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SFMBT2 Scm like with four mbt domains 2 [ Homo sapiens (human) ]

Gene ID: 57713, updated on 2-Nov-2024

Summary

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Official Symbol
SFMBT2provided by HGNC
Official Full Name
Scm like with four mbt domains 2provided by HGNC
Primary source
HGNC:HGNC:20256
See related
Ensembl:ENSG00000198879 MIM:615392; AllianceGenome:HGNC:20256
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
Summary
Enables histone binding activity. Involved in negative regulation of gene expression. Located in aggresome; cytosol; and nuclear speck. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in thyroid (RPKM 4.8), ovary (RPKM 4.5) and 24 other tissues See more
Orthologs
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Genomic context

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See SFMBT2 in Genome Data Viewer
Location:
10p14
Exon count:
29
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (7158624..7411490, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (7158401..7411442, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (7200586..7453452, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:6835894-6836851 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:6836852-6837808 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:6838766-6839721 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:6843478-6844062 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:6844063-6844646 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:6844647-6845230 Neighboring gene long intergenic non-protein coding RNA 707 Neighboring gene uncharacterized LOC105376387 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:6874691-6875192 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:6875193-6875692 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:6918964-6919464 Neighboring gene NANOG hESC enhancer GRCh37_chr10:6952013-6952514 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2970 Neighboring gene nonconserved acetylation island sequence 45 enhancer Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:6975635-6976834 Neighboring gene NANOG hESC enhancer GRCh37_chr10:6995095-6995596 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:7014138-7015337 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16768 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16971 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2110 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:7117931-7118110 Neighboring gene NANOG hESC enhancer GRCh37_chr10:7124870-7125371 Neighboring gene long intergenic non-protein coding RNA 2665 Neighboring gene Sharpr-MPRA regulatory region 5095 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:7212385-7212885 Neighboring gene small nucleolar RNA, C/D box 129 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:7298769-7299968 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:7371119-7371620 Neighboring gene cytochrome c oxidase subunit 6C pseudogene 17 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2973 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2974 Neighboring gene uncharacterized LOC124902372 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:7403871-7405070 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:7407161-7407660 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:7449871-7450766 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2975 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2112 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:7453245-7454165 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:7454166-7455085 Neighboring gene uncharacterized LOC124902373 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:7487564-7487770 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:7488827-7489326 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2977 Neighboring gene NANOG hESC enhancer GRCh37_chr10:7500249-7500813 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2978 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2979 Neighboring gene long intergenic non-protein coding RNA 2642

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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?
  1. Acetylation- and ubiquitination-regulated SFMBT2 acts as a tumor suppressor in clear cell renal cell carcinoma.
    Title: Acetylation- and ubiquitination-regulated SFMBT2 acts as a tumor suppressor in clear cell renal cell carcinoma.
  2. [Effects of circ-SFMBT2 on Proliferation, Migration and Invasion of Acute Myeloid Leukemia Cells by Regulating miR-491-5p/HOXA9 Axis].
    Title: [Effects of circ-SFMBT2 on Proliferation, Migration and Invasion of Acute Myeloid Leukemia Cells by Regulating miR-491-5p/HOXA9 Axis].
  3. Circ-SFMBT2 facilitates the malignant growth of acute myeloid leukemia cells by modulating miR-582-3p/ZBTB20 pathway.
    Title: Circ-SFMBT2 facilitates the malignant growth of acute myeloid leukemia cells by modulating miR-582-3p/ZBTB20 pathway.
  4. Circular RNA SFMBT2 Inhibits the Proliferation and Metastasis of Glioma Cells Through Mir-182-5p/Mtss1 Pathway.
    Title: Circular RNA SFMBT2 Inhibits the Proliferation and Metastasis of Glioma Cells Through Mir-182-5p/Mtss1 Pathway.
  5. CircSFMBT2 facilitates vascular smooth muscle cell proliferation by targeting miR-331-3p/HDAC5.
    Title: CircSFMBT2 facilitates vascular smooth muscle cell proliferation by targeting miR-331-3p/HDAC5.
  6. we revealed that SFMBT2 intervention by siRNA contributed to the catabolic phenotype of human chondrocytes mediated by NF-kB pathway.
    Title: Down-regulated in OA cartilage, SFMBT2 contributes to NF-κB-mediated ECM degradation.
  7. The present study identified Scmlike with four malignant brain tumor domains 2 (SFMBT2) as a novel regulator of SOX9 expression.
    Title: SFMBT2 positively regulates SOX9 and chondrocyte proliferation.
  8. Findings suggest that regulation of SFMBT2 may provide a new therapeutic strategy to control prostate cancer metastasis as well as being a potential biomarker of metastatic prostate cancer.
    Title: SFMBT2 (Scm-like with four mbt domains 2) negatively regulates cell migration and invasion in prostate cancer cells.
  9. SFMBT2 may regulate cell growth via epigenetic regulation of HOXB13 gene expression in prostate cancer cells.
    Title: Regulation of DU145 prostate cancer cell growth by Scm-like with four mbt domains 2.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance.
EBI GWAS Catalog

Variation

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See Variation Viewer (GRCh37.p13)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

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 IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
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 gene expression IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in aggresome IDA
Inferred from Direct Assay
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
located_in nuclear body IDA
Inferred from Direct Assay
more info
  
located_in nuclear speck IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
scm-like with four MBT domains protein 2
Names
Scm-related gene containing four mbt domains 2
scm-like with 4 MBT domains protein 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)

  1. NM_001018039.1 → NP_001018049.1  scm-like with four MBT domains protein 2 isoform 1

    See identical proteins and their annotated locations for NP_001018049.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same protein.
    Source sequence(s)
    AB046837, AL138771, AL590095
    Consensus CDS
    CCDS31138.1
    UniProtKB/Swiss-Prot
    A7MD09, Q5VUG0, Q9HCF5
    UniProtKB/TrEMBL
    A0A669KBL2
    Related
    ENSP00000355109.4, ENST00000361972.8
    Conserved Domains (3) summary
    cd09581
    Location:810 → 894
    SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group
    smart00561
    Location:48 → 144
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam12140
    Location:528 → 643
    SLED; SLED domain

  2. NM_001029880.3 → NP_001025051.1  scm-like with four MBT domains protein 2 isoform 1

    See identical proteins and their annotated locations for NP_001025051.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 both encode the same protein.
    Source sequence(s)
    AB046837, AL138771, AL139125, AL590095, DA152101
    Consensus CDS
    CCDS31138.1
    UniProtKB/Swiss-Prot
    A7MD09, Q5VUG0, Q9HCF5
    UniProtKB/TrEMBL
    A0A669KBL2
    Related
    ENSP00000507767.1, ENST00000683762.1
    Conserved Domains (3) summary
    cd09581
    Location:810 → 894
    SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group
    smart00561
    Location:48 → 144
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam12140
    Location:528 → 643
    SLED; SLED domain

  3. NM_001387889.1 → NP_001374818.1  scm-like with four MBT domains protein 2 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AL138771, AL139125, AL158046, AL590095
    Consensus CDS
    CCDS31138.1
    UniProtKB/Swiss-Prot
    A7MD09, Q5VUG0, Q9HCF5
    UniProtKB/TrEMBL
    A0A669KBL2
    Related
    ENSP00000380353.1, ENST00000397167.6
    Conserved Domains (3) summary
    cd09581
    Location:810 → 894
    SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group
    smart00561
    Location:48 → 144
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam12140
    Location:528 → 643
    SLED; SLED domain

  4. NM_001387890.1 → NP_001374819.1  scm-like with four MBT domains protein 2 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AL138771, AL139125, AL158046, AL590095
    UniProtKB/TrEMBL
    A0A804HLD5
    Conserved Domains (3) summary
    cd09581
    Location:558 → 642
    SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group
    smart00561
    Location:132 → 225
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam12140
    Location:276 → 391
    SLED; SLED domain

  5. NM_001387891.1 → NP_001374820.1  scm-like with four MBT domains protein 2 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AL138771, AL139125, AL158046, AL590095
    Consensus CDS
    CCDS31138.1
    UniProtKB/Swiss-Prot
    A7MD09, Q5VUG0, Q9HCF5
    UniProtKB/TrEMBL
    A0A669KBL2
    Conserved Domains (3) summary
    cd09581
    Location:810 → 894
    SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group
    smart00561
    Location:48 → 144
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam12140
    Location:528 → 643
    SLED; SLED domain

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

  1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    7158624..7411490 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047425568.1 → XP_047281524.1  scm-like with four MBT domains protein 2 isoform X1

    UniProtKB/Swiss-Prot
    A7MD09, Q5VUG0, Q9HCF5

  2. XM_047425567.1 → XP_047281523.1  scm-like with four MBT domains protein 2 isoform X1

    UniProtKB/Swiss-Prot
    A7MD09, Q5VUG0, Q9HCF5

  3. XM_047425570.1 → XP_047281526.1  scm-like with four MBT domains protein 2 isoform X3

  4. XM_006717490.2 → XP_006717553.1  scm-like with four MBT domains protein 2 isoform X2

    UniProtKB/TrEMBL
    A0A804HLD5
    Conserved Domains (4) summary
    cd09581
    Location:641 → 725
    SAM_Scm-like-4MBT1,2; SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group
    smart00454
    Location:652 → 716
    SAM; Sterile alpha motif
    smart00561
    Location:215 → 308
    MBT; Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2
    pfam12140
    Location:359 → 474
    DUF3588; Protein of unknown function (DUF3588)

  5. XM_047425569.1 → XP_047281525.1  scm-like with four MBT domains protein 2 isoform X2

  6. XM_047425573.1 → XP_047281529.1  scm-like with four MBT domains protein 2 isoform X3

  7. XM_047425571.1 → XP_047281527.1  scm-like with four MBT domains protein 2 isoform X4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    7158401..7411442 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054366434.1 → XP_054222409.1  scm-like with four MBT domains protein 2 isoform X1

    UniProtKB/Swiss-Prot
    A7MD09, Q5VUG0, Q9HCF5

  2. XM_054366433.1 → XP_054222408.1  scm-like with four MBT domains protein 2 isoform X1

    UniProtKB/Swiss-Prot
    A7MD09, Q5VUG0, Q9HCF5

  3. XM_054366437.1 → XP_054222412.1  scm-like with four MBT domains protein 2 isoform X3

  4. XM_054366435.1 → XP_054222410.1  scm-like with four MBT domains protein 2 isoform X2

  5. XM_054366436.1 → XP_054222411.1  scm-like with four MBT domains protein 2 isoform X2

  6. XM_054366439.1 → XP_054222414.1  scm-like with four MBT domains protein 2 isoform X3

  7. XM_054366438.1 → XP_054222413.1  scm-like with four MBT domains protein 2 isoform X4

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_020953.1: Suppressed sequence

    Description
    NM_020953.1: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5VUG0.1 GenPept UniProtKB/Swiss-Prot:Q5VUG0

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