Aliases for SCML4 Gene

Aliases for SCML4 Gene

  • Scm Polycomb Group Protein Like 4 2 3 5
  • Sex Comb On Midleg-Like Protein 4 3 4
  • Sex Comb On Midleg Like 4 (Drosophila) 2
  • Sex Comb On Midleg Like 4 3
  • DJ47M23.1 3

External Ids for SCML4 Gene

Previous GeneCards Identifiers for SCML4 Gene

  • GC06M108025
  • GC06M108070
  • GC06M108071
  • GC06M108146
  • GC06M105595
  • GC06M108023
  • GC06M107702
  • GC06M107699

Summaries for SCML4 Gene

GeneCards Summary for SCML4 Gene

SCML4 (Scm Polycomb Group Protein Like 4) is a Protein Coding gene. Diseases associated with SCML4 include Ectrodactyly, Ectodermal Dysplasia, And Cleft Lip/Palate Syndrome 1 and Yunis-Varon Syndrome. An important paralog of this gene is SCMH1.

UniProtKB/Swiss-Prot Summary for SCML4 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 SCML4 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SCML4 Gene

Genomics for SCML4 Gene

GeneHancer (GH) Regulatory Elements for SCML4 Gene

Promoters and enhancers for SCML4 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
GH06J107730 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE dbSUPER 507.8 +117.3 117338 3.4 NCOR1 TCF7 FOXA2 SPI1 GABPB1 HOMEZ ZFP64 RARA RAD21 HSF1 SCML4 lnc-SEC63-5 piR-32314-019
GH06J107847 Promoter/Enhancer 1.5 FANTOM5 ENCODE CraniofacialAtlas 506.8 +0.4 408 0.9 ZNF217 CTCF TEAD4 ZNF10 ZIC2 POLR2A ZBTB11 TARDBP REST ZBTB25 SCML4 SEC63 HSALNG0052530
GH06J107819 Promoter/Enhancer 1.8 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 45.9 +26.0 26044 6 EP300 ZSCAN5C ZNF639 ZNF10 ZIC2 TRIM28 ZNF510 RFX1 ZNF662 EZH2 SCML4 SEC63 HSALNG0052530
GH06J107781 Enhancer 1 Ensembl ENCODE dbSUPER 23.5 +58.3 58258 17.6 EP300 MEF2C CUX1 ATF2 TCF12 EGR1 PBX3 ZNF350 KDM1A JUND SCML4 piR-36393-458 lnc-SEC63-5
GH06J107704 Enhancer 0.9 Ensembl ENCODE dbSUPER 17.8 +144.0 144011 0.7 CTCF REST RAD21 TRIM22 SMC3 ZNF384 NR2F1 ZNF654 HNF4A HLF SCML4 ENSG00000280135 lnc-SOBP-1 lnc-SCML4-1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SCML4 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SCML4

Top Transcription factor binding sites by QIAGEN in the SCML4 gene promoter:
  • Chx10
  • Oct-B1
  • oct-B2
  • oct-B3
  • POU2F1
  • POU2F1a
  • POU2F2
  • POU2F2 (Oct-2.1)
  • POU2F2B
  • POU2F2C

Genomic Locations for SCML4 Gene

Genomic Locations for SCML4 Gene
chr6:107,697,297-107,848,659
(GRCh38/hg38)
Size:
151,363 bases
Orientation:
Minus strand
chr6:108,023,364-108,145,521
(GRCh37/hg19)
Size:
122,158 bases
Orientation:
Minus strand

Genomic View for SCML4 Gene

Genes around SCML4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCML4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCML4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCML4 Gene

Proteins for SCML4 Gene

  • Protein details for SCML4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N228-SCML4_HUMAN
    Recommended name:
    Sex comb on midleg-like protein 4
    Protein Accession:
    Q8N228
    Secondary Accessions:
    • B0QZ10
    • B0QZ11
    • B7ZBX3
    • Q5JXD0
    • Q5T0T6
    • Q8IYY6

    Protein attributes for SCML4 Gene

    Size:
    414 amino acids
    Molecular mass:
    45023 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for SCML4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SCML4 Gene

Post-translational modifications for SCML4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SCML4 Gene

Domains & Families for SCML4 Gene

Gene Families for SCML4 Gene

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

Protein Domains for SCML4 Gene

Blocks:
  • Sterile alpha motif SAM
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SCML4 Gene

GenScript: Design optimal peptide antigens:
  • Sex comb on midleg-like protein 4 (SCML4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8N228

UniProtKB/Swiss-Prot:

SCML4_HUMAN :
  • Belongs to the SCM family.
Family:
  • Belongs to the SCM family.
genes like me logo Genes that share domains with SCML4: view

Function for SCML4 Gene

Molecular function for SCML4 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).

Phenotypes From GWAS Catalog for SCML4 Gene

genes like me logo Genes that share phenotypes with SCML4: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCML4

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SCML4 Gene

Localization for SCML4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCML4 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 SCML4 gene
Compartment Confidence
nucleus 4
mitochondrion 0
cytosol 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SCML4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA --
genes like me logo Genes that share ontologies with SCML4: view

Pathways & Interactions for SCML4 Gene

PathCards logo

SuperPathways for SCML4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SCML4 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for SCML4 Gene

Drugs & Compounds for SCML4 Gene

No Compound Related Data Available

Transcripts for SCML4 Gene

mRNA/cDNA for SCML4 Gene

3 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
11 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 SCML4

Alternative Splicing Database (ASD) splice patterns (SP) for SCML4 Gene

No ASD Table

Relevant External Links for SCML4 Gene

GeneLoc Exon Structure for
SCML4

Expression for SCML4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SCML4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SCML4 Gene

This gene is overexpressed in Whole Blood (x14.2), Small Intestine - Terminal Ileum (x7.2), and Spleen (x6.5).

Protein differential expression in normal tissues from HIPED for SCML4 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (32.0) and CD8 Tcells (31.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SCML4 Gene



Protein tissue co-expression partners for SCML4 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SCML4

SOURCE GeneReport for Unigene cluster for SCML4 Gene:

Hs.486109

Evidence on tissue expression from TISSUES for SCML4 Gene

  • Liver(4.2)
genes like me logo Genes that share expression patterns with SCML4: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SCML4 Gene

Orthologs for SCML4 Gene

This gene was present in the common ancestor of animals.

Orthologs for SCML4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SCML4 31 30
  • 99.52 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SCML4 31 30
  • 89.05 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SCML4 31 30
  • 85.85 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Scml4 17 31 30
  • 81.54 (n)
rat
(Rattus norvegicus)
Mammalia Scml4 30
  • 79.92 (n)
oppossum
(Monodelphis domestica)
Mammalia SCML4 31
  • 76 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 17 (a)
OneToMany
chicken
(Gallus gallus)
Aves SCML4 31 30
  • 72 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SCML4 31
  • 75 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia scml4 30
  • 72.11 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC794170 30
  • 64.7 (n)
scml4 31
  • 46 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta l(3)mbt 31
  • 4 (a)
OneToMany
Species where no ortholog for SCML4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 SCML4 Gene

ENSEMBL:
Gene Tree for SCML4 (if available)
TreeFam:
Gene Tree for SCML4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SCML4: view image

Paralogs for SCML4 Gene

(4) SIMAP similar genes for SCML4 Gene using alignment to 3 proteins:

  • SCML4_HUMAN
  • F2Z2X1_HUMAN
  • Q5T0T5_HUMAN
genes like me logo Genes that share paralogs with SCML4: view

Variants for SCML4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SCML4 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
710965 Benign: not provided 107,707,929(-) C/T SYNONYMOUS_VARIANT
787307 Benign: not provided 107,707,990(-) G/A MISSENSE_VARIANT
rs6934505 - p.Arg126Gln

Additional dbSNP identifiers (rs#s) for SCML4 Gene

Structural Variations from Database of Genomic Variants (DGV) for SCML4 Gene

Variant ID Type Subtype PubMed ID
dgv1823e212 CNV loss 25503493
dgv3360n106 CNV deletion 24896259
esv1367877 CNV deletion 17803354
esv2057606 CNV deletion 18987734
esv23033 CNV gain 19812545
esv2640753 CNV deletion 19546169
esv2660523 CNV deletion 23128226
esv2732553 CNV deletion 23290073
esv3284384 CNV deletion 24192839
esv3540282 CNV deletion 23714750
esv3571344 CNV loss 25503493
esv3610302 CNV loss 21293372
esv3610304 CNV loss 21293372
esv6501 CNV loss 19470904
nsv1073581 CNV deletion 25765185
nsv1114862 CNV deletion 24896259
nsv1137135 CNV deletion 24896259
nsv349488 CNV deletion 16902084
nsv475345 CNV novel sequence insertion 20440878
nsv511910 CNV loss 21212237
nsv604455 CNV loss 21841781
nsv820392 CNV deletion 20802225
nsv830763 CNV gain 17160897
nsv830764 CNV gain 17160897
nsv830765 CNV loss 17160897
nsv950489 CNV deletion 24416366

Variation tolerance for SCML4 Gene

Residual Variation Intolerance Score: 36.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.71; 78.65% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SCML4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCML4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCML4 Gene

Disorders for SCML4 Gene

MalaCards: The human disease database

(2) MalaCards diseases for SCML4 Gene - From: DISEASES

- elite association - COSMIC cancer census association via MalaCards
Search SCML4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SCML4

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SCML4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SCML4 Gene

Publications for SCML4 Gene

  1. Candidate gene/loci studies in cleft lip/palate and dental anomalies finds novel susceptibility genes for clefts. (PMID: 18978678) Vieira AR … Marazita ML (Genetics in medicine : official journal of the American College of Medical Genetics 2008) 3 41 54
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54
  3. Genome-Wide Association and Functional Studies Identify SCML4 and THSD7A as Novel Susceptibility Genes for Coronary Artery Disease. (PMID: 29472232) Li Y … Tian XL (Arteriosclerosis, thrombosis, and vascular biology 2018) 3 54
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 54
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin EL … Gygi SP (Cell 2015) 3 54

Products for SCML4 Gene

Sources for SCML4 Gene