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    Aff3 ALF transcription elongation factor 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 363220, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Aff3provided by RGD
    Official Full Name
    ALF transcription elongation factor 3provided by RGD
    Primary source
    RGD:1308527
    See related
    EnsemblRapid:ENSRNOG00000018830 AllianceGenome:RGD:1308527
    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
    Laf4
    Summary
    Predicted to enable DNA-binding transcription factor activity and double-stranded DNA binding activity. Predicted to be involved in embryonic hindlimb morphogenesis; regulation of DNA-templated transcription; and response to tumor necrosis factor. Predicted to be located in cytosol and nuclear body. Predicted to be part of super elongation complex. Human ortholog(s) of this gene implicated in KINSSHIP syndrome. Orthologous to human AFF3 (ALF transcription elongation factor 3). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Thymus (RPKM 69.2), Spleen (RPKM 44.6) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Aff3 in Genome Data Viewer
    Location:
    9q21-q22
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (47894903..48352380, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (40399099..40856716, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (44837979..45291964, complement)

    Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134480569 Neighboring gene REV1, DNA directed polymerase Neighboring gene transfer RNA threonine (anticodon AGU) 33 Neighboring gene histidine-rich glycoprotein-like Neighboring gene small nucleolar RNA SNORA48 Neighboring gene LON peptidase N-terminal domain and ring finger 2

    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. Triangular tibia with fibular aplasia associated with a microdeletion on 2q11.2 encompassing LAF4. Steichen-Gersdorf E, et al. Clin Genet, 2008 Dec. PMID 18616733
    2. LAF-4 encodes a lymphoid nuclear protein with transactivation potential that is homologous to AF-4, the gene fused to MLL in t(4;11) leukemias. Ma C, et al. Blood, 1996 Jan 15. PMID 8555498
    3. Laf4/Aff3, a gene involved in intellectual disability, is required for cellular migration in the mouse cerebral cortex. Moore JM, et al. PLoS One, 2014. PMID 25162227, Free PMC Article
    4. Investigation of rheumatoid arthritis susceptibility genes identifies association of AFF3 and CD226 variants with response to anti-tumour necrosis factor treatment. Tan RJ, et al. Ann Rheum Dis, 2010 Jun. PMID 20444755, Free PMC Article
    5. 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 DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in embryonic hindlimb morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in response to tumor necrosis factor ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of super elongation complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    AF4/FMR2 family member 3
    Names
    AF4/FMR2 family, member 3
    lymphoid nuclear protein related to AF4

    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_001413892.1 → NP_001400821.1  AF4/FMR2 family member 3

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      Related
      ENSRNOP00000072037.2, ENSRNOT00000083256.3

    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_086027.1 Reference GRCr8

      Range
      47894903..48352380 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039083846.2 → XP_038939774.1  AF4/FMR2 family member 3 isoform X5

      UniProtKB/TrEMBL
      A0A0G2K1Y7, F1M681
      Conserved Domains (2) summary
      pfam05110
      Location:1 → 395
      AF-4; AF-4 proto-oncoprotein
      pfam18876
      Location:898 → 1158
      AF-4_C; AF-4 proto-oncoprotein C-terminal region

    2. XM_039083844.2 → XP_038939772.1  AF4/FMR2 family member 3 isoform X2

      UniProtKB/TrEMBL
      A0A0G2K1Y7
      Related
      ENSRNOP00000106658.1, ENSRNOT00000130248.1
      Conserved Domains (2) summary
      pfam05110
      Location:45 → 497
      AF-4; AF-4 proto-oncoprotein
      pfam18876
      Location:1000 → 1260
      AF-4_C; AF-4 proto-oncoprotein C-terminal region

    3. XM_063267370.1 → XP_063123440.1  AF4/FMR2 family member 3 isoform X3

    4. XM_063267371.1 → XP_063123441.1  AF4/FMR2 family member 3 isoform X4

    5. XM_063267369.1 → XP_063123439.1  AF4/FMR2 family member 3 isoform X1

    Nucleotide Protein Strain
    Heading Accession and Version

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