Human Gene JMJD4 (ENST00000438896.3) from GENCODE V44
  Description: Homo sapiens jumonji domain containing 4 (JMJD4), transcript variant 2, mRNA. (from RefSeq NM_001161465)
Gencode Transcript: ENST00000438896.3
Gencode Gene: ENSG00000081692.13
Transcript (Including UTRs)
   Position: hg38 chr1:227,731,234-227,735,411 Size: 4,178 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg38 chr1:227,732,392-227,735,273 Size: 2,882 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:227,731,234-227,735,411)mRNA (may differ from genome)Protein (401 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDMalacardsMGIneXtProtPubMed
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: JMJD4_HUMAN
DESCRIPTION: RecName: Full=JmjC domain-containing protein 4; AltName: Full=Jumonji domain-containing protein 4;
SIMILARITY: Contains 1 JmjC domain.
CAUTION: It is uncertain whether Met-1 or Met-47 is the initiator.
SEQUENCE CAUTION: Sequence=BAB14366.1; Type=Erroneous initiation; Sequence=CAI23067.1; 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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 36.82 RPKM in Testis
Total median expression: 539.72 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 -71.20138-0.516 Picture PostScript Text
3' UTR -574.001158-0.496 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
IPR003347 - JmjC_dom

ModBase Predicted Comparative 3D Structure on Q9H9V9
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

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


-  Descriptions from all associated GenBank mRNAs
  AK026908 - Homo sapiens cDNA: FLJ23255 fis, clone COL05420.
BC011928 - Homo sapiens jumonji domain containing 4, mRNA (cDNA clone IMAGE:4544682).
AK023030 - Homo sapiens cDNA FLJ12968 fis, clone NT2RP2005815.
AK022579 - Homo sapiens cDNA FLJ12517 fis, clone NT2RM2001784.
JD387258 - Sequence 368282 from Patent EP1572962.
JD421758 - Sequence 402782 from Patent EP1572962.
JD425712 - Sequence 406736 from Patent EP1572962.
JD426453 - Sequence 407477 from Patent EP1572962.
JD545261 - Sequence 526285 from Patent EP1572962.
DQ580730 - Homo sapiens piRNA piR-48842, complete sequence.
JD192689 - Sequence 173713 from Patent EP1572962.
JD535306 - Sequence 516330 from Patent EP1572962.
JD264789 - Sequence 245813 from Patent EP1572962.
JD288123 - Sequence 269147 from Patent EP1572962.
JD078957 - Sequence 59981 from Patent EP1572962.
JD342665 - Sequence 323689 from Patent EP1572962.
JD445323 - Sequence 426347 from Patent EP1572962.
JD400056 - Sequence 381080 from Patent EP1572962.
JD057962 - Sequence 38986 from Patent EP1572962.
JD532961 - Sequence 513985 from Patent EP1572962.
AB528287 - Synthetic construct DNA, clone: pF1KB9537, Homo sapiens JMJD4 gene for jumonji domain containing protein 4, without stop codon, in Flexi system.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000438896.1, ENST00000438896.2, JMJD4_HUMAN, NM_001161465, Q5TBZ1, Q5TBZ6, Q9H970, Q9H9V9, uc001hrc.1, uc001hrc.2, uc001hrc.3, uc001hrc.4, uc001hrc.5
UCSC ID: ENST00000438896.3
RefSeq Accession: NM_001161465
Protein: Q9H9V9 (aka JMJD4_HUMAN)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.