SETD3 SET domain containing 3, actin N3(tau)-histidine methyltransferase [Homo sapiens (human)] - Gene

Summary

Official Symbol: SETD3provided by HGNC
Official Full Name: SET domain containing 3, actin N3(tau)-histidine methyltransferaseprovided by HGNC
Primary source: HGNC:HGNC:20493
See related: Ensembl:ENSG00000183576 MIM:615671; AllianceGenome:HGNC:20493
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: hSETD3; C14orf154
Summary: Enables protein-L-histidine N-tele-methyltransferase activity. Involved in actin modification and peptidyl-histidine methylation. Located in cytoplasm. [provided by Alliance of Genome Resources, Dec 2024]
Expression: Ubiquitous expression in testis (RPKM 33.6), kidney (RPKM 26.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 14q32.2

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (99397748..99486458, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (93629309..93718026, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (99864085..99947196, complement)

Chromosome 14 - NC_000014.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Examining prestructured beta-actin peptides as substrates of histidine methyltransferase SETD3.
Title: Examining prestructured β-actin peptides as substrates of histidine methyltransferase SETD3.
SETD3 functions beyond histidine methylation.
Title: SETD3 functions beyond histidine methylation.
The EV71 2A protease occupies the central cleft of SETD3 and disrupts SETD3-actin interaction.
Title: The EV71 2A protease occupies the central cleft of SETD3 and disrupts SETD3-actin interaction.
The Role of Trp79 in beta-Actin on Histidine Methyltransferase SETD3 Catalysis.
Title: The Role of Trp79 in β-Actin on Histidine Methyltransferase SETD3 Catalysis.
CircSETD3 mediates acquired resistance to gefitinib in non-small lung cancer cells by FXR1/ECT2 pathway.
Title: CircSETD3 mediates acquired resistance to gefitinib in non-small lung cancer cells by FXR1/ECT2 pathway.
Structure-function conservation between the methyltransferases SETD3 and SETD6.
Title: Structure-function conservation between the methyltransferases SETD3 and SETD6.
Proteolytic Activities of Enterovirus 2A Do Not Depend on Its Interaction with SETD3.
Title: Proteolytic Activities of Enterovirus 2A Do Not Depend on Its Interaction with SETD3.
Importance of Ile71 in beta-actin on histidine methyltransferase SETD3 catalysis.
Title: Importance of Ile71 in β-actin on histidine methyltransferase SETD3 catalysis.
Stabilization of SETD3 by deubiquitinase USP27 enhances cell proliferation and hepatocellular carcinoma progression.
Title: Stabilization of SETD3 by deubiquitinase USP27 enhances cell proliferation and hepatocellular carcinoma progression.
The methyltransferase SETD3-mediated histidine methylation: Biological functions and potential implications in cancers.
Title: The methyltransferase SETD3-mediated histidine methylation: Biological functions and potential implications in cancers.

Submit: New GeneRIF Correction See all GeneRIFs (24)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

ECD01521 (e-PCR)
- UniSTS:282624

REN48704 (e-PCR)
- UniSTS:373504

REN48705 (e-PCR)
- UniSTS:373505

REN48706 (e-PCR)
- UniSTS:373506

REN48707 (e-PCR)
- UniSTS:373507

REN48708 (e-PCR)
- UniSTS:373508

REN48709 (e-PCR)
- UniSTS:373509

REN48710 (e-PCR)
- UniSTS:373510

REN48711 (e-PCR)
- UniSTS:373511

REN48712 (e-PCR)
- UniSTS:373512

REN48713 (e-PCR)
- UniSTS:373513

REN48714 (e-PCR)
- UniSTS:373514

REN48715 (e-PCR)
- UniSTS:373515

REN48716 (e-PCR)
- UniSTS:373516

REN48717 (e-PCR)
- UniSTS:373517

ECD13127 (e-PCR)
- UniSTS:294158

REN48718 (e-PCR)
- UniSTS:373518

REN48719 (e-PCR)
- UniSTS:373519

REN48720 (e-PCR)
- UniSTS:373520

REN48721 (e-PCR)
- UniSTS:373521

REN48722 (e-PCR)
- UniSTS:373522

REN48723 (e-PCR)
- UniSTS:373523

REN48724 (e-PCR)
- UniSTS:373524

REN48725 (e-PCR)
- UniSTS:373525

REN48726 (e-PCR)
- UniSTS:373526

ECD00770 (e-PCR)
- UniSTS:281879

REN48727 (e-PCR)
- UniSTS:373527

REN48728 (e-PCR)
- UniSTS:373528

REN48729 (e-PCR)
- UniSTS:373529

ECD12369 (e-PCR)
- UniSTS:293402

REN48730 (e-PCR)
- UniSTS:373530

ECD12370 (e-PCR)
- UniSTS:293403

REN48731 (e-PCR)
- UniSTS:373531

REN48732 (e-PCR)
- UniSTS:373532

REN48733 (e-PCR)
- UniSTS:373533

ECD14433 (e-PCR)
- UniSTS:295454

REN48734 (e-PCR)
- UniSTS:373534

REN48735 (e-PCR)
- UniSTS:373535

REN48736 (e-PCR)
- UniSTS:373536

REN48737 (e-PCR)
- UniSTS:373537

REN48738 (e-PCR)
- UniSTS:373538

REN48739 (e-PCR)
- UniSTS:373539

REN48740 (e-PCR)
- UniSTS:373540

REN48741 (e-PCR)
- UniSTS:373541

REN48742 (e-PCR)
- UniSTS:373542

ECD10840 (e-PCR)
- UniSTS:291879

REN48743 (e-PCR)
- UniSTS:373543

REN48744 (e-PCR)
- UniSTS:373544

REN48745 (e-PCR)
- UniSTS:373545

REN48746 (e-PCR)
- UniSTS:373546

ECD07502 (e-PCR)
- UniSTS:288555

REN48747 (e-PCR)
- UniSTS:373547

RH68701 (e-PCR)
- UniSTS:28716

REN48748 (e-PCR)
- UniSTS:373548

REN48749 (e-PCR)
- UniSTS:373549

REN48750 (e-PCR)
- UniSTS:373550

ECD01052 (e-PCR)
- UniSTS:282159

REN48751 (e-PCR)
- UniSTS:373551

REN48752 (e-PCR)
- UniSTS:373552

REN48753 (e-PCR)
- UniSTS:373553

REN48754 (e-PCR)
- UniSTS:373554

REN48755 (e-PCR)
- UniSTS:373555

REN48756 (e-PCR)
- UniSTS:373556

ECD13166 (e-PCR)
- UniSTS:294197

REN48757 (e-PCR)
- UniSTS:373557

REN48758 (e-PCR)
- UniSTS:373558

REN48759 (e-PCR)
- UniSTS:373559

REN48760 (e-PCR)
- UniSTS:373560

ECD07775 (e-PCR)
- UniSTS:288825

REN48761 (e-PCR)
- UniSTS:373561

REN48762 (e-PCR)
- UniSTS:373562

REN48763 (e-PCR)
- UniSTS:373563

REN48764 (e-PCR)
- UniSTS:373564

REN48765 (e-PCR)
- UniSTS:373565

REN48766 (e-PCR)
- UniSTS:373566

REN48767 (e-PCR)
- UniSTS:373567

ECD16521 (e-PCR)
- UniSTS:297536

REN48768 (e-PCR)
- UniSTS:373568

REN48769 (e-PCR)
- UniSTS:373569

REN48770 (e-PCR)
- UniSTS:373570

REN48771 (e-PCR)
- UniSTS:373571

REN48772 (e-PCR)
- UniSTS:373572

REN48773 (e-PCR)
- UniSTS:373573

REN48774 (e-PCR)
- UniSTS:373574

REN48775 (e-PCR)
- UniSTS:373575

REN48776 (e-PCR)
- UniSTS:373576

REN48777 (e-PCR)
- UniSTS:373577

REN48778 (e-PCR)
- UniSTS:373578

REN48779 (e-PCR)
- UniSTS:373579

REN48780 (e-PCR)
- UniSTS:373580

REN48781 (e-PCR)
- UniSTS:373581

REN48782 (e-PCR)
- UniSTS:373582

REN48783 (e-PCR)
- UniSTS:373583

ECD00322 (e-PCR)
- UniSTS:281435

ECD01099 (e-PCR)
- UniSTS:282206

ECD07813 (e-PCR)
- UniSTS:288863

ECD05757 (e-PCR)
- UniSTS:286819

ECD05758 (e-PCR)
- UniSTS:286820

ECD04734 (e-PCR)
- UniSTS:285805

ECD13479 (e-PCR)
- UniSTS:294509

ECD05512 (e-PCR)
- UniSTS:286576

ECD05513 (e-PCR)
- UniSTS:286577

ECD03193 (e-PCR)
- UniSTS:284278

G36029 (e-PCR)
- UniSTS:17533

SHGC-35053 (e-PCR)
- UniSTS:35980

RH78765 (e-PCR)
- UniSTS:85902

ECD04036 (e-PCR)
- UniSTS:285115

ECD00692 (e-PCR)
- UniSTS:281801

ECD21029 (e-PCR)
- UniSTS:302026

A006R32 (e-PCR)
- UniSTS:16595

SHGC-30385 (e-PCR)
- UniSTS:4821

REN48671 (e-PCR)
- UniSTS:373471

REN48672 (e-PCR)
- UniSTS:373472

REN48673 (e-PCR)
- UniSTS:373473

REN48674 (e-PCR)
- UniSTS:373474

REN48675 (e-PCR)
- UniSTS:373475

REN48676 (e-PCR)
- UniSTS:373476

REN48677 (e-PCR)
- UniSTS:373477

REN48678 (e-PCR)
- UniSTS:373478

REN48679 (e-PCR)
- UniSTS:373479

REN48680 (e-PCR)
- UniSTS:373480

REN48681 (e-PCR)
- UniSTS:373481

REN48682 (e-PCR)
- UniSTS:373482

REN48683 (e-PCR)
- UniSTS:373483

REN48684 (e-PCR)
- UniSTS:373484

ECD03829 (e-PCR)
- UniSTS:284909

ECD22095 (e-PCR)
- UniSTS:303085

REN48685 (e-PCR)
- UniSTS:373485

REN48686 (e-PCR)
- UniSTS:373486

REN48687 (e-PCR)
- UniSTS:373487

REN48688 (e-PCR)
- UniSTS:373488

REN48689 (e-PCR)
- UniSTS:373489

REN48690 (e-PCR)
- UniSTS:373490

ECD07705 (e-PCR)
- UniSTS:288755

REN48691 (e-PCR)
- UniSTS:373491

REN48692 (e-PCR)
- UniSTS:373492

REN48693 (e-PCR)
- UniSTS:373493

REN48694 (e-PCR)
- UniSTS:373494

REN48695 (e-PCR)
- UniSTS:373495

ECD04874 (e-PCR)
- UniSTS:285944

REN48696 (e-PCR)
- UniSTS:373496

REN48697 (e-PCR)
- UniSTS:373497

REN48698 (e-PCR)
- UniSTS:373498

REN48699 (e-PCR)
- UniSTS:373499

REN48700 (e-PCR)
- UniSTS:373500

REN48701 (e-PCR)
- UniSTS:373501

REN48702 (e-PCR)
- UniSTS:373502

REN48703 (e-PCR)
- UniSTS:373503

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA polymerase II-specific DNA-binding transcription factor binding	IEA Inferred from Electronic Annotation more info
enables actin binding	IEA Inferred from Electronic Annotation more info
enables histone H3K36 methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K36 methyltransferase activity	ISS Inferred from Sequence or Structural Similarity more info
enables histone H3K4 methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-L-histidine N-tele-methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein-L-histidine N-tele-methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
NOT enables protein-lysine N-methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables transcription coactivator activity	IBA Inferred from Biological aspect of Ancestor more info
enables transcription coactivator activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in actin modification	IBA Inferred from Biological aspect of Ancestor more info
involved_in actin modification	IDA Inferred from Direct Assay more info	PubMed
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in peptidyl-histidine methylation	IDA Inferred from Direct Assay more info	PubMed
NOT involved_in peptidyl-lysine trimethylation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of muscle cell differentiation	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 regulation of uterine smooth muscle contraction	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of uterine smooth muscle contraction	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in chromatin	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info

General protein information

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Preferred Names: actin-histidine N-methyltransferase

Names: SET domain containing 3, actin histidine methyltransferase; SET domain-containing protein 3; histone-lysine N-methyltransferase setd3; protein-L-histidine N-tele-methyltransferase

NP_115609.2

EC 2.1.1.85

NP_954574.1

EC 2.1.1.85

XP_011535533.2

EC 2.1.1.85

XP_011535534.1

EC 2.1.1.85

XP_011535535.1

EC 2.1.1.85

XP_011535537.1

EC 2.1.1.85

XP_016877188.1

EC 2.1.1.85

XP_016877189.1

EC 2.1.1.85

XP_047287761.1

EC 2.1.1.85

XP_054232780.1

EC 2.1.1.85

XP_054232781.1

EC 2.1.1.85

XP_054232782.1

EC 2.1.1.85

XP_054232783.1

EC 2.1.1.85

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.

mRNA and Protein(s)

NM_032233.3 → NP_115609.2 actin-histidine N-methyltransferase isoform a

See identical proteins and their annotated locations for NP_115609.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).

Source sequence(s)

AK026680, BC037395, BX161471, CB988965

Consensus CDS

CCDS9951.1

UniProtKB/Swiss-Prot

A0PJU3, A5PLP0, B4DZE8, Q0VAQ2, Q659C0, Q86TU7, Q86TU8, Q96GY9, Q9H5U5

Related

ENSP00000327436.5, ENST00000331768.10

Conserved Domains (2) summary

cd19176
Location:80 → 329

SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins

pfam09273
Location:350 → 475

Rubis-subs-bind; Rubisco LSMT substrate-binding
NM_199123.2 → NP_954574.1 actin-histidine N-methyltransferase isoform b

See identical proteins and their annotated locations for NP_954574.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1, that causes a frameshift. The resulting isoform (b) is shorter and has a unique C-terminus compared to isoform a.

Source sequence(s)

BC009054, CB988965

Consensus CDS

CCDS9952.1

UniProtKB/TrEMBL

A6NJ55, Q6NXR6

Related

ENSP00000327910.3, ENST00000329331.7

Conserved Domains (1) summary

cd19176
Location:80 → 282

SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000014.9 Reference GRCh38.p14 Primary Assembly

Range

99397748..99486458 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017021699.2 → XP_016877188.1 actin-histidine N-methyltransferase isoform X1

UniProtKB/Swiss-Prot

A0PJU3, A5PLP0, B4DZE8, Q0VAQ2, Q659C0, Q86TU7, Q86TU8, Q96GY9, Q9H5U5

Conserved Domains (2) summary

cd19176
Location:80 → 329

SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins

pfam09273
Location:350 → 475

Rubis-subs-bind; Rubisco LSMT substrate-binding
XM_011537233.3 → XP_011535535.1 actin-histidine N-methyltransferase isoform X2

Conserved Domains (2) summary

pfam09273
Location:292 → 417

Rubis-subs-bind; Rubisco LSMT substrate-binding

cd19176
Location:80 → 271

SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins
XM_011537231.3 → XP_011535533.2 actin-histidine N-methyltransferase isoform X1

UniProtKB/Swiss-Prot

A0PJU3, A5PLP0, B4DZE8, Q0VAQ2, Q659C0, Q86TU7, Q86TU8, Q96GY9, Q9H5U5

Conserved Domains (2) summary

cd19176
Location:80 → 329

SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins

pfam09273
Location:350 → 475

Rubis-subs-bind; Rubisco LSMT substrate-binding
XM_011537232.4 → XP_011535534.1 actin-histidine N-methyltransferase isoform X1

See identical proteins and their annotated locations for XP_011535534.1

UniProtKB/Swiss-Prot

A0PJU3, A5PLP0, B4DZE8, Q0VAQ2, Q659C0, Q86TU7, Q86TU8, Q96GY9, Q9H5U5

Conserved Domains (2) summary

cd19176
Location:80 → 329

SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins

pfam09273
Location:350 → 475

Rubis-subs-bind; Rubisco LSMT substrate-binding
XM_047431805.1 → XP_047287761.1 actin-histidine N-methyltransferase isoform X1

UniProtKB/Swiss-Prot

A0PJU3, A5PLP0, B4DZE8, Q0VAQ2, Q659C0, Q86TU7, Q86TU8, Q96GY9, Q9H5U5
XM_017021700.2 → XP_016877189.1 actin-histidine N-methyltransferase isoform X1

UniProtKB/Swiss-Prot

A0PJU3, A5PLP0, B4DZE8, Q0VAQ2, Q659C0, Q86TU7, Q86TU8, Q96GY9, Q9H5U5

Conserved Domains (2) summary

cd19176
Location:80 → 329

SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins

pfam09273
Location:350 → 475

Rubis-subs-bind; Rubisco LSMT substrate-binding
XM_011537235.1 → XP_011535537.1 actin-histidine N-methyltransferase isoform X3

See identical proteins and their annotated locations for XP_011535537.1

UniProtKB/TrEMBL

A6NJ55, Q6NXR6

Conserved Domains (1) summary

cd19176
Location:80 → 282

SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins