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] See more...

Aliases for SCML2 Gene

Aliases for SCML2 Gene

  • Scm Polycomb Group Protein Like 2 2 3 5
  • Sex Comb On Midleg-Like Protein 2 3 4
  • Sex Comb On Midleg (Drosophila)-Like 2 2
  • Sex Comb On Midleg Like 2 (Drosophila) 2
  • Sex Comb On Midleg Like 2 3
  • SCML2 5

External Ids for SCML2 Gene

Previous GeneCards Identifiers for SCML2 Gene

  • GC0XM017801
  • GC0XM016923
  • GC0XM017459
  • GC0XM017618
  • GC0XM018017
  • GC0XM016015

Summaries for SCML2 Gene

Entrez Gene Summary for SCML2 Gene

  • 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]

GeneCards Summary for SCML2 Gene

SCML2 (Scm Polycomb Group Protein Like 2) is a Protein Coding gene. Diseases associated with SCML2 include Retinitis Pigmentosa 24 and Central Nervous System Mesenchymal Non-Meningothelial Tumor. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and sequence-specific DNA binding. An important paralog of this gene is SCMH1.

UniProtKB/Swiss-Prot Summary for SCML2 Gene

  • Putative Polycomb group (PcG) protein. PcG proteins act by forming multiprotein complexes, which are required to maintain the transcriptionally repressive state of homeotic genes throughout development (By similarity).

Additional gene information for SCML2 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SCML2 Gene

Genomics for SCML2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SCML2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ018353 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 600.7 +0.6 588 2.6 RNF2 ZIC2 RBFOX2 POLR2A PATZ1 NR2C1 CTCF YY1 SOX6 GATAD2B SCML2 lnc-CDKL5-1 RF00017-8189 RF00017-8188 BEND2
GH0XJ017593 Enhancer 0.7 Ensembl ENCODE 4.1 +758.9 758873 4.8 SP1 BCL11A NFIC NFIB FOXA1 JUN MTA2 NHS SCML1 SCML2 piR-33804-169 piR-55194-428
GH0XJ017588 Enhancer 0.3 Ensembl 4.1 +766.7 766688 0.4 NFE2 SCML2 piR-55194-428 piR-33804-169 SCML1 NHS
GH0XJ018351 Enhancer 0.5 Ensembl 0.7 +3.2 3188 0.6 EZH2 FOXA2 FOSL2 FEZF1 PRDM6 JUND ZNF384 SP7 RF00017-8189 SCML2 RF00017-8188 BEND2
GH0XJ018348 Enhancer 0.7 Ensembl 0.4 +6.9 6888 0.8 ZNF341 ZBTB44 ZXDB TSHZ1 OSR2 SCRT1 PRDM4 HIC1 ZNF366 ZNF843 RF00017-8189 SCML2 TMSB10P2 RF00017-8188 BEND2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SCML2 on the GeneHancer Hub at the UCSC Golden Path

Top Transcription factor binding sites by QIAGEN in the SCML2 gene promoter:
  • HOXA5
  • ISGF-3
  • Lhx3a
  • LHX3b
  • NF-kappaB1
  • Nkx6-1
  • RelA
  • SREBP-1a
  • SREBP-1b
  • SREBP-1c

Genomic Locations for SCML2 Gene

Genomic Locations for SCML2 Gene
chrX:18,239,313-18,355,089
(GRCh38/hg38)
Size:
115,777 bases
Orientation:
Minus strand
chrX:18,257,433-18,372,847
(GRCh37/hg19)
Size:
115,415 bases
Orientation:
Minus strand

Genomic View for SCML2 Gene

Genes around SCML2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCML2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCML2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCML2 Gene

Proteins for SCML2 Gene

  • Protein details for SCML2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UQR0-SCML2_HUMAN
    Recommended name:
    Sex comb on midleg-like protein 2
    Protein Accession:
    Q9UQR0
    Secondary Accessions:
    • Q5JXE6
    • Q86U98
    • Q8IWD0
    • Q8NDP2
    • Q9UGC5

    Protein attributes for SCML2 Gene

    Size:
    700 amino acids
    Molecular mass:
    77257 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAH51913.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SCML2 Gene

    Alternative splice isoforms for SCML2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SCML2 Gene

Post-translational modifications for SCML2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SCML2 Gene

Domains & Families for SCML2 Gene

Gene Families for SCML2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for SCML2 Gene

InterPro:
Blocks:
  • Sterile alpha motif SAM
ProtoNet:

Suggested Antigen Peptide Sequences for SCML2 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ60333, highly similar to Sex comb on midleg-like protein 2 (B4DRC2_HUMAN)
  • cDNA FLJ54781, highly similar to Sex comb on midleg-like protein 2 (B4DZR9_HUMAN)
  • Sex comb on midleg-like 2 (Drosophila) (Q5JXE7_HUMAN)
  • Sex comb on midleg-like protein 2 (SCML2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9UQR0

UniProtKB/Swiss-Prot:

SCML2_HUMAN :
  • Belongs to the SCM family.
Family:
  • Belongs to the SCM family.
genes like me logo Genes that share domains with SCML2: view

Function for SCML2 Gene

Molecular function for SCML2 Gene

UniProtKB/Swiss-Prot Function:
Putative Polycomb group (PcG) protein. PcG proteins act by forming multiprotein complexes, which are required to maintain the transcriptionally repressive state of homeotic genes throughout development (By similarity).
GENATLAS Biochemistry:
Drosophila sex comb on midleg-like 2 homolog,member of the polycomb group (PcG),involved in transcriptional repression of HOX genes,clustered with SCML1

Gene Ontology (GO) - Molecular Function for SCML2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding TAS --
GO:0003682 chromatin binding IBA 21873635
GO:0003700 DNA-binding transcription factor activity TAS --
GO:0005515 protein binding IPI 24358021
GO:0042393 histone binding IBA 21873635
genes like me logo Genes that share ontologies with SCML2: view
genes like me logo Genes that share phenotypes with SCML2: view

Animal Model Products

CRISPR Products

miRNA for SCML2 Gene

miRTarBase miRNAs that target SCML2

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCML2

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SCML2 Gene

Localization for SCML2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCML2 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SCML2 gene
Compartment Confidence
nucleus 5
cytosol 3
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoli (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SCML2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 21282530
GO:0031519 PcG protein complex IDA 21282530
genes like me logo Genes that share ontologies with SCML2: view

Pathways & Interactions for SCML2 Gene

PathCards logo

SuperPathways for SCML2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SCML2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0009653 anatomical structure morphogenesis TAS,IMP 10331946
GO:0045892 negative regulation of transcription, DNA-templated IBA 21873635
genes like me logo Genes that share ontologies with SCML2: view

No data available for Pathways by source and SIGNOR curated interactions for SCML2 Gene

Drugs & Compounds for SCML2 Gene

No Compound Related Data Available

Transcripts for SCML2 Gene

mRNA/cDNA for SCML2 Gene

1 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCML2

Alternative Splicing Database (ASD) splice patterns (SP) for SCML2 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12a · 12b · 12c · 12d ^ 13a · 13b · 13c ^ 14 ^ 15a · 15b · 15c ^ 16 ^
SP1:
SP2: - -
SP3: - -
SP4: -
SP5:
SP6: -
SP7: -
SP8:
SP9:

ExUns: 17a · 17b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for SCML2 Gene

GeneLoc Exon Structure for
SCML2

Expression for SCML2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SCML2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SCML2 Gene

This gene is overexpressed in Testis (x4.7).

Protein differential expression in normal tissues from HIPED for SCML2 Gene

This gene is overexpressed in Testis (23.7), Bone marrow mesenchymal stem cell (17.4), Fetal ovary (14.8), and Ovary (8.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SCML2 Gene



Protein tissue co-expression partners for SCML2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SCML2

SOURCE GeneReport for Unigene cluster for SCML2 Gene:

Hs.495774

mRNA Expression by UniProt/SwissProt for SCML2 Gene:

Q9UQR0-SCML2_HUMAN
Tissue specificity: Highly expressed in placenta, thymus and testis. Detected at lower levels in brain, liver, skeletal muscle, pancreas and ovary.

Evidence on tissue expression from TISSUES for SCML2 Gene

  • Liver(4.2)
genes like me logo Genes that share expression patterns with SCML2: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SCML2 Gene

Orthologs for SCML2 Gene

This gene was present in the common ancestor of animals.

Orthologs for SCML2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SCML2 30 31
  • 99.42 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SCML2 30 31
  • 85.73 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SCML2 30 31
  • 83.1 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia RGD1564289 30
  • 75 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia SCML2 31
  • 63 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SCML2 31
  • 60 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Scml2 31
  • 35 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SCML2 30 31
  • 70.58 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SCML2 31
  • 58 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia scml2 30
  • 62.8 (n)
Str.20296 30
Zebrafish
(Danio rerio)
Actinopterygii scml2 30
  • 58.43 (n)
SCML2 31
  • 48 (a)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Scm 31 32
  • 26 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.6357 31
  • 30 (a)
OneToMany
Species where no ortholog for SCML2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for SCML2 Gene

ENSEMBL:
Gene Tree for SCML2 (if available)
TreeFam:
Gene Tree for SCML2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SCML2: view image

Paralogs for SCML2 Gene

(2) SIMAP similar genes for SCML2 Gene using alignment to 3 proteins:

  • SCML2_HUMAN
  • B4DRC2_HUMAN
  • H0Y6S1_HUMAN

Pseudogenes.org Pseudogenes for SCML2 Gene

genes like me logo Genes that share paralogs with SCML2: view

Variants for SCML2 Gene

Additional dbSNP identifiers (rs#s) for SCML2 Gene

Structural Variations from Database of Genomic Variants (DGV) for SCML2 Gene

Variant ID Type Subtype PubMed ID
dgv2231e212 CNV gain 25503493
esv24903 CNV loss 19812545
esv2663102 CNV deletion 23128226
esv3330943 CNV insertion 20981092
nsv1075309 CNV deletion 25765185
nsv6819 CNV insertion 18451855

Variation tolerance for SCML2 Gene

Residual Variation Intolerance Score: 9.62% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.57; 12.34% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SCML2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCML2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SCML2 Gene

Disorders for SCML2 Gene

MalaCards: The human disease database

(4) MalaCards diseases for SCML2 Gene - From: DISEASES

Disorder Aliases PubMed IDs
retinitis pigmentosa 24
  • rp24
central nervous system mesenchymal non-meningothelial tumor
  • central nervous system mesenchymal non-meningothelial tumour
osteogenesis imperfecta, type i
  • oi1
retinitis pigmentosa
  • retinitis pigmentosa 1
- elite association - COSMIC cancer census association via MalaCards
Search SCML2 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with SCML2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SCML2 Gene

Publications for SCML2 Gene

  1. Identification of SCML2, a second human gene homologous to the Drosophila sex comb on midleg (Scm): A new gene cluster on Xp22. (PMID: 10331946) Montini E … Franco B (Genomics 1999) 2 3 4
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  3. Crystal structure of the malignant brain tumor (MBT) repeats in Sex Comb on Midleg-like 2 (SCML2). (PMID: 12952983) Sathyamurthy A … Bycroft M (The Journal of biological chemistry 2003) 3 4
  4. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  5. Mapping the Ku Interactome Using Proximity-Dependent Biotin Identification in Human Cells. (PMID: 30585729) Abbasi S … Schild-Poulter C (Journal of proteome research 2019) 3

Products for SCML2 Gene

Sources for SCML2 Gene