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    Aff3 AF4/FMR2 family, member 3 [ Mus musculus (house mouse) ]

    Gene ID: 16764, updated on 9-Dec-2024

    Summary

    Official Symbol
    Aff3provided by MGI
    Official Full Name
    AF4/FMR2 family, member 3provided by MGI
    Primary source
    MGI:MGI:106927
    See related
    Ensembl:ENSMUSG00000037138 AllianceGenome:MGI:106927
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Laf4; LAF-4; A730046J16; 3222402O04Rik
    Summary
    Enables DNA-binding transcription factor activity and double-stranded DNA binding activity. Involved in embryonic hindlimb morphogenesis and regulation of DNA-templated transcription. Located in nucleus. Is expressed in several structures, including alimentary system; genitourinary system; limb bud; nervous system; and sensory organ. Used to study KINSSHIP syndrome. 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, Dec 2024]
    Expression
    Broad expression in thymus adult (RPKM 9.9), spleen adult (RPKM 7.6) and 19 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Aff3 in Genome Data Viewer
    Location:
    1 B; 1 16.58 cM
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (38212936..38704036, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (38175393..38630178, complement)

    Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_00689 Neighboring gene STARR-seq mESC enhancer starr_00690 Neighboring gene eukaryotic translation initiation factor 5B Neighboring gene STARR-seq mESC enhancer starr_00691 Neighboring gene REV1, DNA directed polymerase Neighboring gene predicted gene 5099 Neighboring gene predicted gene 16150 Neighboring gene STARR-seq mESC enhancer starr_00693 Neighboring gene predicted gene 16152 Neighboring gene STARR-seq mESC enhancer starr_00694 Neighboring gene nucleoside diphosphate kinase, mitochondrial pseudogene Neighboring gene STARR-seq mESC enhancer starr_00697 Neighboring gene STARR-seq mESC enhancer starr_00698 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:38714500-38714733 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:38721813-38722000 Neighboring gene predicted gene, 34596 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:38752992-38753101 Neighboring gene predicted gene, 57569 Neighboring gene STARR-seq mESC enhancer starr_00700 Neighboring gene STARR-positive B cell enhancer ABC_E8770 Neighboring gene STARR-seq mESC enhancer starr_00701 Neighboring gene LON peptidase N-terminal domain and ring finger 2

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (6)  1 citation
    • Targeted (1) 
    • Transposon induced (1) 

    General gene information

    Markers

    Gene Ontology Provided by MGI

    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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

    Preferred Names
    AF4/FMR2 family member 3
    Names
    lymphoid nuclear protein 4
    lymphoid nuclear protein related to AF4
    protein LAF-4

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001290814.2NP_001277743.1  AF4/FMR2 family member 3

      Status: VALIDATED

      Source sequence(s)
      AC117789, AC132381, AC138386
      Consensus CDS
      CCDS69884.1
      UniProtKB/TrEMBL
      D3YYI6, F8WJA7
      Related
      ENSMUSP00000092637.3, ENSMUST00000095027.9
      Conserved Domains (3) summary
      PRK12323
      Location:533630
      PRK12323; DNA polymerase III subunit gamma/tau
      pfam05110
      Location:20475
      AF-4; AF-4 proto-oncoprotein
      pfam18876
      Location:9681228
      AF-4_C; AF-4 proto-oncoprotein C-terminal region

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000067.7 Reference GRCm39 C57BL/6J

      Range
      38212936..38704036 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030251556.2XP_030107416.1  AF4/FMR2 family member 3 isoform X6

      UniProtKB/TrEMBL
      F8WJA7
      Conserved Domains (1) summary
      pfam05110
      Location:621234
      AF-4; AF-4 proto-oncoprotein
    2. XM_006495737.5XP_006495800.1  AF4/FMR2 family member 3 isoform X4

      UniProtKB/TrEMBL
      F8WJA7
      Conserved Domains (1) summary
      pfam05110
      Location:621262
      AF-4; AF-4 proto-oncoprotein
    3. XM_011238447.4XP_011236749.1  AF4/FMR2 family member 3 isoform X5

      UniProtKB/Swiss-Prot
      P51827, Q80WS6
      Conserved Domains (1) summary
      pfam05110
      Location:871260
      AF-4; AF-4 proto-oncoprotein
    4. XM_011238444.4XP_011236746.1  AF4/FMR2 family member 3 isoform X2

      UniProtKB/Swiss-Prot
      P51827, Q80WS6
      Conserved Domains (1) summary
      pfam05110
      Location:871286
      AF-4; AF-4 proto-oncoprotein
    5. XM_011238446.4XP_011236748.1  AF4/FMR2 family member 3 isoform X3

      UniProtKB/Swiss-Prot
      P51827, Q80WS6
      Conserved Domains (1) summary
      pfam05110
      Location:871271
      AF-4; AF-4 proto-oncoprotein
    6. XM_011238443.4XP_011236745.1  AF4/FMR2 family member 3 isoform X1

      UniProtKB/Swiss-Prot
      P51827, Q80WS6
      Related
      ENSMUSP00000159147.2, ENSMUST00000238906.2
      Conserved Domains (1) summary
      pfam05110
      Location:871287
      AF-4; AF-4 proto-oncoprotein

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_010678.2: Suppressed sequence

      Description
      NM_010678.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.