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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 4-Nov-2022

Summary

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
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Genomic context

See Smarcad1 in Genome Data Viewer
Location:
6 C1; 6 30.11 cM
Exon count:
31
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (65019575..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 sorting nexin 10 pseudogene 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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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
PubMed 
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
PubMed 
enables DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
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 cellular response to DNA damage stimulus 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 histone H3 deacetylation ISO
Inferred from Sequence Orthology
more info
 
involved_in histone H4 deacetylation 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
 
located_in 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
PubMed 
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

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_031984.1
XP_006505573.1
XP_006505575.1
XP_006505576.1
XP_036021704.1
XP_036021705.1
XP_036021706.1
XP_036021707.1

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_001253392.1NP_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:286808
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cd17998
    Location:307489
    DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
  2. NM_001355248.2NP_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
    Related
    ENSMUSP00000144776.2, ENSMUST00000204696.3
  3. NM_001355249.2NP_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
    Related
    ENSMUSP00000145340.2, ENSMUST00000205118.3
  4. NM_001355250.2NP_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
    Q3UYR6
    Conserved Domains (2) summary
    PLN03142
    Location:471993
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cd17998
    Location:492674
    DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
  5. NM_001409790.1NP_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_001409791.1NP_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_007958.3NP_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, Q3UYR6
    Related
    ENSMUSP00000031984.7, ENSMUST00000031984.9
    Conserved Domains (2) summary
    PLN03142
    Location:471993
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cd17998
    Location:492674
    DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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
    65019575..65093045
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036165811.1XP_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:471964
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cd17998
    Location:492674
    DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
  2. XM_036165814.1XP_036021707.1  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:286808
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cd17998
    Location:307489
    DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
  3. XM_036165812.1XP_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:471964
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cd17998
    Location:492674
    DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
  4. XM_036165813.1XP_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:286808
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cd17998
    Location:307489
    DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
  5. XM_006505510.4XP_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, Q3UYR6
    Conserved Domains (2) summary
    PLN03142
    Location:471993
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cd17998
    Location:492674
    DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
  6. XM_006505512.5XP_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:286808
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cd17998
    Location:307489
    DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
  7. XM_006505513.5XP_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:46568
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cd17998
    Location:67249
    DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

RNA

  1. XR_003956162.2 RNA Sequence

  2. XR_003956163.2 RNA Sequence