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SCML1 Scm polycomb group protein like 1 [ Homo sapiens (human) ]

Gene ID: 6322, updated on 2-Nov-2024

Summary

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Official Symbol
SCML1provided by HGNC
Official Full Name
Scm polycomb group protein like 1provided by HGNC
Primary source
HGNC:HGNC:10580
See related
Ensembl:ENSG00000047634 MIM:300227; AllianceGenome:HGNC:10580
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
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 located in female germ cell nucleus and male germ cell nucleus. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in testis (RPKM 14.0), ovary (RPKM 6.6) and 24 other tissues See more
Orthologs
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Genomic context

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See SCML1 in Genome Data Viewer
Location:
Xp22.13
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (17737128..17754985)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (17319668..17337595)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (17755613..17773105)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene NHS actin remodeling regulator Neighboring gene uncharacterized LOC105373142 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:17653158-17653816 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:17674013-17674724 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:17674725-17675435 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20684 Neighboring gene CHP1 pseudogene 3 Neighboring gene MED14-independent group 3 enhancer GRCh37_chrX:17767905-17769104 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:17804670-17805440 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:17805441-17806211 Neighboring gene family with sequence similarity 136 member A pseudogene Neighboring gene retinoic acid induced 2

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. Characterization of SCML1, a new gene in Xp22, with homology to developmental polycomb genes. van de Vosse E, et al. Genomics, 1998 Apr 1. PMID 9570953
  2. Adaptive evolution of SCML1 in primates, a gene involved in male reproduction. Wu HH, et al. BMC Evol Biol, 2008 Jul 5. PMID 18601738, Free PMC Article
  3. A novel Xp22.13 microdeletion in Nance-Horan syndrome. Accogli A, et al. Birth Defects Res, 2017 Jul 3. PMID 28464487
  4. PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes. Gao Z, et al. Mol Cell, 2012 Feb 10. PMID 22325352, Free PMC Article
  5. Myotubularin-related proteins 3 and 4 interact with polo-like kinase 1 and centrosomal protein of 55 kDa to ensure proper abscission. St-Denis N, et al. Mol Cell Proteomics, 2015 Apr. PMID 25659891, Free PMC Article

See all (30) citations in PubMed

GeneRIFs: Gene References Into Functions

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

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 1
Names
sex comb on midleg like 1

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_001037535.3 → NP_001032624.1  sex comb on midleg-like protein 1 isoform c

    See identical proteins and their annotated locations for NP_001032624.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks two exons and uses an alternate splice site in the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) has a shorter N-terminus, compared to isoform a. Both variants 3 and 4 encode the same isoform (c).
    Source sequence(s)
    AA382395, AF160728, BC026159
    Consensus CDS
    CCDS35211.1
    Related
    ENSP00000381154.1, ENST00000398080.5
    Conserved Domains (2) summary
    cd09578
    Location:131 → 202
    SAM_Scm; SAM domain of Scm proteins of Polycomb group
    smart00454
    Location:134 → 202
    SAM; Sterile alpha motif

  2. NM_001037536.3 → NP_001032625.1  sex comb on midleg-like protein 1 isoform c

    See identical proteins and their annotated locations for NP_001032625.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks two exons in the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) has a shorter N-terminus, compared to isoform a. Both variants 3 and 4 encode the same isoform (c).
    Source sequence(s)
    AA382395, AF160728, BC026159
    Consensus CDS
    CCDS35211.1
    Related
    ENSP00000369384.3, ENST00000380045.7
    Conserved Domains (2) summary
    cd09578
    Location:131 → 202
    SAM_Scm; SAM domain of Scm proteins of Polycomb group
    smart00454
    Location:134 → 202
    SAM; Sterile alpha motif

  3. NM_001037540.3 → NP_001032629.1  sex comb on midleg-like protein 1 isoform a

    See identical proteins and their annotated locations for NP_001032629.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AA382395, AF160728, BC026159, BI461014
    Consensus CDS
    CCDS35210.1
    UniProtKB/Swiss-Prot
    B0FZN6, B2RA08, Q5H968, Q5H969, Q9UN30
    Related
    ENSP00000369380.3, ENST00000380041.8
    Conserved Domains (2) summary
    cd09578
    Location:252 → 323
    SAM_Scm; SAM domain of Scm proteins of Polycomb group
    smart00454
    Location:255 → 323
    SAM; Sterile alpha motif

  4. NM_006746.6 → NP_006737.2  sex comb on midleg-like protein 1 isoform b

    See identical proteins and their annotated locations for NP_006737.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an exon and uses an alternate splice site in the 5' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (b) is shorter than isoform a.
    Source sequence(s)
    AA382395, AF160728, BC026159
    Consensus CDS
    CCDS14182.2
    Related
    ENSP00000369382.3, ENST00000380043.7
    Conserved Domains (2) summary
    cd09578
    Location:225 → 296
    SAM_Scm; SAM domain of Scm proteins of Polycomb group
    smart00454
    Location:228 → 296
    SAM; Sterile alpha motif

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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    17737128..17754985
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047442348.1 → XP_047298304.1  sex comb on midleg-like protein 1 isoform X1

  2. XM_047442350.1 → XP_047298306.1  sex comb on midleg-like protein 1 isoform X5

  3. XM_047442349.1 → XP_047298305.1  sex comb on midleg-like protein 1 isoform X5

  4. XM_011545564.4 → XP_011543866.1  sex comb on midleg-like protein 1 isoform X1

    See identical proteins and their annotated locations for XP_011543866.1

    Conserved Domains (1) summary
    cd09578
    Location:253 → 324
    SAM_Scm; SAM domain of Scm proteins of Polycomb group

  5. XM_006724508.5 → XP_006724571.1  sex comb on midleg-like protein 1 isoform X2

    See identical proteins and their annotated locations for XP_006724571.1

    UniProtKB/Swiss-Prot
    B0FZN6, B2RA08, Q5H968, Q5H969, Q9UN30
    Conserved Domains (2) summary
    cd09578
    Location:252 → 323
    SAM_Scm; SAM domain of Scm proteins of Polycomb group
    smart00454
    Location:255 → 323
    SAM; Sterile alpha motif

  6. XM_017029723.3 → XP_016885212.1  sex comb on midleg-like protein 1 isoform X3

    Conserved Domains (2) summary
    cd09578
    Location:225 → 296
    SAM_Scm; SAM domain of Scm proteins of Polycomb group
    smart00454
    Location:228 → 296
    SAM; Sterile alpha motif

  7. XM_006724509.5 → XP_006724572.1  sex comb on midleg-like protein 1 isoform X4

    See identical proteins and their annotated locations for XP_006724572.1

    Conserved Domains (2) summary
    cd09578
    Location:224 → 295
    SAM_Scm; SAM domain of Scm proteins of Polycomb group
    smart00454
    Location:227 → 295
    SAM; Sterile alpha motif

  8. XM_005274578.3 → XP_005274635.1  sex comb on midleg-like protein 1 isoform X1

    See identical proteins and their annotated locations for XP_005274635.1

    Conserved Domains (1) summary
    cd09578
    Location:253 → 324
    SAM_Scm; SAM domain of Scm proteins of Polycomb group

  9. XM_005274579.3 → XP_005274636.1  sex comb on midleg-like protein 1 isoform X4

    See identical proteins and their annotated locations for XP_005274636.1

    Conserved Domains (2) summary
    cd09578
    Location:224 → 295
    SAM_Scm; SAM domain of Scm proteins of Polycomb group
    smart00454
    Location:227 → 295
    SAM; Sterile alpha motif

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    17319668..17337595
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054327562.1 → XP_054183537.1  sex comb on midleg-like protein 1 isoform X5

  2. XM_054327556.1 → XP_054183531.1  sex comb on midleg-like protein 1 isoform X1

  3. XM_054327558.1 → XP_054183533.1  sex comb on midleg-like protein 1 isoform X2

    UniProtKB/Swiss-Prot
    B0FZN6, B2RA08, Q5H968, Q5H969, Q9UN30

  4. XM_054327559.1 → XP_054183534.1  sex comb on midleg-like protein 1 isoform X3

  5. XM_054327560.1 → XP_054183535.1  sex comb on midleg-like protein 1 isoform X4

  6. XM_054327557.1 → XP_054183532.1  sex comb on midleg-like protein 1 isoform X1

  7. XM_054327561.1 → XP_054183536.1  sex comb on midleg-like protein 1 isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UN30.2 GenPept UniProtKB/Swiss-Prot:Q9UN30

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