SCML2 Scm polycomb group protein like 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SCML2provided by HGNC
Official Full Name: Scm polycomb group protein like 2provided by HGNC
Primary source: HGNC:HGNC:10581
See related: Ensembl:ENSG00000102098 MIM:300208; AllianceGenome:HGNC:10581
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary: This gene encodes a member of the Polycomb group proteins. These proteins form the Polycomb repressive complexes which are involved in transcriptional repression. The encoded protein binds histone peptides that are monomethylated at lysine residues and may be involved in regulating homeotic gene expression during development. [provided by RefSeq, Jun 2010]
Expression: Broad expression in testis (RPKM 5.8), adrenal (RPKM 1.8) and 19 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: Xp22.13

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (18239313..18355118, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	X	NC_060947.1 (17821927..17937732, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (18257433..18372808, complement)

Chromosome X - NC_000023.11 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: 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?

Sex Comb on Midleg Like-2 Accelerates Hepatocellular Carcinoma Cell Proliferation and Metastasis by Activating Wnt/beta-Catenin/EMT Signaling.
Title: Sex Comb on Midleg Like-2 Accelerates Hepatocellular Carcinoma Cell Proliferation and Metastasis by Activating Wnt/β-Catenin/EMT Signaling.
SCML2A, an SCML2 isoform tightly associated to chromatin, contributes to PRC1 localization and also directly enforces repression of certain Polycomb target genes.
Title: Interactions with RNA direct the Polycomb group protein SCML2 to chromatin where it represses target genes.
SCML2 directly interacts with USP7 and drives its localization. SCML2 connects USP7 to PRC1.4, allowing for the stabilization of BMI1, and USP7 is found on SCML2 and BMI1 target genes.
Title: USP7 cooperates with SCML2 to regulate the activity of PRC1.
Because PRC1 complexes localize to the promoters of a specific subset of developmental genes in vivo, the SLED domain of Scml2 may provide an important link connecting the PRC1 complexes to their target genes.
Title: Solution NMR structure of the DNA-binding domain from Scml2 (sex comb on midleg-like 2).
The malignant brain tumor repeats of SCML2 preferentially bind histone peptides monomethylated at lysine residues. The crystal structure of the complex reveals that the modified amino acid binds to an aromatic rich pocket.
Title: The malignant brain tumor repeats of human SCML2 bind to peptides containing monomethylated lysine.
1.78-A crystal structure of the two MBT repeats of SCML2 show significant structural similarities to the Tudor, PWWP, and chromo domains, suggesting probable evolutionary relationships and functional similarities between the MBT repeats and these domains.
Title: Crystal structure of the malignant brain tumor (MBT) repeats in Sex Comb on Midleg-like 2 (SCML2).

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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

STS-R07875 (e-PCR)
- UniSTS:77312

D10S275 (e-PCR)
- UniSTS:147992

D11S2560 (e-PCR)
- UniSTS:37928

STS-N74417 (e-PCR)
- UniSTS:23238

G06175 (e-PCR)
- UniSTS:24810

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 protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in anatomical structure morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of PcG protein complex	IDA Inferred from Direct Assay more info	PubMed
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: sex comb on midleg-like protein 2

Names: sex comb on midleg like 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.

Genomic

NG_021431.2 RefSeqGene

Range

5037..120412

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_006089.3 → NP_006080.1 sex comb on midleg-like protein 2

See identical proteins and their annotated locations for NP_006080.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the functional protein.

Source sequence(s)

BC040497, BC064617

Consensus CDS

CCDS14185.1

UniProtKB/Swiss-Prot

Q5JXE6, Q86U98, Q8IWD0, Q8NDP2, Q9UGC5, Q9UQR0

UniProtKB/TrEMBL

B4DZR9, E7ERN2

Related

ENSP00000251900.4, ENST00000251900.9

Conserved Domains (4) summary

cd09578
Location:625 → 696

SAM_Scm; SAM domain of Scm proteins of Polycomb group

smart00454
Location:628 → 696

SAM; Sterile alpha motif

smart00561
Location:142 → 240

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

pfam12140
Location:356 → 465

DUF3588; Protein of unknown function (DUF3588)

RNA

NR_033717.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an internal segment, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

BC040497, BC051913

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_000023.11 Reference GRCh38.p14 Primary Assembly

Range

18239313..18355118 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017029219.2 → XP_016884708.1 sex comb on midleg-like protein 2 isoform X1

UniProtKB/Swiss-Prot

Q5JXE6, Q86U98, Q8IWD0, Q8NDP2, Q9UGC5, Q9UQR0

UniProtKB/TrEMBL

B4DZR9, E7ERN2

Conserved Domains (4) summary

cd09578
Location:625 → 696

SAM_Scm; SAM domain of Scm proteins of Polycomb group

smart00454
Location:628 → 696

SAM; Sterile alpha motif

smart00561
Location:142 → 240

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

pfam12140
Location:356 → 465

DUF3588; Protein of unknown function (DUF3588)
XM_006724458.1 → XP_006724521.1 sex comb on midleg-like protein 2 isoform X2

UniProtKB/TrEMBL

B4DZR9, E7ERN2

Conserved Domains (2) summary

smart00561
Location:142 → 240

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

pfam12140
Location:356 → 465

DUF3588; Protein of unknown function (DUF3588)
XM_017029220.3 → XP_016884709.1 sex comb on midleg-like protein 2 isoform X1

UniProtKB/Swiss-Prot

Q5JXE6, Q86U98, Q8IWD0, Q8NDP2, Q9UGC5, Q9UQR0

UniProtKB/TrEMBL

B4DZR9, E7ERN2

Conserved Domains (4) summary

cd09578
Location:625 → 696

SAM_Scm; SAM domain of Scm proteins of Polycomb group

smart00454
Location:628 → 696

SAM; Sterile alpha motif

smart00561
Location:142 → 240

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

pfam12140
Location:356 → 465

DUF3588; Protein of unknown function (DUF3588)
XM_017029222.2 → XP_016884711.1 sex comb on midleg-like protein 2 isoform X3