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    Samd11 sterile alpha motif domain containing 11 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 102549710, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Samd11provided by RGD
    Official Full Name
    sterile alpha motif domain containing 11provided by RGD
    Primary source
    RGD:1310271
    See related
    EnsemblRapid:ENSRNOG00000020342 AllianceGenome:RGD:1310271
    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
    RGD1310271
    Summary
    Predicted to enable several functions, including DNA-binding transcription repressor activity, RNA polymerase II-specific; identical protein binding activity; and protein domain specific binding activity. Predicted to be involved in negative regulation of DNA-templated transcription and retinal rod cell development. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II. Predicted to be part of PRC1 complex. Predicted to be active in nucleus. Orthologous to human SAMD11 (sterile alpha motif domain containing 11). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Kidney (RPKM 35.4), Liver (RPKM 24.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Samd11 in Genome Data Viewer
    Location:
    5q36
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (172113900..172142026, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (166831681..166859805, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (173672413..173689360, complement)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene PPARGC1 and ESRR induced regulator, muscle 1 Neighboring gene pleckstrin homology domain containing N1 Neighboring gene kelch-like family member 17 Neighboring gene NOC2-like nucleolar associated transcriptional repressor

    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. Cloning and characterization of mr-s, a novel SAM domain protein, predominantly expressed in retinal photoreceptor cells. Inoue T, et al. BMC Dev Biol, 2006 Mar 16. PMID 16539743, Free PMC Article
    2. Gene and alternative splicing annotation with AIR. Florea L, et al. Genome Res, 2005 Jan. PMID 15632090, 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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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables PH domain binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables SAM domain binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in negative regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in retinal rod cell development ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of PRC1 complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    sterile alpha motif domain-containing protein 11

    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_001415981.1 → NP_001402910.1  sterile alpha motif domain-containing protein 11

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000005
      UniProtKB/TrEMBL
      A0A8I5ZXL4
      Related
      ENSRNOP00000084329.1, ENSRNOT00000096699.2

    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_086023.1 Reference GRCr8

      Range
      172113900..172142026 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039109114.2 → XP_038965042.1  sterile alpha motif domain-containing protein 11 isoform X3

      UniProtKB/TrEMBL
      D3ZMX5
      Conserved Domains (1) summary
      cd09579
      Location:525 → 592
      SAM_Samd7,11; SAM domain of Samd7,11 subfamily of Polycomb group

    2. XM_039109112.2 → XP_038965040.1  sterile alpha motif domain-containing protein 11 isoform X1

      Conserved Domains (2) summary
      cd09579
      Location:693 → 760
      SAM_Samd7,11; SAM domain of Samd7,11 subfamily of Polycomb group
      pfam01342
      Location:113 → 185
      SAND; SAND domain

    3. XM_039109113.2 → XP_038965041.1  sterile alpha motif domain-containing protein 11 isoform X2

      Conserved Domains (2) summary
      cd09579
      Location:676 → 743
      SAM_Samd7,11; SAM domain of Samd7,11 subfamily of Polycomb group
      pfam01342
      Location:113 → 185
      SAND; SAND domain

    4. XM_039109116.2 → XP_038965044.1  sterile alpha motif domain-containing protein 11 isoform X4

      UniProtKB/TrEMBL
      D3ZMX5
      Conserved Domains (1) summary
      cd09579
      Location:504 → 571
      SAM_Samd7,11; SAM domain of Samd7,11 subfamily of Polycomb group

    5. XM_039109119.2 → XP_038965047.1  sterile alpha motif domain-containing protein 11 isoform X5

      Conserved Domains (1) summary
      pfam01342
      Location:113 → 185
      SAND; SAND domain

    RNA

    1. XR_005504352.2 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001305446.1: Suppressed sequence

      Description
      NM_001305446.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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