Human Gene JMY (uc003kfx.4)
  Description: Homo sapiens junction mediating and regulatory protein, p53 cofactor (JMY), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr5:78,531,925-78,623,038 Size: 91,114 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr5:78,532,474-78,612,130 Size: 79,657 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:78,531,925-78,623,038)mRNA (may differ from genome)Protein (988 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMalacardsMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: JMY_HUMAN
DESCRIPTION: RecName: Full=Junction-mediating and -regulatory protein;
FUNCTION: Acts both as a nuclear p53/TP53-cofactor and a cytoplasmic regulator of actin dynamics depending on conditions. In nucleus, acts as a cofactor that increases p53/TP53 response via its interaction with p300/EP300. Increases p53/TP53-dependent transcription and apoptosis, suggesting an important role in p53/TP53 stress response such as DNA damage. In cytoplasm, acts as a nucleation-promoting factor for both branched and unbranched actin filaments. Activates the Arp2/3 complex to induce branched actin filament networks. Also catalyzes actin polymerization in the absence of Arp2/3, creating unbranched filaments. Contributes to cell motility by controlling actin dynamics. May promote the rapid formation of a branched actin network by first nucleating new mother filaments and then activating Arp2/3 to branch off these filaments. The p53/TP53-cofactor and actin activator activities are regulated via its subcellular location (By similarity).
SUBUNIT: Interacts with p300/EP300, the complex being recruited to activated p53/TP53. Interacts with TTC5 (By similarity).
INTERACTION: Q00987:MDM2; NbExp=2; IntAct=EBI-866435, EBI-389668;
SUBCELLULAR LOCATION: Nucleus (By similarity). Cytoplasm, cytoskeleton. Note=Localizes to the nucleus in most cell types. Accumulates in nucleus under DNA damage conditions, increasing p53/TP53 transcription response and reducing its influence on cell motility (By similarity). In primary neutrophils, it colocalizes with actin filaments at the leading edge and is excluded from the nucleus. Localization correlates with motility, because it moves from the nucleus to the cytoplasmic compartment when cells are differentiated from nonmotile cells into highly motile neutrophil- like cells.
INDUCTION: By E2F.
PTM: Ubiquitinated by MDM2, leading to its subsequent degradation by the proteasome. In case of DNA damage, the interaction with MDM2 is altered, preventing degradation and allowing interaction with p300/EP300 and its function in p53/TP53 stress response (By similarity).
SIMILARITY: Belongs to the JMY family.
SIMILARITY: Contains 1 WH2 domain.
SEQUENCE CAUTION: Sequence=AAI30625.1; Type=Erroneous initiation; Sequence=BAC04495.1; Type=Erroneous initiation; Sequence=EAW95834.1; Type=Erroneous gene model prediction;

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): JMY
CDC HuGE Published Literature: JMY

-  MalaCards Disease Associations
  MalaCards Gene Search: JMY
Diseases sorted by gene-association score: usher syndrome, type 1b (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D013749 Tetrachlorodibenzodioxin
  • C517041 (4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)
  • C495626 14-deoxy-11,12-didehydroandrographolide
  • C029497 2,3-bis(3'-hydroxybenzyl)butyrolactone
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
  • D016604 Aflatoxin B1
  • C408982 CPG-oligonucleotide
  • D002117 Calcitriol
  • D003300 Copper
          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: 8.76 RPKM in Ovary
Total median expression: 225.34 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 -279.20549-0.509 Picture PostScript Text
3' UTR -1450.845613-0.258 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
IPR003124 - WH2_dom

Pfam Domains:
PF02205 - WH2 motif
PF15871 - Junction-mediating and -regulatory protein
PF15920 - N-terminal of Junction-mediating and WASP homolog-associated

ModBase Predicted Comparative 3D Structure on Q8N9B5
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 orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003713 transcription coactivator activity
GO:0003779 actin binding
GO:0005515 protein binding
GO:0071933 Arp2/3 complex binding

Biological Process:
GO:0006281 DNA repair
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006974 cellular response to DNA damage stimulus
GO:0007050 cell cycle arrest
GO:0034314 Arp2/3 complex-mediated actin nucleation
GO:0043065 positive regulation of apoptotic process
GO:0051091 positive regulation of sequence-specific DNA binding transcription factor activity
GO:0070060 'de novo' actin filament nucleation
GO:0070358 actin polymerization-dependent cell motility
GO:0072332 intrinsic apoptotic signaling pathway by p53 class mediator
GO:1901796 regulation of signal transduction by p53 class mediator

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005856 cytoskeleton
GO:0031252 cell leading edge


-  Descriptions from all associated GenBank mRNAs
  LF384943 - JP 2014500723-A/192446: Polycomb-Associated Non-Coding RNAs.
LF332281 - JP 2014500723-A/139784: Polycomb-Associated Non-Coding RNAs.
AB590691 - Synthetic construct DNA, clone: pFN21AB0466, Homo sapiens JMY gene for junction mediating and regulatory protein, p53 cofactor, without stop codon, in Flexi system.
LF332280 - JP 2014500723-A/139783: Polycomb-Associated Non-Coding RNAs.
BC130624 - Homo sapiens junction mediating and regulatory protein, p53 cofactor, mRNA (cDNA clone MGC:163496 IMAGE:40146655), complete cds.
AK095189 - Homo sapiens cDNA FLJ37870 fis, clone BRSSN2017682, highly similar to Mus musculus p300 transcriptional cofactor JMY mRNA.
HQ258469 - Synthetic construct Homo sapiens clone IMAGE:100072898 Unknown protein gene, encodes complete protein.
KJ903784 - Synthetic construct Homo sapiens clone ccsbBroadEn_13178 JMY gene, encodes complete protein.
LF332277 - JP 2014500723-A/139780: Polycomb-Associated Non-Coding RNAs.
LF332274 - JP 2014500723-A/139777: Polycomb-Associated Non-Coding RNAs.
LF332273 - JP 2014500723-A/139776: Polycomb-Associated Non-Coding RNAs.
LF332271 - JP 2014500723-A/139774: Polycomb-Associated Non-Coding RNAs.
BX648731 - Homo sapiens mRNA; cDNA DKFZp451P2410 (from clone DKFZp451P2410).
LF332268 - JP 2014500723-A/139771: Polycomb-Associated Non-Coding RNAs.
LF332267 - JP 2014500723-A/139770: Polycomb-Associated Non-Coding RNAs.
LF332266 - JP 2014500723-A/139769: Polycomb-Associated Non-Coding RNAs.
LF332263 - JP 2014500723-A/139766: Polycomb-Associated Non-Coding RNAs.
JD131943 - Sequence 112967 from Patent EP1572962.
JD503523 - Sequence 484547 from Patent EP1572962.
JD435908 - Sequence 416932 from Patent EP1572962.
JD328500 - Sequence 309524 from Patent EP1572962.
JD534106 - Sequence 515130 from Patent EP1572962.
JD093402 - Sequence 74426 from Patent EP1572962.
JD350309 - Sequence 331333 from Patent EP1572962.
LF332262 - JP 2014500723-A/139765: Polycomb-Associated Non-Coding RNAs.
BX648048 - Homo sapiens mRNA; cDNA DKFZp686E06203 (from clone DKFZp686E06203).
LF332261 - JP 2014500723-A/139764: Polycomb-Associated Non-Coding RNAs.
LF332260 - JP 2014500723-A/139763: Polycomb-Associated Non-Coding RNAs.
LF332259 - JP 2014500723-A/139762: Polycomb-Associated Non-Coding RNAs.
AK092475 - Homo sapiens cDNA FLJ35156 fis, clone PLACE6011057.
LF332258 - JP 2014500723-A/139761: Polycomb-Associated Non-Coding RNAs.
LF332257 - JP 2014500723-A/139760: Polycomb-Associated Non-Coding RNAs.
LF332256 - JP 2014500723-A/139759: Polycomb-Associated Non-Coding RNAs.
LF332255 - JP 2014500723-A/139758: Polycomb-Associated Non-Coding RNAs.
LF332254 - JP 2014500723-A/139757: Polycomb-Associated Non-Coding RNAs.
LF332253 - JP 2014500723-A/139756: Polycomb-Associated Non-Coding RNAs.
MA620520 - JP 2018138019-A/192446: Polycomb-Associated Non-Coding RNAs.
MA567858 - JP 2018138019-A/139784: Polycomb-Associated Non-Coding RNAs.
MA567857 - JP 2018138019-A/139783: Polycomb-Associated Non-Coding RNAs.
MA567854 - JP 2018138019-A/139780: Polycomb-Associated Non-Coding RNAs.
MA567851 - JP 2018138019-A/139777: Polycomb-Associated Non-Coding RNAs.
MA567850 - JP 2018138019-A/139776: Polycomb-Associated Non-Coding RNAs.
MA567848 - JP 2018138019-A/139774: Polycomb-Associated Non-Coding RNAs.
MA567845 - JP 2018138019-A/139771: Polycomb-Associated Non-Coding RNAs.
MA567844 - JP 2018138019-A/139770: Polycomb-Associated Non-Coding RNAs.
MA567843 - JP 2018138019-A/139769: Polycomb-Associated Non-Coding RNAs.
MA567840 - JP 2018138019-A/139766: Polycomb-Associated Non-Coding RNAs.
MA567839 - JP 2018138019-A/139765: Polycomb-Associated Non-Coding RNAs.
MA567838 - JP 2018138019-A/139764: Polycomb-Associated Non-Coding RNAs.
MA567837 - JP 2018138019-A/139763: Polycomb-Associated Non-Coding RNAs.
MA567836 - JP 2018138019-A/139762: Polycomb-Associated Non-Coding RNAs.
MA567835 - JP 2018138019-A/139761: Polycomb-Associated Non-Coding RNAs.
MA567834 - JP 2018138019-A/139760: Polycomb-Associated Non-Coding RNAs.
MA567833 - JP 2018138019-A/139759: Polycomb-Associated Non-Coding RNAs.
MA567832 - JP 2018138019-A/139758: Polycomb-Associated Non-Coding RNAs.
MA567831 - JP 2018138019-A/139757: Polycomb-Associated Non-Coding RNAs.
MA567830 - JP 2018138019-A/139756: Polycomb-Associated Non-Coding RNAs.

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

Protein Q8N9B5 (Reactome details) participates in the following event(s):

R-HSA-6804229 JMY, TTC5 and EP300 bind
R-HSA-6804253 MDM2 ubiquitinates JMY
R-HSA-6804242 TP53 binds the complex of JMY, EP300 and TTC5
R-HSA-6804379 PRMT5 binds TTC5
R-HSA-6804383 PRMT5 methylates TP53
R-HSA-6804760 Regulation of TP53 Activity through Methylation
R-HSA-5633007 Regulation of TP53 Activity
R-HSA-3700989 Transcriptional Regulation by TP53
R-HSA-212436 Generic Transcription Pathway
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: A1L4P5, B5MDS2, B5MDT0, JMY_HUMAN, NM_152405, NP_689618, Q8N9B5
UCSC ID: uc003kfx.4
RefSeq Accession: NM_152405
Protein: Q8N9B5 (aka JMY_HUMAN)
CCDS: CCDS4047.3

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_152405.4
exon count: 11CDS single in 3' UTR: no RNA size: 9145
ORF size: 2967CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5142.00frame shift in genome: no % Coverage: 99.83
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.