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

    Gene ID: 16764, updated on 27-Nov-2024

    Summary

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    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, Nov 2024]
    Expression
    Broad expression in thymus adult (RPKM 9.9), spleen adult (RPKM 7.6) and 19 other tissues See more
    Orthologs
    human all
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    Genomic context

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    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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Deletions, Inversions, Duplications: Engineering of Structural Variants using CRISPR/Cas in Mice. Kraft K, et al. Cell Rep, 2015 Feb 10. PMID 25660031
    2. The mouse Laf4 gene: exon/intron organization, cDNA sequence, alternative splicing, and expression during central nervous system development. Britanova O, et al. Genomics, 2002 Jul. PMID 12079280
    3. Variants in the degron of AFF3 are associated with intellectual disability, mesomelic dysplasia, horseshoe kidney, and epileptic encephalopathy. Voisin N, et al. Am J Hum Genet, 2021 May 6. PMID 33961779, Free PMC Article
    4. 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
    5. 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

    See all (40) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. AFF3 is associated with the Kruppel-like zinc finger protein ZFP281 in embryonic stem (ES) cells. ZFP281 recruits AFF3 to the Meg3 enhancer within the imprinted Dlk1-Dio3 locus, thus regulating the allele-specific expression of the Meg3 polycistron.
      Title: A permissive chromatin state regulated by ZFP281-AFF3 in controlling the imprinted Meg3 polycistron.
    2. The neuronal migration deficit caused by loss of Laf4 can be partially rescued by Mdga2 over-expression, revealing an important functional relationship between these genes in a mouse model of intellectual disability.
      Title: Laf4/Aff3, a gene involved in intellectual disability, is required for cellular migration in the mouse cerebral cortex.
    3. Alternatively spliced forms encode several forms of putative protein with potentially different transactivation functions.
      Title: The mouse Laf4 gene: exon/intron organization, cDNA sequence, alternative splicing, and expression during central nervous system development.
    Submit: New GeneRIF Correction

    Variation

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    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

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within DNA-templated transcription TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in embryonic hindlimb morphogenesis IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in embryonic hindlimb morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in response to tumor necrosis factor IEA
    Inferred from Electronic Annotation
    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 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

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    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)

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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_001290814.2 → NP_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:533 → 630
      PRK12323; DNA polymerase III subunit gamma/tau
      pfam05110
      Location:20 → 475
      AF-4; AF-4 proto-oncoprotein
      pfam18876
      Location:968 → 1228
      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_030251556.2 → XP_030107416.1  AF4/FMR2 family member 3 isoform X6

      UniProtKB/TrEMBL
      F8WJA7
      Conserved Domains (1) summary
      pfam05110
      Location:62 → 1234
      AF-4; AF-4 proto-oncoprotein

    2. XM_006495737.5 → XP_006495800.1  AF4/FMR2 family member 3 isoform X4

      UniProtKB/TrEMBL
      F8WJA7
      Conserved Domains (1) summary
      pfam05110
      Location:62 → 1262
      AF-4; AF-4 proto-oncoprotein

    3. XM_011238447.4 → XP_011236749.1  AF4/FMR2 family member 3 isoform X5

      UniProtKB/Swiss-Prot
      P51827, Q80WS6
      Conserved Domains (1) summary
      pfam05110
      Location:87 → 1260
      AF-4; AF-4 proto-oncoprotein

    4. XM_011238444.4 → XP_011236746.1  AF4/FMR2 family member 3 isoform X2

      UniProtKB/Swiss-Prot
      P51827, Q80WS6
      Conserved Domains (1) summary
      pfam05110
      Location:87 → 1286
      AF-4; AF-4 proto-oncoprotein

    5. XM_011238446.4 → XP_011236748.1  AF4/FMR2 family member 3 isoform X3

      UniProtKB/Swiss-Prot
      P51827, Q80WS6
      Conserved Domains (1) summary
      pfam05110
      Location:87 → 1271
      AF-4; AF-4 proto-oncoprotein

    6. XM_011238443.4 → XP_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:87 → 1287
      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.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P51827.2 GenPept UniProtKB/Swiss-Prot:P51827

    Gene LinkOut

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