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

    Gene ID: 312398, updated on 14-Nov-2024

    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 several processes, including DNA double-strand break processing; chromosome separation; and regulation of gene expression. 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 (SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1). [provided by Alliance of Genome Resources, Nov 2024]
    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
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    D3Z9Z9.1 GenPept UniProtKB/Swiss-Prot:D3Z9Z9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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