Human Gene KDM4B (ENST00000159111.9_10) from GENCODE V47lift37
  Description: lysine demethylase 4B, transcript variant 1 (from RefSeq NM_015015.3)
Gencode Transcript: ENST00000159111.9_10
Gencode Gene: ENSG00000127663.16_17
Transcript (Including UTRs)
   Position: hg19 chr19:4,969,124-5,153,609 Size: 184,486 Total Exon Count: 23 Strand: +
Coding Region
   Position: hg19 chr19:5,032,902-5,151,522 Size: 118,621 Coding Exon Count: 21 

Page IndexSequence and LinksPrimersCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureOther SpeciesmRNA DescriptionsOther NamesModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:4,969,124-5,153,609)mRNA (may differ from genome)Protein (1096 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  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
  • D001564 Benzo(a)pyrene
  • D002945 Cisplatin
  • D005472 Fluorouracil
  • D013749 Tetrachlorodibenzodioxin
  • C006780 bisphenol A
  • 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
  • C547126 AZM551248
  • D002117 Calcitriol
          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: 17.26 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 390.98 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 -98.60226-0.436 Picture PostScript Text
3' UTR -864.202087-0.414 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.

-  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 SorterGene Sorter    
 RGDEnsembl   
      
      

-  Descriptions from all associated GenBank mRNAs
  LF385210 - JP 2014500723-A/192713: Polycomb-Associated Non-Coding RNAs.
AB020683 - Homo sapiens KIAA0876 mRNA for KIAA0876 protein.
BC063889 - Homo sapiens jumonji domain containing 2B, mRNA (cDNA clone IMAGE:30389696), complete cds.
BC136611 - Homo sapiens jumonji domain containing 2B, mRNA (cDNA clone MGC:168224 IMAGE:9020601), complete cds.
BC144292 - Homo sapiens jumonji domain containing 2B, mRNA (cDNA clone MGC:177829 IMAGE:9052812), complete cds.
AB384028 - Synthetic construct DNA, clone: pF1KSDA0876, Homo sapiens JMJD2B gene for jmjC domain-containing histone demethylation protein 3B, complete cds, without stop codon, in Flexi system.
KJ902267 - Synthetic construct Homo sapiens clone ccsbBroadEn_11661 KDM4B gene, encodes complete protein.
AK126854 - Homo sapiens cDNA FLJ44906 fis, clone BRAMY3007078, highly similar to JmjC domain-containing histone demethylation protein 3B (EC 1.14.11.-).
AK026040 - Homo sapiens cDNA: FLJ22387 fis, clone HRC07655.
MA620787 - JP 2018138019-A/192713: Polycomb-Associated Non-Coding RNAs.
JD128055 - Sequence 109079 from Patent EP1572962.
JD445762 - Sequence 426786 from Patent EP1572962.
JD394402 - Sequence 375426 from Patent EP1572962.
JD115735 - Sequence 96759 from Patent EP1572962.
CU687848 - Synthetic construct Homo sapiens gateway clone IMAGE:100022863 5' read JMJD2B mRNA.
AK090405 - Homo sapiens mRNA for FLJ00291 protein.
LF341754 - JP 2014500723-A/149257: Polycomb-Associated Non-Coding RNAs.
MA577331 - JP 2018138019-A/149257: Polycomb-Associated Non-Coding RNAs.
AL133622 - Homo sapiens mRNA; cDNA DKFZp434P1721 (from clone DKFZp434P1721).
LF341756 - JP 2014500723-A/149259: Polycomb-Associated Non-Coding RNAs.
LF341757 - JP 2014500723-A/149260: Polycomb-Associated Non-Coding RNAs.
DQ575864 - Homo sapiens piRNA piR-43976, complete sequence.
LF341758 - JP 2014500723-A/149261: Polycomb-Associated Non-Coding RNAs.
LF341759 - JP 2014500723-A/149262: Polycomb-Associated Non-Coding RNAs.
JD408574 - Sequence 389598 from Patent EP1572962.
JD220227 - Sequence 201251 from Patent EP1572962.
JD389406 - Sequence 370430 from Patent EP1572962.
JD126544 - Sequence 107568 from Patent EP1572962.
AF052144 - Homo sapiens clone 24573 and 24786 mRNA sequences.
JD068731 - Sequence 49755 from Patent EP1572962.
JD298189 - Sequence 279213 from Patent EP1572962.
JD036354 - Sequence 17378 from Patent EP1572962.
JD453186 - Sequence 434210 from Patent EP1572962.
JD108233 - Sequence 89257 from Patent EP1572962.
JD477069 - Sequence 458093 from Patent EP1572962.
JD465264 - Sequence 446288 from Patent EP1572962.
JD418668 - Sequence 399692 from Patent EP1572962.
JD406252 - Sequence 387276 from Patent EP1572962.
JD537477 - Sequence 518501 from Patent EP1572962.
JD537478 - Sequence 518502 from Patent EP1572962.
JD458339 - Sequence 439363 from Patent EP1572962.
JD192120 - Sequence 173144 from Patent EP1572962.
JD217029 - Sequence 198053 from Patent EP1572962.
JD456683 - Sequence 437707 from Patent EP1572962.
JD255924 - Sequence 236948 from Patent EP1572962.
JD547854 - Sequence 528878 from Patent EP1572962.
JD535048 - Sequence 516072 from Patent EP1572962.
JD392611 - Sequence 373635 from Patent EP1572962.
JD177223 - Sequence 158247 from Patent EP1572962.
JD216651 - Sequence 197675 from Patent EP1572962.
JD254182 - Sequence 235206 from Patent EP1572962.
BC046167 - Homo sapiens, clone IMAGE:4444834, mRNA.
JD407165 - Sequence 388189 from Patent EP1572962.
JD195419 - Sequence 176443 from Patent EP1572962.
JD525232 - Sequence 506256 from Patent EP1572962.
JD416535 - Sequence 397559 from Patent EP1572962.
JD278780 - Sequence 259804 from Patent EP1572962.
BC015378 - Homo sapiens jumonji domain containing 2B, mRNA (cDNA clone IMAGE:4432212), with apparent retained intron.
JD199509 - Sequence 180533 from Patent EP1572962.
BC040014 - Homo sapiens jumonji domain containing 2B, mRNA (cDNA clone IMAGE:5785435), partial cds.
JD565650 - Sequence 546674 from Patent EP1572962.
JD565651 - Sequence 546675 from Patent EP1572962.
JD561204 - Sequence 542228 from Patent EP1572962.
JD215032 - Sequence 196056 from Patent EP1572962.
JD135008 - Sequence 116032 from Patent EP1572962.
JD223831 - Sequence 204855 from Patent EP1572962.
JD545827 - Sequence 526851 from Patent EP1572962.
JD487489 - Sequence 468513 from Patent EP1572962.
JD472716 - Sequence 453740 from Patent EP1572962.
JD472717 - Sequence 453741 from Patent EP1572962.
JD559714 - Sequence 540738 from Patent EP1572962.
JD266727 - Sequence 247751 from Patent EP1572962.
JD371372 - Sequence 352396 from Patent EP1572962.
JD217882 - Sequence 198906 from Patent EP1572962.
JD316900 - Sequence 297924 from Patent EP1572962.
JD165716 - Sequence 146740 from Patent EP1572962.
JD365510 - Sequence 346534 from Patent EP1572962.
JD122550 - Sequence 103574 from Patent EP1572962.
LF341760 - JP 2014500723-A/149263: Polycomb-Associated Non-Coding RNAs.
JD151188 - Sequence 132212 from Patent EP1572962.
JD425781 - Sequence 406805 from Patent EP1572962.
JD297627 - Sequence 278651 from Patent EP1572962.
LF341761 - JP 2014500723-A/149264: Polycomb-Associated Non-Coding RNAs.
JD314277 - Sequence 295301 from Patent EP1572962.
MA577333 - JP 2018138019-A/149259: Polycomb-Associated Non-Coding RNAs.
MA577334 - JP 2018138019-A/149260: Polycomb-Associated Non-Coding RNAs.
MA577335 - JP 2018138019-A/149261: Polycomb-Associated Non-Coding RNAs.
MA577336 - JP 2018138019-A/149262: Polycomb-Associated Non-Coding RNAs.
MA577337 - JP 2018138019-A/149263: Polycomb-Associated Non-Coding RNAs.
MA577338 - JP 2018138019-A/149264: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: A0A0C4DFL8, A0A0C4DFL8_HUMAN, ENST00000159111.1, ENST00000159111.2, ENST00000159111.3, ENST00000159111.4, ENST00000159111.5, ENST00000159111.6, ENST00000159111.7, ENST00000159111.8, KDM4B , NM_015015, uc317cce.1, uc317cce.2
UCSC ID: ENST00000159111.9_10
RefSeq Accession: NM_015015.3

-  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.