Human Gene NSD3 (ENST00000316985.7_5) from GENCODE V47lift37
  Description: nuclear receptor binding SET domain protein 3, transcript variant short (from RefSeq NM_017778.3)
Gencode Transcript: ENST00000316985.7_5
Gencode Gene: ENSG00000147548.17_18
Transcript (Including UTRs)
   Position: hg19 chr8:38,173,935-38,239,790 Size: 65,856 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg19 chr8:38,175,474-38,205,689 Size: 30,216 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsGene 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 (chr8:38,173,935-38,239,790)mRNA (may differ from genome)Protein (645 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsMalacardsMGI
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NSD3_HUMAN
DESCRIPTION: RecName: Full=Histone-lysine N-methyltransferase NSD3; EC=2.1.1.43; AltName: Full=Nuclear SET domain-containing protein 3; AltName: Full=Protein whistle; AltName: Full=WHSC1-like 1 isoform 9 with methyltransferase activity to lysine; AltName: Full=Wolf-Hirschhorn syndrome candidate 1-like protein 1; Short=WHSC1-like protein 1;
FUNCTION: Histone methyltransferase. Preferentially methylates 'Lys-4' and 'Lys-27' of histone H3. H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation, while 'Lys-27' is a mark for transcriptional repression.
CATALYTIC ACTIVITY: S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
SUBCELLULAR LOCATION: Nucleus (By similarity). Chromosome (By similarity).
TISSUE SPECIFICITY: Highly expressed in brain, heart and skeletal muscle. Expressed at lower level in liver and lung.
DISEASE: Note=Defects in WHSC1L1 may be involved in non small cell lung carcinomas (NSCLC). Amplified or overexpressed in NSCLC.
DISEASE: Note=A chromosomal aberration involving WHSC1L1 is found in childhood acute myeloid leukemia. Translocation t(8;11)(p11.2;p15) with NUP98.
SIMILARITY: Belongs to the histone-lysine methyltransferase family. SET2 subfamily.
SIMILARITY: Contains 1 AWS domain.
SIMILARITY: Contains 4 PHD-type zinc fingers.
SIMILARITY: Contains 1 post-SET domain.
SIMILARITY: Contains 2 PWWP domains.
SIMILARITY: Contains 1 SET domain.
SEQUENCE CAUTION: Sequence=AAG44637.1; Type=Frameshift; Positions=Several; Sequence=AAI07735.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=BAA91110.1; Type=Erroneous initiation;
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/WHSC1L1NSD3ID42810ch8p11.html";

-  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: NSD3
Diseases sorted by gene-association score: leukemia, acute myeloid* (162), wolf-hirschhorn syndrome (18)
* = Manually curated disease association

+  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: 11.70 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 302.26 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 -254.50518-0.491 Picture PostScript Text
3' UTR -378.401539-0.246 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
IPR006560 - AWS
IPR003616 - Post-SET_dom
IPR000313 - PWWP
IPR001214 - SET_dom
IPR019786 - Zinc_finger_PHD-type_CS
IPR011011 - Znf_FYVE_PHD
IPR001965 - Znf_PHD
IPR019787 - Znf_PHD-finger
IPR001841 - Znf_RING
IPR013083 - Znf_RING/FYVE/PHD

Pfam Domains:
PF00855 - PWWP domain

SCOP Domains:
63748 - Tudor/PWWP/MBT

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2DAQ - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q9BZ95
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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 SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0016740 transferase activity
GO:0018024 histone-lysine N-methyltransferase activity
GO:0046872 metal ion binding

Biological Process:
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0016571 histone methylation
GO:0032259 methylation
GO:0034968 histone lysine methylation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome


-  Descriptions from all associated GenBank mRNAs
  AJ295990 - Homo sapiens mRNA for putative chromatin modulator, alternative splice NSD3L.
AJ295991 - Homo sapiens mRNA for Putative Chromatin modulator, alternative splice NSD3L2.
AF332469 - Homo sapiens putative protein WHSC1L1l (WHSC1L1) mRNA, complete cds, alternatively spliced.
LF385434 - JP 2014500723-A/192937: Polycomb-Associated Non-Coding RNAs.
BC101717 - Homo sapiens Wolf-Hirschhorn syndrome candidate 1-like 1, transcript variant long, mRNA (cDNA clone MGC:126766 IMAGE:8069223), complete cds.
BC113469 - Homo sapiens Wolf-Hirschhorn syndrome candidate 1-like 1, mRNA (cDNA clone MGC:142029 IMAGE:8322521), complete cds.
BC143510 - Homo sapiens Wolf-Hirschhorn syndrome candidate 1-like 1, mRNA (cDNA clone MGC:177035 IMAGE:9052018), complete cds.
BC115006 - Homo sapiens Wolf-Hirschhorn syndrome candidate 1-like 1, mRNA (cDNA clone MGC:131572 IMAGE:7961962), complete cds.
BC115007 - Homo sapiens cDNA clone IMAGE:7961965, containing frame-shift errors.
AB384816 - Synthetic construct DNA, clone: pF1KB3497, Homo sapiens WHSC1L1 gene for histone-lysine N-methyltransferase NSD3, complete cds, without stop codon, in Flexi system.
MA621011 - JP 2018138019-A/192937: Polycomb-Associated Non-Coding RNAs.
AK000360 - Homo sapiens cDNA FLJ20353 fis, clone HEP14780.
AJ295992 - Homo sapiens mRNA for putative chromatin modulator, alternative splice NSD3S.
AF332468 - Homo sapiens putative protein WHSC1L1s (WHSC1L1) mRNA, complete cds, alternatively spliced.
LF384349 - JP 2014500723-A/191852: Polycomb-Associated Non-Coding RNAs.
JD090444 - Sequence 71468 from Patent EP1572962.
JD120199 - Sequence 101223 from Patent EP1572962.
AK022560 - Homo sapiens cDNA FLJ12498 fis, clone NT2RM2001668, weakly similar to Homo sapiens putative WHSC1 protein (WHSC1) mRNA, alternative splice product ending in intron 11.
AF255649 - Homo sapiens DC28 mRNA, complete cds.
JD280934 - Sequence 261958 from Patent EP1572962.
JD538107 - Sequence 519131 from Patent EP1572962.
JD413569 - Sequence 394593 from Patent EP1572962.
JD244256 - Sequence 225280 from Patent EP1572962.
JD148864 - Sequence 129888 from Patent EP1572962.
JD552742 - Sequence 533766 from Patent EP1572962.
BC062631 - Homo sapiens Wolf-Hirschhorn syndrome candidate 1-like 1, mRNA (cDNA clone IMAGE:5246860), complete cds.
JD284971 - Sequence 265995 from Patent EP1572962.
JD379105 - Sequence 360129 from Patent EP1572962.
JD355129 - Sequence 336153 from Patent EP1572962.
JD085177 - Sequence 66201 from Patent EP1572962.
BC012059 - Homo sapiens Wolf-Hirschhorn syndrome candidate 1-like 1, mRNA (cDNA clone IMAGE:4552610), complete cds.
JD104260 - Sequence 85284 from Patent EP1572962.
JF432144 - Synthetic construct Homo sapiens clone IMAGE:100073288 Wolf-Hirschhorn syndrome candidate 1-like 1 (WHSC1L1) gene, encodes complete protein.
KJ906205 - Synthetic construct Homo sapiens clone ccsbBroadEn_15875 WHSC1L1 gene, encodes complete protein.
LF371772 - JP 2014500723-A/179275: Polycomb-Associated Non-Coding RNAs.
BC073858 - Homo sapiens Wolf-Hirschhorn syndrome candidate 1-like 1, mRNA (cDNA clone IMAGE:4179405).
LF371770 - JP 2014500723-A/179273: Polycomb-Associated Non-Coding RNAs.
LF371769 - JP 2014500723-A/179272: Polycomb-Associated Non-Coding RNAs.
LF371768 - JP 2014500723-A/179271: Polycomb-Associated Non-Coding RNAs.
AK127594 - Homo sapiens cDNA FLJ45689 fis, clone FCBBF3024911.
LF371766 - JP 2014500723-A/179269: Polycomb-Associated Non-Coding RNAs.
CU680186 - Synthetic construct Homo sapiens gateway clone IMAGE:100018382 5' read WHSC1L1 mRNA.
LF371765 - JP 2014500723-A/179268: Polycomb-Associated Non-Coding RNAs.
BC000030 - Homo sapiens Wolf-Hirschhorn syndrome candidate 1-like 1, mRNA (cDNA clone IMAGE:3505788), partial cds.
AF318339 - Homo sapiens pp14328 mRNA, complete cds.
BC107734 - Homo sapiens Wolf-Hirschhorn syndrome candidate 1-like 1, mRNA (cDNA clone IMAGE:4770567), partial cds.
BC007787 - Homo sapiens Wolf-Hirschhorn syndrome candidate 1-like 1, mRNA (cDNA clone IMAGE:3546345), partial cds.
LF371763 - JP 2014500723-A/179266: Polycomb-Associated Non-Coding RNAs.
LF371762 - JP 2014500723-A/179265: Polycomb-Associated Non-Coding RNAs.
JD387403 - Sequence 368427 from Patent EP1572962.
JD054408 - Sequence 35432 from Patent EP1572962.
JD385932 - Sequence 366956 from Patent EP1572962.
JD460216 - Sequence 441240 from Patent EP1572962.
JD186846 - Sequence 167870 from Patent EP1572962.
LF371751 - JP 2014500723-A/179254: Polycomb-Associated Non-Coding RNAs.
MA619926 - JP 2018138019-A/191852: Polycomb-Associated Non-Coding RNAs.
MA607349 - JP 2018138019-A/179275: Polycomb-Associated Non-Coding RNAs.
MA607347 - JP 2018138019-A/179273: Polycomb-Associated Non-Coding RNAs.
MA607346 - JP 2018138019-A/179272: Polycomb-Associated Non-Coding RNAs.
MA607345 - JP 2018138019-A/179271: Polycomb-Associated Non-Coding RNAs.
MA607343 - JP 2018138019-A/179269: Polycomb-Associated Non-Coding RNAs.
MA607342 - JP 2018138019-A/179268: Polycomb-Associated Non-Coding RNAs.
MA607340 - JP 2018138019-A/179266: Polycomb-Associated Non-Coding RNAs.
MA607339 - JP 2018138019-A/179265: Polycomb-Associated Non-Coding RNAs.
MA607328 - JP 2018138019-A/179254: Polycomb-Associated Non-Coding RNAs.

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

Protein Q9BZ95 (Reactome details) participates in the following event(s):

R-HSA-5159245 SETD3, SETD7 (KMT7), WHSC1L1 (KMT3F), Core MLL complex methylate lysine-5 of histone H3 (H3K4)
R-HSA-5637686 WHSC1L1 (KMT3F), Core MLL complex, SMYD3 (KMT3E) methylate methyl-lysine-5 of histone H3 (H3K4)
R-HSA-5638333 WHSC1 (KMT3G) methylates lysine-28 of histone H3 (H3K27)
R-HSA-5649800 WHSC1L1 (KMT3F) methylates methyl-lysine-28 of histone H3 (H3K27)
R-HSA-5649802 WHSC1L1 (KMT3F) methylates dimethyl-lysine-28 of histone H3 (H3K27)
R-HSA-3214841 PKMTs methylate histone lysines
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-4839726 Chromatin organization

-  Other Names for This Gene
  Alternate Gene Symbols: B7ZL11, D3DSX1, DC28, ENST00000316985.1, ENST00000316985.2, ENST00000316985.3, ENST00000316985.4, ENST00000316985.5, ENST00000316985.6, NM_017778, NSD3 , NSD3_HUMAN, Q1RMD3, Q3B796, Q6ZSA5, Q9BYU8, Q9BYU9, Q9BZ95, Q9H2M8, Q9H9W9, Q9NXA6, uc317qdf.1, uc317qdf.2, WHSC1L1
UCSC ID: ENST00000316985.7_5
RefSeq Accession: NM_017778.3
Protein: Q9BZ95 (aka NSD3_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.