LOC4342575 DNA (cytosine-5)-methyltransferase 1B-like [Oryza sativa Japonica Group (Japanese rice)] - Gene

Summary

Gene symbol: LOC4342575
Gene description: DNA (cytosine-5)-methyltransferase 1B-like
Locus tag: OSNPB_070182900
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Oryza sativa Japonica Group
Lineage: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
Also known as: MET1; MET1B; MET1-2; OsMET1b; OsMET1-2; OJ1506_G02.17
Expression: Broad expression in flower buds (RPKM 6.4), milk grains (RPKM 5.1) and 5 other tissues See more
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Genomic context

Location:: chromosome: 7

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_06	current	ASM3414082v1 (GCF_034140825.1)	7	NC_089041.1 (4441776..4452645)
102	previous assembly	IRGSP-1.0 (GCF_001433935.1)	7	NC_029262.1 (4381088..4391957)

Chromosome 7 - NC_089041.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Transcriptome profiling of various organs at different developmental stages in rice
Description: Transcriptom profiling in flower buds, flowers, flag leaves and roots sampled before flowering and after flowering, milk grains and mature seeds
BioProject: PRJNA243371
Publication: PMID 26387578
Analysis date: Fri Dec 15 20:02:59 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Loss of OsMet1 expression by RNAi does not significantly affect levels and patterns of de novo DNA methylation or post-transcriptional mRNA suppression.
Title: De novo DNA methylation induced by siRNA targeted to endogenous transcribed sequences is gene-specific and OsMet1-independent in rice.

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General gene information

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Gene Ontology Provided by RefSeq

Function	Evidence Code	Pubs
enables DNA (cytosine-5-)-methyltransferase activity	IEA Inferred from Electronic Annotation more info	PubMed
enables DNA binding	IEA Inferred from Electronic Annotation more info	PubMed
enables chromatin binding	IEA Inferred from Electronic Annotation more info	PubMed

Process	Evidence Code	Pubs
involved_in negative regulation of gene expression via chromosomal CpG island methylation	IEA Inferred from Electronic Annotation more info	PubMed

Component	Evidence Code	Pubs
located_in nucleus	IEA Inferred from Electronic Annotation more info	PubMed

General protein information

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Preferred Names: dNA (cytosine-5)-methyltransferase 1B

Names: DNA (cytosine-5)-methyltransferase 1B; DNA methyltransferase 1-2; LOC_Os07g08500; putative DNA methyltransferase; putative cytosine-5 DNA methyltransferase

NP_001409175.1

EC 2.1.1.37

XP_025882910.1

EC 2.1.1.37

XP_066168055.1

EC 2.1.1.37

XP_066168056.1

EC 2.1.1.37

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_001422246.1 → NP_001409175.1 dNA (cytosine-5)-methyltransferase 1B

Status: VALIDATED

Source sequence(s)

AP014963

UniProtKB/Swiss-Prot

A0A0P0X2V1, B1Q3J6, B1Q3J7, Q0D857, Q69W70, Q7PC77

UniProtKB/TrEMBL

B9FVV0

RefSeqs of Annotated Genomes: GCF_034140825.1-RS_2024_06

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

Reference ASM3414082v1 Primary Assembly

Genomic

NC_089041.1 Reference ASM3414082v1 Primary Assembly

Range

4441776..4452645

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_066311959.1 → XP_066168056.1 dNA (cytosine-5)-methyltransferase 1B isoform X3
XM_066311958.1 → XP_066168055.1 dNA (cytosine-5)-methyltransferase 1B isoform X1
XM_026027125.2 → XP_025882910.1 dNA (cytosine-5)-methyltransferase 1B isoform X2

UniProtKB/Swiss-Prot

A0A0P0X2V1, B1Q3J6, B1Q3J7, Q0D857, Q69W70, Q7PC77

UniProtKB/TrEMBL

B9FVV0

Conserved Domains (4) summary

cd04708
Location:905 → 1105

BAH_plantDCM_II; BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects ...

pfam12047
Location:107 → 240

DNMT1-RFD; Cytosine specific DNA methyltransferase replication foci domain

cl02608
Location:738 → 873

BAH; or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in ...

cl17173
Location:1093 → 1522

AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...