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

    Gene ID: 256380, updated on 2-Nov-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 DNA-templated transcription. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in lymph node (RPKM 2.2), appendix (RPKM 1.5) and 13 other tissues See more
    Orthologs
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (107702154..107846038, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (108881077..109024211, complement)
    RS_2024_09 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. In-Depth In Vivo Crosslinking in Minutes by a Compact, Membrane-Permeable, and Alkynyl-Enrichable Crosslinker. Gao H, et al. Anal Chem, 2022 May 31. PMID 35575683
    4. The BioPlex Network: A Systematic Exploration of the Human Interactome. Huttlin EL, et al. Cell, 2015 Jul 16. PMID 26186194, Free PMC Article
    5. A reference map of the human binary protein interactome. Luck K, et al. Nature, 2020 Apr. PMID 32296183, Free PMC Article

    See all (10) 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
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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_2024_08

    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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