set-16 PHD-type domain-containing protein [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: set-16
Official Full Name: PHD-type domain-containing protein
Primary source: WormBase:WBGene00011729
Locus tag: CELE_T12D8.1
See related: AllianceGenome:WB:WBGene00011729
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Caenorhabditis elegans (strain: Bristol N2)
Lineage: Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
Summary: Enables histone H3K4 methyltransferase activity. Involved in programmed cell death and regulation of vulval development. Part of MLL3/4 complex. Is expressed in several structures, including P3.p hermaphrodite; P4.p hermaphrodite; P5.p hermaphrodite; germ line; and linker cell. Human ortholog(s) of this gene implicated in Kabuki syndrome; Kleefstra syndrome 2; carcinoma (multiple); intracranial aneurysm; and stomach cancer (multiple). Orthologous to several human genes including KMT2D (lysine methyltransferase 2D). [provided by Alliance of Genome Resources, Nov 2024]
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Genomic context

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See set-16 in Genome Data Viewer

Location:: chromosome: III

Exon count:: 15

Sequence:: Chromosome: III; NC_003281.10 (13643916..13656637)

Chromosome III - NC_003281.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003281.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

T12D8.2 (e-PCR)
- UniSTS:321064

T12D8.1 (e-PCR)
- UniSTS:308017

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables histone H3 methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K4 methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K4 methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein-lysine N-methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables transcription coactivator activity	IBA Inferred from Biological aspect of Ancestor more info
enables transferase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in programmed cell death	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of vulval development	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
part_of MLL3/4 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of MLL3/4 complex	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: PHD-type domain-containing protein

NP_499819.3

Confirmed by transcript evidence

NCBI Reference Sequences (RefSeq)

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Genome Annotation

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

Reference assembly

Genomic

NC_003281.10 Reference assembly

Range

13643916..13656637

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_067418.7 → NP_499819.3 PHD-type domain-containing protein [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_499819.3

Status: REVIEWED

UniProtKB/TrEMBL

G5EGI1

Conserved Domains (9) summary

smart00542
Location:2112 → 2199

FYRC; FY-rich domain, C-terminal region

smart00317
Location:2333 → 2457

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

cd15489
Location:42 → 84

PHD_SF; PHD finger superfamily

cd15512
Location:427 → 477

PHD4_KMT2C_like; PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD domain 3 found in KMT2D

cd15513
Location:479 → 524

PHD5_KMT2C_like; PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D

cd15514
Location:554 → 604

PHD6_KMT2C_like; PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 5 found in KMT2D

cd15666
Location:1904 → 2008

ePHD2_KMT2C_like; Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D)

pfam05964
Location:2055 → 2104

FYRN; F/Y-rich N-terminus

pfam07083
Location:1060 → 1163

DUF1351; Protein of unknown function (DUF1351)