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SCML4 Scm polycomb group protein like 4 [ Homo sapiens (human) ]

Gene ID: 256380, updated on 17-Aug-2024

Summary

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Official Symbol
SCML4provided by HGNC
Official Full Name
Scm polycomb group protein like 4provided by HGNC
Primary source
HGNC:HGNC:21397
See related
Ensembl:ENSG00000146285 AllianceGenome:HGNC:21397
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
Also known as
dJ47M23.1
Summary
Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in negative regulation of transcription, DNA-templated. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in lymph node (RPKM 2.2), appendix (RPKM 1.5) and 13 other tissues See more
Orthologs
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Genomic context

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See SCML4 in Genome Data Viewer
Location:
6q21
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (107702154..107846038, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (108881077..109024211, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (108023358..108145517, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17440 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17441 Neighboring gene sine oculis binding protein homolog Neighboring gene NANOG hESC enhancer GRCh37_chr6:107906855-107907747 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107925473-107925974 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107925975-107926474 Neighboring gene Sharpr-MPRA regulatory region 6907 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107978733-107979310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107979311-107979887 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107989710-107990210 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107990211-107990711 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24906 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:107994533-107995032 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:107995930-107996511 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:107996512-107997092 Neighboring gene uncharacterized LOC124901367 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17442 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24908 Neighboring gene Sharpr-MPRA regulatory region 13974 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:108181119-108181688 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:108181689-108182258 Neighboring gene MPRA-validated peak6008 silencer Neighboring gene SEC63 homolog, protein translocation regulator Neighboring gene RNA, U6 small nuclear 437, pseudogene Neighboring gene ribosomal protein L23a pseudogene 50

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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Related articles in PubMed

  1. Genome-Wide Association and Functional Studies Identify SCML4 and THSD7A as Novel Susceptibility Genes for Coronary Artery Disease. Li Y, et al. Arterioscler Thromb Vasc Biol, 2018 Apr. PMID 29472232
  2. Candidate gene/loci studies in cleft lip/palate and dental anomalies finds novel susceptibility genes for clefts. Vieira AR, et al. Genet Med, 2008 Sep. PMID 18978678, Free PMC Article
  3. The BioPlex Network: A Systematic Exploration of the Human Interactome. Huttlin EL, et al. Cell, 2015 Jul 16. PMID 26186194, Free PMC Article
  4. A reference map of the human binary protein interactome. Luck K, et al. Nature, 2020 Apr. PMID 32296183, Free PMC Article
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039

See all (9) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SCML4 and THSD7A are identified as novel susceptibility genes for coronary artery disease.
    Title: Genome-Wide Association and Functional Studies Identify SCML4 and THSD7A as Novel Susceptibility Genes for Coronary Artery Disease.
  2. Observational study of gene-disease association. (HuGE Navigator)
    Title: Candidate gene/loci studies in cleft lip/palate and dental anomalies finds novel susceptibility genes for clefts.
Submit: New GeneRIF Correction

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)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ36252

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
  
Process Evidence Code Pubs
involved_in negative regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
sex comb on midleg-like protein 4
Names
sex comb on midleg like 4

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_001286408.2 → NP_001273337.1  sex comb on midleg-like protein 4 isoform b

    See identical proteins and their annotated locations for NP_001273337.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an exon that results in the loss of a portion of the 5' UTR and 5' coding region, and it initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AK093571, AL096816, BC021582, BC033286, BE349472
    Consensus CDS
    CCDS69163.1
    UniProtKB/Swiss-Prot
    Q8N228
    Related
    ENSP00000358018.2, ENST00000369022.6
    Conserved Domains (3) summary
    cd09578
    Location:282 → 353
    SAM_Scm; SAM domain of Scm proteins of Polycomb group
    smart00454
    Location:285 → 353
    SAM; Sterile alpha motif
    pfam12140
    Location:37 → 147
    DUF3588; Protein of unknown function (DUF3588)

  2. NM_001286409.2 → NP_001273338.1  sex comb on midleg-like protein 4 isoform c

    See identical proteins and their annotated locations for NP_001273338.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains alternate 5' exon structure and it thus differs in its 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AL096816, BC021582, BE349472
    Consensus CDS
    CCDS75500.1
    UniProtKB/TrEMBL
    A0A0B4J1S9
    Related
    ENSP00000358021.2, ENST00000369025.6
    Conserved Domains (1) summary
    cd09578
    Location:98 → 169
    SAM_Scm; SAM domain of Scm proteins of Polycomb group

  3. NM_198081.5 → NP_932347.2  sex comb on midleg-like protein 4 isoform a

    See identical proteins and their annotated locations for NP_932347.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AK093571, AK303562, AL096816, BC021582, BC033286, BE349472
    Consensus CDS
    CCDS5060.2
    UniProtKB/Swiss-Prot
    B0QZ10, B0QZ11, B7ZBX3, Q5JXD0, Q5T0T6, Q8IYY6, Q8N228
    Related
    ENSP00000358016.3, ENST00000369020.8
    Conserved Domains (3) summary
    cd09578
    Location:340 → 411
    SAM_Scm; SAM domain of Scm proteins of Polycomb group
    smart00454
    Location:343 → 411
    SAM; Sterile alpha motif
    pfam12140
    Location:95 → 205
    DUF3588; Protein of unknown function (DUF3588)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    107702154..107846038 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047418598.1 → XP_047274554.1  sex comb on midleg-like protein 4 isoform X1

  2. XM_011535706.2 → XP_011534008.1  sex comb on midleg-like protein 4 isoform X4

    See identical proteins and their annotated locations for XP_011534008.1

    UniProtKB/Swiss-Prot
    Q8N228
    Conserved Domains (3) summary
    cd09578
    Location:282 → 353
    SAM_Scm; SAM domain of Scm proteins of Polycomb group
    smart00454
    Location:285 → 353
    SAM; Sterile alpha motif
    pfam12140
    Location:37 → 147
    DUF3588; Protein of unknown function (DUF3588)

  3. XM_047418596.1 → XP_047274552.1  sex comb on midleg-like protein 4 isoform X1

  4. XM_011535703.3 → XP_011534005.1  sex comb on midleg-like protein 4 isoform X3

    See identical proteins and their annotated locations for XP_011534005.1

    Conserved Domains (3) summary
    cd09578
    Location:311 → 382
    SAM_Scm; SAM domain of Scm proteins of Polycomb group
    smart00454
    Location:314 → 382
    SAM; Sterile alpha motif
    pfam12140
    Location:66 → 176
    DUF3588; Protein of unknown function (DUF3588)

  5. XM_047418595.1 → XP_047274551.1  sex comb on midleg-like protein 4 isoform X1

  6. XM_047418597.1 → XP_047274553.1  sex comb on midleg-like protein 4 isoform X2

  7. XM_011535704.3 → XP_011534006.1  sex comb on midleg-like protein 4 isoform X3

    See identical proteins and their annotated locations for XP_011534006.1

    Conserved Domains (3) summary
    cd09578
    Location:311 → 382
    SAM_Scm; SAM domain of Scm proteins of Polycomb group
    smart00454
    Location:314 → 382
    SAM; Sterile alpha motif
    pfam12140
    Location:66 → 176
    DUF3588; Protein of unknown function (DUF3588)

  8. XM_011535709.3 → XP_011534011.1  sex comb on midleg-like protein 4 isoform X5

    See identical proteins and their annotated locations for XP_011534011.1

    UniProtKB/TrEMBL
    A0A0B4J1S9
    Conserved Domains (1) summary
    cd09578
    Location:98 → 169
    SAM_Scm; SAM domain of Scm proteins of Polycomb group

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    108881077..109024211 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054355067.1 → XP_054211042.1  sex comb on midleg-like protein 4 isoform X1

  2. XM_054355071.1 → XP_054211046.1  sex comb on midleg-like protein 4 isoform X4

  3. XM_054355066.1 → XP_054211041.1  sex comb on midleg-like protein 4 isoform X1

  4. XM_054355069.1 → XP_054211044.1  sex comb on midleg-like protein 4 isoform X3

  5. XM_054355065.1 → XP_054211040.1  sex comb on midleg-like protein 4 isoform X1

  6. XM_054355068.1 → XP_054211043.1  sex comb on midleg-like protein 4 isoform X2

  7. XM_054355070.1 → XP_054211045.1  sex comb on midleg-like protein 4 isoform X3

  8. XM_054355072.1 → XP_054211047.1  sex comb on midleg-like protein 4 isoform X5

    UniProtKB/TrEMBL
    A0A0B4J1S9
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N228.2 GenPept UniProtKB/Swiss-Prot:Q8N228

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