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    Smarcad1 SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 [ Mus musculus (house mouse) ]

    Gene ID: 13990, updated on 3-Apr-2024

    Summary

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    Official Symbol
    Smarcad1provided by MGI
    Official Full Name
    SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1provided by MGI
    Primary source
    MGI:MGI:95453
    See related
    Ensembl:ENSMUSG00000029920 AllianceGenome:MGI:95453
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Etl1; etl-1; D6Pas1; mKIAA1122
    Summary
    Predicted to enable ATP-dependent activity, acting on DNA; DNA binding activity; and chromatin binding activity. Predicted to be involved in several processes, including DNA double-strand break processing; chromosome separation; and histone deacetylation. Predicted to act upstream of or within DNA repair and chromatin organization. Located in heterochromatin and nucleus. Is expressed in several structures, including alimentary system; central nervous system; eye; genitourinary system; and integumental system. Used to study asphyxiating thoracic dystrophy. Human ortholog(s) of this gene implicated in BASAN syndrome and adermatoglyphia. Orthologous to human SMARCAD1 (SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in CNS E11.5 (RPKM 9.6), CNS E14 (RPKM 8.1) and 22 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Smarcad1 in Genome Data Viewer
    Location:
    6 C1; 6 30.11 cM
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (65019577..65093045)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (65042591..65116061)

    Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene lurcher transcript 1 Neighboring gene STARR-seq mESC enhancer starr_16119 Neighboring gene sorting nexin 10 pseudogene Neighboring gene STARR-seq mESC enhancer starr_16124 Neighboring gene STARR-seq mESC enhancer starr_16125 Neighboring gene STARR-seq mESC enhancer starr_16130 Neighboring gene STARR-positive B cell enhancer ABC_E8107 Neighboring gene 7,8-dihydro-8-oxoguanine triphosphatase-like Neighboring gene hematopoietic prostaglandin D synthase Neighboring gene zinc finger protein 706 pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Smarcad1 mediates microbiota-induced inflammation in mouse and coordinates gene expression in the intestinal epithelium. Kazakevych J, et al. Genome Biol, 2020 Mar 11. PMID 32160911, Free PMC Article
    2. SMARCAD1 ATPase activity is required to silence endogenous retroviruses in embryonic stem cells. Sachs P, et al. Nat Commun, 2019 Mar 22. PMID 30902974, Free PMC Article
    3. SMARCAD1 Contributes to the Regulation of Naive Pluripotency by Interacting with Histone Citrullination. Xiao S, et al. Cell Rep, 2017 Mar 28. PMID 28355564, Free PMC Article
    4. Skeletal dysplasias, growth retardation, reduced postnatal survival, and impaired fertility in mice lacking the SNF2/SWI2 family member ETL1. Schoor M, et al. Mech Dev, 1999 Jul. PMID 10415348
    5. The mouse Enhancer trap locus 1 (Etl-1): a novel mammalian gene related to Drosophila and yeast transcriptional regulator genes. Soininen R, et al. Mech Dev, 1992 Nov. PMID 1489724

    See all (40) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The Conserved Chromatin Remodeler SMARCAD1 Interacts with TFIIIC and Architectural Proteins in Human and Mouse.
      Title: The Conserved Chromatin Remodeler SMARCAD1 Interacts with TFIIIC and Architectural Proteins in Human and Mouse.
    2. Smarcad1 mediates microbiota-induced inflammation in mouse and coordinates gene expression in the intestinal epithelium.
      Title: Smarcad1 mediates microbiota-induced inflammation in mouse and coordinates gene expression in the intestinal epithelium.
    3. Role of the ATP-dependent chromatin remodeling enzyme Fun30/Smarcad1 in the regulation of mRNA splicing.
      Title: Role of the ATP-dependent chromatin remodeling enzyme Fun30/Smarcad1 in the regulation of mRNA splicing.
    4. These findings uncover a role for the enzymatic activity of SMARCAD1 in cooperating with KAP1 to silence Endogenous retroviruses.
      Title: SMARCAD1 ATPase activity is required to silence endogenous retroviruses in embryonic stem cells.
    5. These data suggest a model in which SMARCAD1 regulates naive pluripotency by interacting with H3 arginine 26 citrullination and suppressing heterochromatin formation.
      Title: SMARCAD1 Contributes to the Regulation of Naive Pluripotency by Interacting with Histone Citrullination.
    6. Results suggest a novel model for gene regulation via the SMARCAD1/KIAA1122 protein complex.
      Title: The novel protein complex with SMARCAD1/KIAA1122 binds to the vicinity of TSS.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from PubChem

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    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 MGI

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent activity, acting on DNA IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ATP-dependent chromatin remodeler activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ubiquitin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within DNA damage response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in DNA double-strand break processing ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within DNA repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in chromosome separation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of DNA recombination ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of heterochromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear replication fork ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in site of double-strand break ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1
    Names
    ATP-dependent helicase SMARCAD1
    enhancer trap locus 1
    enhancer trap locus homolog 1
    NP_001240321.1
    NP_001342177.1
    NP_001342178.1
    NP_001342179.1
    NP_001396719.1
    NP_001396720.1
    NP_031984.1
    XP_006505573.1
    XP_006505575.1
    XP_006505576.1
    XP_036021704.1
    XP_036021705.1
    XP_036021706.1

    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_001253392.1 → NP_001240321.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform 2

      See identical proteins and their annotated locations for NP_001240321.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon which results in the use of a downstream start codon, compared to variant 1. The resulting protein (isoform 2) is shorter when it is compared to isoform 1. Variants 2 and 6 both encode the same isoform (2).
      Source sequence(s)
      AK122454, AK147884, X69942
      UniProtKB/Swiss-Prot
      Q04692
      Conserved Domains (2) summary
      PLN03142
      Location:286 → 808
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd17998
      Location:307 → 489
      DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

    2. NM_001355248.2 → NP_001342177.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks several exons and includes an alternate 3' terminal exon, compared to variant 1. The encoded protein (isoform 3) is shorter and has a distinct C-terminus, compared to isoform 1. Variants 3, 4, and 7 all encode the same protein (isoform 3).
      Source sequence(s)
      AC138622
      Consensus CDS
      CCDS90055.1
      UniProtKB/TrEMBL
      A0A0N4SUQ5, A0A0N4SVS7
      Related
      ENSMUSP00000144776.2, ENSMUST00000204696.3

    3. NM_001355249.2 → NP_001342178.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, lacks several exons and includes an alternate 3' terminal exon, compared to variant 1. The encoded protein (isoform 3) is shorter and has a distinct C-terminus, compared to isoform 1. Variants 3, 4, and 7 all encode the same protein (isoform 3).
      Source sequence(s)
      AC138622
      Consensus CDS
      CCDS90055.1
      UniProtKB/TrEMBL
      A0A0N4SUQ5, A0A0N4SVS7
      Related
      ENSMUSP00000145340.2, ENSMUST00000205118.3

    4. NM_001355250.2 → NP_001342179.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, compared to variant 1, and encodes isoform 1. Variants 1 and 5 encode the same protein (isoform 1).
      Source sequence(s)
      AC138622, AC143330
      Consensus CDS
      CCDS20204.1
      UniProtKB/Swiss-Prot
      Q04692, Q3UGK6, Q3UYR6
      Conserved Domains (2) summary
      PLN03142
      Location:471 → 993
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd17998
      Location:492 → 674
      DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

    5. NM_001409790.1 → NP_001396719.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC138622, AC143330

    6. NM_001409791.1 → NP_001396720.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC138622
      UniProtKB/TrEMBL
      A0A0N4SUQ5

    7. NM_007958.3 → NP_031984.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform 1

      See identical proteins and their annotated locations for NP_031984.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest protein (isoform 1). Variants 1 and 5 encode the same protein (isoform 1).
      Source sequence(s)
      AC138622, AC143330
      Consensus CDS
      CCDS20204.1
      UniProtKB/Swiss-Prot
      Q04692, Q3UGK6, Q3UYR6
      Related
      ENSMUSP00000031984.7, ENSMUST00000031984.9
      Conserved Domains (2) summary
      PLN03142
      Location:471 → 993
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd17998
      Location:492 → 674
      DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000072.7 Reference GRCm39 C57BL/6J

      Range
      65019577..65093045
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036165811.1 → XP_036021704.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X2

      Conserved Domains (2) summary
      PLN03142
      Location:471 → 964
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd17998
      Location:492 → 674
      DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

    2. XM_036165812.1 → XP_036021705.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X2

      Conserved Domains (2) summary
      PLN03142
      Location:471 → 964
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd17998
      Location:492 → 674
      DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

    3. XM_036165813.1 → XP_036021706.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X3

      Conserved Domains (2) summary
      PLN03142
      Location:286 → 808
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd17998
      Location:307 → 489
      DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

    4. XM_006505510.4 → XP_006505573.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X1

      See identical proteins and their annotated locations for XP_006505573.1

      UniProtKB/Swiss-Prot
      Q04692, Q3UGK6, Q3UYR6
      Conserved Domains (2) summary
      PLN03142
      Location:471 → 993
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd17998
      Location:492 → 674
      DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

    5. XM_006505512.5 → XP_006505575.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X3

      See identical proteins and their annotated locations for XP_006505575.1

      UniProtKB/Swiss-Prot
      Q04692
      Conserved Domains (2) summary
      PLN03142
      Location:286 → 808
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd17998
      Location:307 → 489
      DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

    6. XM_006505513.5 → XP_006505576.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X4

      Conserved Domains (2) summary
      PLN03142
      Location:46 → 568
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd17998
      Location:67 → 249
      DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

    RNA

    1. XR_003956162.2 RNA Sequence

    2. XR_003956163.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q04692.2 GenPept UniProtKB/Swiss-Prot:Q04692

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