Sfmbt2 Scm-like with four mbt domains 2 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Sfmbt2provided by MGI
Official Full Name: Scm-like with four mbt domains 2provided by MGI
Primary source: MGI:MGI:2447794
See related: Ensembl:ENSMUSG00000061186 AllianceGenome:MGI:2447794
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: D2Wsu23e; D330030P06Rik
Summary: Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in negative regulation of DNA-templated transcription and negative regulation of gene expression. Predicted to be located in aggresome; cytosol; and nuclear speck. Predicted to be active in nucleus. Is expressed in several structures, including extraembryonic component; liver; lung; placenta; and spleen. Orthologous to human SFMBT2 (Scm like with four mbt domains 2). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in placenta adult (RPKM 7.9) and testis adult (RPKM 2.9) See more
Orthologs: human all
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Genomic context

Location:: 2 A1; 2 7.81 cM

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (10375251..10600064)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (10370440..10595253)

Chromosome 2 - NC_000068.8 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: 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?

Data indicate that in transgenic mice overexpressing Sfmbt2 10th intron-hosted miR-466a-3p, significant down-regulation of Nfat5 and many other osmoregulation-related genes was observed in both the renal cortex and medulla.
Title: Sfmbt2 10th intron-hosted miR-466(a/e)-3p are important epigenetic regulators of Nfat5 signaling, osmoregulation and urine concentration in mice.
loss of SFMBT2 results in defects in maintenance of trophoblast cell types necessary for development of the extra-embryonic tissues, the placenta in particular.
Title: The imprinted polycomb group gene Sfmbt2 is required for trophoblast maintenance and placenta development.
Data show that the expression of Sfmbt2 miRNAs is dependent on Dicer.
Title: Genome-wide impact of a recently expanded microRNA cluster in mouse.
a large miRNA gene cluster in intron 10 of the Sfmbt2 gene
Title: Modeling the asymmetric evolution of a mouse and rat-specific microRNA gene cluster intron 10 of the Sfmbt2 gene.

Submit: New GeneRIF Correction

Variation

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Alleles

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

Endonuclease-mediated (6) 1 citation
Gene trapped (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AI013758 (e-PCR)
- UniSTS:250368

RH125679 (e-PCR)
- UniSTS:142376

NoName (e-PCR)
- UniSTS:234327

NoName (e-PCR)
- UniSTS:234328

RH124592 (e-PCR)
- UniSTS:161414

Sfmbt2 (e-PCR), detects polymorphism
- UniSTS:502712

NoName (e-PCR)
- UniSTS:488649

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables histone binding	ISO Inferred from Sequence Orthology more info
enables histone binding	ISS Inferred from Sequence or Structural Similarity more info
enables transcription corepressor activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in negative regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of gene expression	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in aggresome	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in nuclear body	ISO Inferred from Sequence Orthology more info
located_in nuclear speck	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: scm-like with four MBT domains protein 2

Names: Scm-related gene containing four mbt domain 2

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_001198808.1 → NP_001185737.1 scm-like with four MBT domains protein 2 isoform 2

See identical proteins and their annotated locations for NP_001185737.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) has multiple differences in the presence and absence of exons, compared to variant 1, which results in a shorter transcript encoding a longer protein (isoform 2), compared to isoform 1.

Source sequence(s)

AK147557, AK147651, BC145610, BQ033024

Consensus CDS

CCDS57152.1

UniProtKB/Swiss-Prot

Q5DTW2, Q80VG7

UniProtKB/TrEMBL

Q3UH63

Conserved Domains (3) summary

cd09581
Location:893 → 975

SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group

smart00561
Location:47 → 143

MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2

pfam12140
Location:528 → 643

SLED; SLED domain
NM_001198809.1 → NP_001185738.1 scm-like with four MBT domains protein 2 isoform 3

See identical proteins and their annotated locations for NP_001185738.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an exon in the 5' UTR and contains an extra segment at its 3' terminus, compared to variant 1, which results in a much shorter transcript encoding a much shorter protein (isoform 3) with a novel C-terminus, compared to isoform 1.

Source sequence(s)

AK049505, BB636293, BC115511

Consensus CDS

CCDS57153.1

UniProtKB/TrEMBL

Q3TH50, Q8BG70

Related

ENSMUSP00000110514.3, ENSMUST00000114864.9

Conserved Domains (1) summary

smart00561
Location:47 → 143

MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
NM_001369078.1 → NP_001356007.1 scm-like with four MBT domains protein 2 isoform 1

Status: VALIDATED

Source sequence(s)

AL772216, AL953853

Consensus CDS

CCDS38046.1

UniProtKB/Swiss-Prot

Q5DTW2, Q80VG7

UniProtKB/TrEMBL

Q3UH07

Conserved Domains (3) summary

cd09581
Location:860 → 942

SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group

smart00561
Location:47 → 143

MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2

pfam12140
Location:528 → 643

SLED; SLED domain
NM_177386.5 → NP_796360.2 scm-like with four MBT domains protein 2 isoform 1

See identical proteins and their annotated locations for NP_796360.2

Status: VALIDATED

Description

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

Source sequence(s)

AK147651, BB636293, BQ033024

Consensus CDS

CCDS38046.1

UniProtKB/Swiss-Prot

Q5DTW2, Q80VG7

UniProtKB/TrEMBL

Q3UH07

Related

ENSMUSP00000112293.3, ENSMUST00000116594.9

Conserved Domains (3) summary

cd09581
Location:860 → 942

SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group

smart00561
Location:47 → 143

MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2

pfam12140
Location:528 → 643

SLED; SLED domain

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_000068.8 Reference GRCm39 C57BL/6J

Range

10375251..10600064

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006497491.4 → XP_006497554.1 scm-like with four MBT domains protein 2 isoform X1

See identical proteins and their annotated locations for XP_006497554.1

UniProtKB/Swiss-Prot

Q5DTW2, Q80VG7

UniProtKB/TrEMBL

Q3UH63

Conserved Domains (3) summary

cd09581
Location:893 → 975

SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group

smart00561
Location:47 → 143

MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2

pfam12140
Location:528 → 643

SLED; SLED domain
XM_006497498.4 → XP_006497561.1 scm-like with four MBT domains protein 2 isoform X2

See identical proteins and their annotated locations for XP_006497561.1

UniProtKB/Swiss-Prot

Q5DTW2, Q80VG7

UniProtKB/TrEMBL

Q3UH07

Conserved Domains (3) summary

cd09581
Location:860 → 942

SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group

smart00561
Location:47 → 143

MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2

pfam12140
Location:528 → 643

SLED; SLED domain
XM_030251809.2 → XP_030107669.1 scm-like with four MBT domains protein 2 isoform X5

UniProtKB/TrEMBL

Q3TH50, Q8BG70

Related

ENSMUSP00000110512.2, ENSMUST00000114862.8

Conserved Domains (1) summary

smart00561
Location:47 → 143

MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
XM_006497490.5 → XP_006497553.1 scm-like with four MBT domains protein 2 isoform X1

See identical proteins and their annotated locations for XP_006497553.1

UniProtKB/Swiss-Prot

Q5DTW2, Q80VG7

UniProtKB/TrEMBL

Q3UH63

Conserved Domains (3) summary

cd09581
Location:893 → 975

SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group

smart00561
Location:47 → 143

MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2

pfam12140
Location:528 → 643

SLED; SLED domain
XM_006497494.5 → XP_006497557.1 scm-like with four MBT domains protein 2 isoform X1

See identical proteins and their annotated locations for XP_006497557.1

UniProtKB/Swiss-Prot

Q5DTW2, Q80VG7

UniProtKB/TrEMBL

Q3UH63

Conserved Domains (3) summary

cd09581
Location:893 → 975

SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group

smart00561
Location:47 → 143

MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2

pfam12140
Location:528 → 643

SLED; SLED domain
XM_006497492.4 → XP_006497555.1 scm-like with four MBT domains protein 2 isoform X1

See identical proteins and their annotated locations for XP_006497555.1

UniProtKB/Swiss-Prot

Q5DTW2, Q80VG7

UniProtKB/TrEMBL

Q3UH63

Related

ENSMUSP00000040575.7, ENSMUST00000041105.7

Conserved Domains (3) summary

cd09581
Location:893 → 975

SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group

smart00561
Location:47 → 143

MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2

pfam12140
Location:528 → 643

SLED; SLED domain
XM_030251810.2 → XP_030107670.1 scm-like with four MBT domains protein 2 isoform X5

UniProtKB/TrEMBL

Q3TH50, Q8BG70

Conserved Domains (1) summary

smart00561
Location:47 → 143

MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
XM_006497493.4 → XP_006497556.1 scm-like with four MBT domains protein 2 isoform X1

See identical proteins and their annotated locations for XP_006497556.1

UniProtKB/Swiss-Prot

Q5DTW2, Q80VG7

UniProtKB/TrEMBL

Q3UH63

Conserved Domains (3) summary

cd09581
Location:893 → 975

SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group

smart00561
Location:47 → 143

MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2

pfam12140
Location:528 → 643

SLED; SLED domain
XM_006497496.5 → XP_006497559.1 scm-like with four MBT domains protein 2 isoform X1

See identical proteins and their annotated locations for XP_006497559.1

UniProtKB/Swiss-Prot

Q5DTW2, Q80VG7

UniProtKB/TrEMBL

Q3UH63

Conserved Domains (3) summary

cd09581
Location:893 → 975

SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group

smart00561
Location:47 → 143

MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2

pfam12140
Location:528 → 643

SLED; SLED domain
XM_006497499.3 → XP_006497562.1 scm-like with four MBT domains protein 2 isoform X3

Conserved Domains (4) summary

cd09581
Location:655 → 737

SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group

smart00561
Location:145 → 237

MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2

pfam12140
Location:290 → 405

SLED; SLED domain

cl17705
Location:52 → 133

MBT; mbt repeat
XM_006497500.4 → XP_006497563.1 scm-like with four MBT domains protein 2 isoform X4

Conserved Domains (3) summary

cd09581
Location:617 → 699

SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group

smart00561
Location:107 → 199

MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2

pfam12140
Location:252 → 367

SLED; SLED domain