Setd1b SET domain containing 1B [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Setd1bprovided by MGI
Official Full Name: SET domain containing 1Bprovided by MGI
Primary source: MGI:MGI:2652820
See related: Ensembl:ENSMUSG00000038384 AllianceGenome:MGI:2652820
Gene type: protein coding
RefSeq status: INFERRED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: KMT2G; mKIAA1076
Summary: Predicted to enable RNA binding activity and histone-lysine N-methyltransferase activity. Predicted to contribute to histone methyltransferase activity (H3-K4 specific). Predicted to be involved in histone H3-K4 dimethylation; histone H3-K4 monomethylation; and histone H3-K4 trimethylation. Predicted to act upstream of or within chromatin organization and methylation. Located in nucleus. Is expressed in several structures, including brain; cranium; early conceptus; oocyte; and sensory organ. Orthologous to human SETD1B (SET domain containing 1B, histone lysine methyltransferase). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in thymus adult (RPKM 17.1), adrenal adult (RPKM 12.0) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 5 F; 5 62.8 cM

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	5	NC_000071.7 (123280109..123306693)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	5	NC_000071.6 (123142040..123168630)

Chromosome 5 - NC_000071.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Expression of the histone lysine methyltransferases SETD1B, SETDB1, SETD2, and CFP1 exhibits significant changes in the oocytes and granulosa cells of aged mouse ovaries.
Title: Expression of the histone lysine methyltransferases SETD1B, SETDB1, SETD2, and CFP1 exhibits significant changes in the oocytes and granulosa cells of aged mouse ovaries.
Postnatal expression of the lysine methyltransferase SETD1B is essential for learning and the regulation of neuron-enriched genes.
Title: Postnatal expression of the lysine methyltransferase SETD1B is essential for learning and the regulation of neuron-enriched genes.
Setd1b is essential for hematopoietic stem and progenitor cell homeostasis in mice.
Title: The H3K4 methyltransferase Setd1b is essential for hematopoietic stem and progenitor cell homeostasis in mice.
Expression profiling of Setd1b(Gdf9) cKO MII oocytes revealed (1) that Setd1b promotes the expression of the major oocyte transcription factors including Obox1, 2, 5, 7, Meis2 and Sall4; and (2) twice as many mRNAs were upregulated than downregulated, suggesting that Setd1b also promotes the expression of negative regulators of oocyte development with multiple Zfp-KRAB factors implicated.
Title: Setd1b, encoding a histone 3 lysine 4 methyltransferase, is a maternal effect gene required for the oogenic gene expression program.
The H3K4 methyltransferase Setd1a is first required at the epiblast stage, whereas Setd1b becomes essential after gastrulation.
Title: The H3K4 methyltransferase Setd1a is first required at the epiblast stage, whereas Setd1b becomes essential after gastrulation.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (4) 1 citation
Endonuclease-mediated (2)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Setd1b (e-PCR), detects polymorphism
- UniSTS:479137

RH124405 (e-PCR)
- UniSTS:161227

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables histone H3K4 methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
contributes_to histone H3K4 methyltransferase activity	ISO Inferred from Sequence Orthology more info
enables histone H3K4 monomethyltransferase activity	IEA Inferred from Electronic Annotation more info
enables methyltransferase activity	IEA Inferred from Electronic Annotation more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables transferase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within chromatin organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within methylation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of Set1C/COMPASS complex	IBA Inferred from Biological aspect of Ancestor more info
part_of Set1C/COMPASS complex	ISO Inferred from Sequence Orthology more info
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
part_of histone methyltransferase complex	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: histone-lysine N-methyltransferase SETD1B

Names: SET domain-containing protein 1B

NP_001035488.2

EC 2.1.1.364

XP_006530300.1

EC 2.1.1.364

XP_006530301.1

EC 2.1.1.364

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_001040398.2 → NP_001035488.2 histone-lysine N-methyltransferase SETD1B

See identical proteins and their annotated locations for NP_001035488.2

Status: INFERRED

Source sequence(s)

AC158114, AI463740, AK141316, BC038367, CF536496

Consensus CDS

CCDS59684.1

UniProtKB/Swiss-Prot

Q80TK9, Q8CFQ8, Q8CFT2, Q8CGD1

Related

ENSMUSP00000133933.2, ENSMUST00000163030.9

Conserved Domains (3) summary

cd19169
Location:1834 → 1981

SET_SETD1; SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and similar proteins

cd12549
Location:100 → 192

RRM_Set1B; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B)

pfam11764
Location:1698 → 1840

N-SET; COMPASS (Complex proteins associated with Set1p) component N

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000071.7 Reference GRCm39 C57BL/6J

Range

123280109..123306693

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006530238.5 → XP_006530301.1 histone-lysine N-methyltransferase SETD1B isoform X1

See identical proteins and their annotated locations for XP_006530301.1

Conserved Domains (3) summary

cd12549
Location:100 → 192

RRM_Set1B; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B)

pfam11764
Location:1698 → 1841

N-SET; COMPASS (Complex proteins associated with Set1p) component N

cd19169
Location:1835 → 1982

SET_SETD1; SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and similar proteins
XM_006530237.4 → XP_006530300.1 histone-lysine N-methyltransferase SETD1B isoform X1

See identical proteins and their annotated locations for XP_006530300.1

Conserved Domains (3) summary

cd12549
Location:100 → 192

RRM_Set1B; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B)

pfam11764
Location:1698 → 1841

N-SET; COMPASS (Complex proteins associated with Set1p) component N

cd19169
Location:1835 → 1982

SET_SETD1; SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and similar proteins

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_177581.2: Suppressed sequence

Description

NM_177581.2: This RefSeq was suppressed temporarily based on the calculation that the annotated protein was shorter than a protein or proteins from a putative ortholog.