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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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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

Gene LinkOut

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