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NSD3 nuclear receptor binding SET domain protein 3 [ Homo sapiens (human) ]

Gene ID: 54904, updated on 25-Jan-2024

Summary

Official Symbol
NSD3provided by HGNC
Official Full Name
nuclear receptor binding SET domain protein 3provided by HGNC
Primary source
HGNC:HGNC:12767
See related
Ensembl:ENSG00000147548 MIM:607083; AllianceGenome:HGNC:12767
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
KMT3F; KMT3G; WHISTLE; WHSC1L1; pp14328
Summary
This gene is related to the Wolf-Hirschhorn syndrome candidate-1 gene and encodes a protein with PWWP (proline-tryptophan-tryptophan-proline) domains. This protein methylates histone H3 at lysine residues 4 and 27, which represses gene transcription. Two alternatively spliced variants have been described. [provided by RefSeq, May 2015]
Expression
Ubiquitous expression in ovary (RPKM 10.0), brain (RPKM 9.8) and 25 other tissues See more
Orthologs
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Genomic context

See NSD3 in Genome Data Viewer
Location:
8p11.23
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (38269704..38382271, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (38546659..38659240, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (38127222..38239789, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:38033837-38034694 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27246 Neighboring gene BAG cochaperone 4 Neighboring gene Sharpr-MPRA regulatory region 4585 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19117 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:38089405-38089904 Neighboring gene DDHD domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19119 Neighboring gene phospholipid phosphatase 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19120 Neighboring gene NUP98-NSD3 recombination region Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27247 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38235530-38236031 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38238312-38238846 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:38239137-38239927 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19122 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19123 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:38242638-38243268 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr8:38243269-38243898 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38244052-38244553 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19125 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38247000-38247501 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38248280-38248781 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38257600-38258101 Neighboring gene uncharacterized LOC102723716 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:38261681-38262180 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38262831-38263332 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19126 Neighboring gene leucine zipper and EF-hand containing transmembrane protein 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38269931-38270603 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:38270604-38271277 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38272896-38273666 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr8:38274107-38274772 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38275681-38276444 Neighboring gene OCT4 hESC enhancer GRCh37_chr8:38277305-38277806 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38277908-38278453 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38278454-38278998 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:38278999-38279544 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:38279545-38280088 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr8:38280202-38280702 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr8:38280703-38281203 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:38282951-38283642 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38285189-38286186 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38287183-38288180 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38289284-38289961 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38289962-38290638 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr8:38292133-38292640 Neighboring gene fibroblast growth factor receptor 1 Neighboring gene ribosomal protein S20 pseudogene 22

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ20353, MGC126766, MGC142029, DKFZp667H044

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
more info
 
involved_in methylation IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
 
Component Evidence Code Pubs
part_of chromatin IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleus IMP
Inferred from Mutant Phenotype
more info
PubMed 

General protein information

Preferred Names
histone-lysine N-methyltransferase NSD3
Names
Wolf-Hirschhorn syndrome candidate 1-like 1
nuclear SET domain-containing protein 3
protein whistle
NP_060248.2
NP_075447.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_023292.2 RefSeqGene

    Range
    5000..117567
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_017778.3NP_060248.2  histone-lysine N-methyltransferase NSD3 isoform short

    See identical proteins and their annotated locations for NP_060248.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (short) contains an alternative 3' end sequence. The shorter protein encoded has a different carboxy terminus than the protein encoded by variant long.
    Source sequence(s)
    AF332468
    Consensus CDS
    CCDS6105.1
    UniProtKB/Swiss-Prot
    Q9BZ95
    Related
    ENSP00000313410.3, ENST00000316985.7
    Conserved Domains (1) summary
    cd05837
    Location:267383
    MSH6_like; The PWWP domain is present in MSH6, a mismatch repair protein homologous to bacterial MutS. The PWWP domain of histone-lysine N-methyltransferase, also known as Nuclear SET domain-containing protein 3, is also included. Mutations in MSH6 have been ...
  2. NM_023034.2NP_075447.1  histone-lysine N-methyltransferase NSD3 isoform long

    See identical proteins and their annotated locations for NP_075447.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (long) contains an alternative 3' end sequence. The longer protein encoded has a different carboxy terminus than the protein encoded by variant short.
    Source sequence(s)
    AC087362, AF332469
    Consensus CDS
    CCDS43729.1
    UniProtKB/Swiss-Prot
    B7ZL11, D3DSX1, Q1RMD3, Q3B796, Q6ZSA5, Q9BYU8, Q9BYU9, Q9BZ95, Q9H2M8, Q9H9W9, Q9NXA6
    Related
    ENSP00000313983.7, ENST00000317025.13
    Conserved Domains (10) summary
    cd05837
    Location:267383
    MSH6_like; The PWWP domain is present in MSH6, a mismatch repair protein homologous to bacterial MutS. The PWWP domain of histone-lysine N-methyltransferase, also known as Nuclear SET domain-containing protein 3, is also included. Mutations in MSH6 have been ...
    cd05838
    Location:9581051
    WHSC1_related; The PWWP domain was first identified in the WHSC1 (Wolf-Hirschhorn syndrome candidate 1) protein, a protein implicated in Wolf-Hirschhorn syndrome (WHS). When translocated, WHSC1 plays a role in lymphoid multiple myeloma (MM) disease, also known as ...
    smart00570
    Location:10941144
    AWS; associated with SET domains
    smart00317
    Location:11451268
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    COG5034
    Location:602746
    TNG2; Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
    cd15649
    Location:703746
    PHD1_NSD3; PHD finger 1 found in nuclear SET domain-containing protein 3 (NSD3)
    cd15652
    Location:751797
    PHD2_NSD3; PHD finger 2 found in nuclear SET domain-containing protein 3 (NSD3)
    cd15655
    Location:798850
    PHD3_NSD3; PHD finger 3 found in nuclear SET domain-containing protein 3 (NSD3)
    cd15658
    Location:917952
    PHD4_NSD3; PHD finger 4 found in nuclear SET domain-containing protein 3 (NSD3)
    cd15661
    Location:13231365
    PHD5_NSD3; PHD finger 5 found in nuclear SET domain-containing protein 3 (NSD3)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    38269704..38382271 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    38546659..38659240 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)