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    Skic2 SKI2 subunit of superkiller complex [ Rattus norvegicus (Norway rat) ]

    Gene ID: 294260, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Skic2provided by RGD
    Official Full Name
    SKI2 subunit of superkiller complexprovided by RGD
    Primary source
    RGD:1303059
    See related
    EnsemblRapid:ENSRNOG00000000421 AllianceGenome:RGD:1303059
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Skiv2l
    Summary
    Predicted to enable 3'-5' RNA helicase activity. Predicted to be involved in nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay and rescue of stalled ribosome. Predicted to be part of Ski complex. Human ortholog(s) of this gene implicated in trichohepatoenteric syndrome 2. Orthologous to human SKIC2 (SKI2 subunit of superkiller complex). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Adrenal (RPKM 117.0), Kidney (RPKM 104.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Skic2 in Genome Data Viewer
    Location:
    20p12
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (3987130..3997887)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (3982494..3993261)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (4519457..4530177, complement)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene complement factor B Neighboring gene negative elongation factor complex member E Neighboring gene decapping exoribonuclease Neighboring gene serine/threonine kinase 19

    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 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 human DEVH-box protein Ski2w from the HLA is localized in nucleoli and ribosomes. Qu X, et al. Nucleic Acids Res, 1998 Sep 1. PMID 9705521, Free PMC Article
    2. The human PAF complex coordinates transcription with events downstream of RNA synthesis. Zhu B, et al. Genes Dev, 2005 Jul 15. PMID 16024656, Free PMC Article
    3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables 3'-5' RNA helicase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA helicase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in rescue of stalled ribosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of Ski complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of Ski complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    superkiller complex protein 2
    Names
    SKI2 homolog, superkiller viralicidic activity 2-like
    Ski2 like RNA helicase
    helicase SKI2W
    superkiller viralicidic activity 2-like
    NP_998724.1
    XP_006255985.1

    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_213559.2 → NP_998724.1  superkiller complex protein 2

      See identical proteins and their annotated locations for NP_998724.1

      Status: VALIDATED

      Source sequence(s)
      BX883045
      UniProtKB/TrEMBL
      A6KTK7, F1LP39, Q6MG76
      Conserved Domains (6) summary
      smart00490
      Location:618 → 702
      HELICc; helicase superfamily c-terminal domain
      COG4581
      Location:285 → 1239
      Dob10; Superfamily II RNA helicase [Replication, recombination and repair]
      pfam00270
      Location:309 → 456
      DEAD; DEAD/DEAH box helicase
      pfam08148
      Location:1067 → 1233
      DSHCT; DSHCT (NUC185) domain
      pfam13234
      Location:759 → 1037
      rRNA_proc-arch; rRNA-processing arch domain
      pfam15345
      Location:216 → 274
      TMEM51; Transmembrane protein 51

    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_086038.1 Reference GRCr8

      Range
      3987130..3997887
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006255923.4 → XP_006255985.1  superkiller complex protein 2 isoform X1

      UniProtKB/TrEMBL
      A6KTK7
      Related
      ENSRNOP00000098071.1, ENSRNOT00000120389.2
      Conserved Domains (6) summary
      smart00490
      Location:621 → 705
      HELICc; helicase superfamily c-terminal domain
      COG4581
      Location:288 → 1242
      Dob10; Superfamily II RNA helicase [Replication, recombination and repair]
      pfam00270
      Location:312 → 459
      DEAD; DEAD/DEAH box helicase
      pfam08148
      Location:1070 → 1236
      DSHCT; DSHCT (NUC185) domain
      pfam13234
      Location:762 → 1040
      rRNA_proc-arch; rRNA-processing arch domain
      pfam15345
      Location:219 → 277
      TMEM51; Transmembrane protein 51
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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