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Smarcad1 SNF2 related chromatin remodeling ATPase with DExD box 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 312398, updated on 4-Jan-2025

Summary

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Official Symbol
Smarcad1provided by RGD
Official Full Name
SNF2 related chromatin remodeling ATPase with DExD box 1provided by RGD
Primary source
RGD:1309640
See related
EnsemblRapid:ENSRNOG00000006391 AllianceGenome:RGD:1309640
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to enable DNA binding activity; chromatin binding activity; and nucleosome array spacer activity. Predicted to be involved in DNA double-strand break processing; chromosome separation; and regulation of macromolecule metabolic process. Predicted to be located in chromosome and nucleoplasm. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in BASAN syndrome and adermatoglyphia. Orthologous to human SMARCAD1 (SNF2 related chromatin remodeling ATPase with DExD box 1). [provided by Alliance of Genome Resources, Jan 2025]
Expression
Biased expression in Spleen (RPKM 169.0), Thymus (RPKM 135.5) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Smarcad1 in Genome Data Viewer
Location:
4q31
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (95639722..95709055)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (94311441..94379184)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (95884020..95945248)

Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA48 Neighboring gene non-POU domain containing, octamer-binding, pseudogene 10 Neighboring gene oxidized purine nucleoside triphosphate hydrolase-like Neighboring gene hematopoietic prostaglandin D synthase Neighboring gene tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta, pseudogene 4

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. The Etl-1 gene encodes a nuclear protein differentially expressed during early mouse development. Schoor M, et al. Dev Dyn, 1993 Jul. PMID 8219362
  2. SMARCAD1, a novel human helicase family-defining member associated with genetic instability: cloning, expression, and mapping to 4q22-q23, a band rich in breakpoints and deletion mutants involved in several human diseases. Adra CN, et al. Genomics, 2000 Oct 15. PMID 11031099
  3. The novel protein complex with SMARCAD1/KIAA1122 binds to the vicinity of TSS. Okazaki N, et al. J Mol Biol, 2008 Oct 3. PMID 18675275
  4. The yeast Fun30 and human SMARCAD1 chromatin remodellers promote DNA end resection. Costelloe T, et al. Nature, 2012 Sep 27. PMID 22960744, Free PMC Article
  5. Maintenance of silent chromatin through replication requires SWI/SNF-like chromatin remodeler SMARCAD1. Rowbotham SP, et al. Mol Cell, 2011 May 6. PMID 21549307

See all (6) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables ATP hydrolysis activity IEA
Inferred from Electronic Annotation
more info
  
enables ATP-dependent H2AZ histone chaperone activity IEA
Inferred from Electronic Annotation
more info
  
enables ATP-dependent H3-H4 histone complex chaperone activity IEA
Inferred from Electronic Annotation
more info
  
enables ATP-dependent chromatin remodeler activity ISO
Inferred from Sequence Orthology
more info
  
enables ATP-dependent chromatin remodeler activity ISS
Inferred from Sequence or Structural Similarity
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 DNA clamp loader activity IEA
Inferred from Electronic Annotation
more info
  
enables chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables chromatin extrusion motor activity IEA
Inferred from Electronic Annotation
more info
  
enables cohesin loader activity IEA
Inferred from Electronic Annotation
more info
  
enables double-stranded DNA helicase activity IEA
Inferred from Electronic Annotation
more info
  
enables forked DNA-dependent helicase activity IEA
Inferred from Electronic Annotation
more info
  
enables four-way junction helicase activity IEA
Inferred from Electronic Annotation
more info
  
enables helicase activity IEA
Inferred from Electronic Annotation
more info
  
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
enables nucleosome array spacer activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables single-stranded 3'-5' DNA helicase activity 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 IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in DNA double-strand break processing ISO
Inferred from Sequence Orthology
more info
  
involved_in DNA double-strand break processing ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in DNA duplex unwinding IEA
Inferred from Electronic Annotation
more info
  
involved_in DNA repair IEA
Inferred from Electronic Annotation
more info
  
involved_in chromatin looping IEA
Inferred from Electronic Annotation
more info
  
involved_in 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 chromosome separation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in heterochromatin formation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of DNA recombination ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in chromatin IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in chromosome IEA
Inferred from Electronic Annotation
more info
  
located_in heterochromatin ISO
Inferred from Sequence Orthology
more info
  
located_in heterochromatin ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nuclear replication fork ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm IEA
Inferred from Electronic Annotation
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 IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in site of double-strand break ISO
Inferred from Sequence Orthology
more info
  
located_in site of double-strand break ISS
Inferred from Sequence or Structural Similarity
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
SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1
SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1`
NP_001101334.2
XP_006236662.1
XP_038963492.1
XP_038963493.1
XP_063142113.1

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_001107864.2 → NP_001101334.2  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1

    See identical proteins and their annotated locations for NP_001101334.2

    Status: PROVISIONAL

    Source sequence(s)
    JAXUCZ010000004
    UniProtKB/Swiss-Prot
    D3Z9Z9
    UniProtKB/TrEMBL
    A0A8I6G898
    Conserved Domains (3) summary
    cd00046
    Location:515 → 657
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    pfam00176
    Location:498 → 785
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:851 → 965
    Helicase_C; Helicase conserved C-terminal domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086022.1 Reference GRCr8

    Range
    95639722..95709055
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039107564.2 → XP_038963492.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X1

    UniProtKB/TrEMBL
    A0A8I6G898
    Conserved Domains (3) summary
    PLN03142
    Location:474 → 996
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cd17998
    Location:495 → 677
    DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
    NF033845
    Location:18 → 247
    MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

  2. XM_006236600.5 → XP_006236662.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X2

    See identical proteins and their annotated locations for XP_006236662.1

    UniProtKB/Swiss-Prot
    D3Z9Z9
    UniProtKB/TrEMBL
    A0A8I6G898
    Related
    ENSRNOP00000008585.3, ENSRNOT00000008585.5
    Conserved Domains (3) summary
    cd00046
    Location:515 → 657
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    pfam00176
    Location:498 → 785
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:851 → 965
    Helicase_C; Helicase conserved C-terminal domain

  3. XM_039107565.2 → XP_038963493.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X1

    UniProtKB/TrEMBL
    A0A8I6G898
    Conserved Domains (3) summary
    PLN03142
    Location:474 → 996
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cd17998
    Location:495 → 677
    DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
    NF033845
    Location:18 → 247
    MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

  4. XM_063286043.1 → XP_063142113.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X2

    UniProtKB/Swiss-Prot
    D3Z9Z9
    UniProtKB/TrEMBL
    A0A8I6G898
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
D3Z9Z9.1 GenPept UniProtKB/Swiss-Prot:D3Z9Z9

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