
GO:0022624 proteasome accessory complex


-  Descriptions from all associated GenBank mRNAs
  U24704 - Human antisecretory factor-1 mRNA, complete cds.
JD126020 - Sequence 107044 from Patent EP1572962.
JD409498 - Sequence 390522 from Patent EP1572962.
U51007 - Human 26S protease subunit S5a mRNA, complete cds.
BC072008 - Homo sapiens proteasome (prosome, macropain) 26S subunit, non-ATPase, 4, mRNA (cDNA clone MGC:88714 IMAGE:6285035), complete cds.
AB033605 - Homo sapiens mRNA for pUb-R5, complete cds.
BC002365 - Homo sapiens proteasome (prosome, macropain) 26S subunit, non-ATPase, 4, mRNA (cDNA clone MGC:8410 IMAGE:2820813), complete cds.
JD343920 - Sequence 324944 from Patent EP1572962.
AB527552 - Synthetic construct DNA, clone: pF1KB6593, Homo sapiens PSMD4 gene for proteasome (prosome, macropain) 26S subunit, non-ATPase, 4, without stop codon, in Flexi system.
JF432522 - Synthetic construct Homo sapiens clone IMAGE:100073744 proteasome (prosome, macropain) 26S subunit, non-ATPase, 4 (PSMD4) gene, encodes complete protein.
KJ891926 - Synthetic construct Homo sapiens clone ccsbBroadEn_01320 PSMD4 gene, encodes complete protein.
U72664 - Human S5a/antisecretory factor protein mRNA, partial cds.
JD174032 - Sequence 155056 from Patent EP1572962.
JD439277 - Sequence 420301 from Patent EP1572962.
JD185674 - Sequence 166698 from Patent EP1572962.
JD183021 - Sequence 164045 from Patent EP1572962.
JD392651 - Sequence 373675 from Patent EP1572962.
JD463449 - Sequence 444473 from Patent EP1572962.
JD538795 - Sequence 519819 from Patent EP1572962.
JD401141 - Sequence 382165 from Patent EP1572962.
JD118820 - Sequence 99844 from Patent EP1572962.
JD042734 - Sequence 23758 from Patent EP1572962.
JD049506 - Sequence 30530 from Patent EP1572962.
JD095943 - Sequence 76967 from Patent EP1572962.
JD063604 - Sequence 44628 from Patent EP1572962.

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

Protein P55036 (Reactome details) participates in the following event(s):

R-HSA-5665871 ADRM1 binds 26S proteasome
R-HSA-8956140 NEDD8 and UBD bind NUB1 and the 26S proteasome
R-HSA-5665854 ADRM1:26S proteaseome binds UCHL5
R-HSA-5689539 ADRM1:26S proteaseome binds USP14
R-HSA-5689603 UCH proteinases
R-HSA-8951664 Neddylation
R-HSA-5689880 Ub-specific processing proteases
R-HSA-5688426 Deubiquitination
R-HSA-597592 Post-translational protein modification
R-HSA-68827 CDT1 association with the CDC6:ORC:origin complex
R-HSA-68949 Orc1 removal from chromatin
R-HSA-69017 CDK-mediated phosphorylation and removal of Cdc6
R-HSA-69601 Ubiquitin Mediated Degradation of Phosphorylated Cdc25A
R-HSA-69229 Ubiquitin-dependent degradation of Cyclin D1
R-HSA-174178 APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1
R-HSA-174154 APC/C:Cdc20 mediated degradation of Securin
R-HSA-2467813 Separation of Sister Chromatids
R-HSA-174113 SCF-beta-TrCP mediated degradation of Emi1
R-HSA-174184 Cdc20:Phospho-APC/C mediated degradation of Cyclin A
R-HSA-180534 Vpu mediated degradation of CD4
R-HSA-180585 Vif-mediated degradation of APOBEC3G
R-HSA-9020702 Interleukin-1 signaling
R-HSA-211733 Regulation of activated PAK-2p34 by proteasome mediated degradation
R-HSA-349425 Autodegradation of the E3 ubiquitin ligase COP1
R-HSA-350562 Regulation of ornithine decarboxylase (ODC)
R-HSA-450408 AUF1 (hnRNP D0) binds and destabilizes mRNA
R-HSA-983168 Antigen processing: Ubiquitination & Proteasome degradation
R-HSA-1169091 Activation of NF-kappaB in B cells
R-HSA-1234176 Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha
R-HSA-1236974 ER-Phagosome pathway
R-HSA-1236978 Cross-presentation of soluble exogenous antigens (endosomes)
R-HSA-4641258 Degradation of DVL
R-HSA-195253 Degradation of beta-catenin by the destruction complex
R-HSA-4641257 Degradation of AXIN
R-HSA-4608870 Asymmetric localization of PCP proteins
R-HSA-5358346 Hedgehog ligand biogenesis
R-HSA-5362768 Hh mutants that don't undergo autocatalytic processing are degraded by ERAD
R-HSA-202424 Downstream TCR signaling
R-HSA-2871837 FCERI mediated NF-kB activation
R-HSA-5607764 CLEC7A (Dectin-1) signaling
R-HSA-5607761 Dectin-1 mediated noncanonical NF-kB signaling
R-HSA-5676590 NIK-->noncanonical NF-kB signaling
R-HSA-5610785 GLI3 is processed to GLI3R by the proteasome
R-HSA-5610783 Degradation of GLI2 by the proteasome
R-HSA-5610780 Degradation of GLI1 by the proteasome
R-HSA-5632684 Hedgehog 'on' state
R-HSA-5658442 Regulation of RAS by GAPs
R-HSA-5668541 TNFR2 non-canonical NF-kB pathway
R-HSA-5687128 MAPK6/MAPK4 signaling
R-HSA-8948751 Regulation of PTEN stability and activity
R-HSA-69481 G2/M Checkpoints
R-HSA-8852276 The role of GTSE1 in G2/M progression after G2 checkpoint
R-HSA-8854050 FBXL7 down-regulates AURKA during mitotic entry and in early mitosis
R-HSA-382556 ABC-family proteins mediated transport
R-HSA-5678895 Defective CFTR causes cystic fibrosis
R-HSA-8939236 RUNX1 regulates transcription of genes involved in differentiation of HSCs
R-HSA-8939902 Regulation of RUNX2 expression and activity
R-HSA-9010553 Regulation of expression of SLITs and ROBOs
R-HSA-174084 Autodegradation of Cdh1 by Cdh1:APC/C
R-HSA-187577 SCF(Skp2)-mediated degradation of p27/p21
R-HSA-8941858 Regulation of RUNX3 expression and activity
R-HSA-392499 Metabolism of proteins
R-HSA-68867 Assembly of the pre-replicative complex
R-HSA-69052 Switching of origins to a post-replicative state
R-HSA-69610 p53-Independent DNA Damage Response
R-HSA-75815 Ubiquitin-dependent degradation of Cyclin D
R-HSA-174143 APC/C-mediated degradation of cell cycle proteins
R-HSA-176409 APC/C:Cdc20 mediated degradation of mitotic proteins
R-HSA-68882 Mitotic Anaphase
R-HSA-176408 Regulation of APC/C activators between G1/S and early anaphase
R-HSA-179419 APC:Cdc20 mediated degradation of cell cycle proteins prior to satisfation of the cell cycle checkpoint
R-HSA-162909 Host Interactions of HIV factors
R-HSA-446652 Interleukin-1 family signaling
R-HSA-169911 Regulation of Apoptosis
R-HSA-69541 Stabilization of p53
R-HSA-351202 Metabolism of polyamines
R-HSA-450531 Regulation of mRNA stability by proteins that bind AU-rich elements
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-1168372 Downstream signaling events of B Cell Receptor (BCR)
R-HSA-1234174 Regulation of Hypoxia-inducible Factor (HIF) by oxygen
R-HSA-1236975 Antigen processing-Cross presentation
R-HSA-201681 TCF dependent signaling in response to WNT
R-HSA-195721 Signaling by WNT
R-HSA-4086400 PCP/CE pathway
R-HSA-5358351 Signaling by Hedgehog
R-HSA-5387390 Hh mutants abrogate ligand secretion
R-HSA-202403 TCR signaling
R-HSA-2454202 Fc epsilon receptor (FCERI) signaling
R-HSA-5621481 C-type lectin receptors (CLRs)
R-HSA-5610787 Hedgehog 'off' state
R-HSA-5673001 RAF/MAP kinase cascade
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-5683057 MAPK family signaling cascades
R-HSA-6807070 PTEN Regulation
R-HSA-69620 Cell Cycle Checkpoints
R-HSA-69275 G2/M Transition
R-HSA-382551 Transport of small molecules
R-HSA-5619084 ABC transporter disorders
R-HSA-8878171 Transcriptional regulation by RUNX1
R-HSA-8878166 Transcriptional regulation by RUNX2
R-HSA-376176 Signaling by ROBO receptors
R-HSA-69202 Cyclin E associated events during G1/S transition
R-HSA-69656 Cyclin A:Cdk2-associated events at S phase entry
R-HSA-8878159 Transcriptional regulation by RUNX3
R-HSA-69002 DNA Replication Pre-Initiation
R-HSA-69239 Synthesis of DNA
R-HSA-69613 p53-Independent G1/S DNA damage checkpoint
R-HSA-69242 S Phase
R-HSA-453276 Regulation of mitotic cell cycle
R-HSA-176814 Activation of APC/C and APC/C:Cdc20 mediated degradation of mitotic proteins
R-HSA-2555396 Mitotic Metaphase and Anaphase
R-HSA-162906 HIV Infection
R-HSA-449147 Signaling by Interleukins
R-HSA-109581 Apoptosis
R-HSA-69563 p53-Dependent G1 DNA Damage Response
R-HSA-71291 Metabolism of nitrogenous molecules
R-HSA-8953854 Metabolism of RNA
R-HSA-1280218 Adaptive Immune System
R-HSA-983705 Signaling by the B Cell Receptor (BCR)
R-HSA-2262749 Cellular response to hypoxia
R-HSA-162582 Signal Transduction
R-HSA-3858494 Beta-catenin independent WNT signaling
R-HSA-5663202 Diseases of signal transduction
R-HSA-168249 Innate Immune System
R-HSA-5684996 MAPK1/MAPK3 signaling
R-HSA-168256 Immune System
R-HSA-1257604 PIP3 activates AKT signaling
R-HSA-1640170 Cell Cycle
R-HSA-453274 Mitotic G2-G2/M phases
R-HSA-5619115 Disorders of transmembrane transporters
R-HSA-212436 Generic Transcription Pathway
R-HSA-422475 Axon guidance
R-HSA-69206 G1/S Transition
R-HSA-68874 M/G1 Transition
R-HSA-69306 DNA Replication
R-HSA-69615 G1/S DNA Damage Checkpoints
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-68886 M Phase
R-HSA-5663205 Infectious disease
R-HSA-5357801 Programmed Cell Death
R-HSA-69580 p53-Dependent G1/S DNA damage checkpoint
R-HSA-1430728 Metabolism
R-HSA-2262752 Cellular responses to stress
R-HSA-1643685 Disease
R-HSA-9006925 Intracellular signaling by second messengers
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-1266738 Developmental Biology
R-HSA-453279 Mitotic G1-G1/S phases
R-HSA-8953897 Cellular responses to external stimuli
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: D3DV16, ENST00000368884.1, ENST00000368884.2, ENST00000368884.3, ENST00000368884.4, ENST00000368884.5, ENST00000368884.6, ENST00000368884.7, MCB1, NM_002810, P55036, PSMD4_HUMAN, Q5VWC5, Q9NS92, uc318hdm.1, uc318hdm.2
UCSC ID: ENST00000368884.8_10
RefSeq Accession: NM_002810.4
Protein: P55036 (aka PSMD4_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.