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

Gene ID: 16764, updated on 11-Apr-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 regulation of transcription, DNA-templated. Acts upstream of or within embryonic hindlimb morphogenesis. Located in nucleus. Is expressed in several structures, including alimentary system; genitourinary system; limb bud; nervous system; and sensory organ. Orthologous to human AFF3 (AF4/FMR2 family member 3). [provided by Alliance of Genome Resources, Apr 2022]
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. 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
  3. 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
  4. A permissive chromatin state regulated by ZFP281-AFF3 in controlling the imprinted Meg3 polycistron. Wang Y, et al. Nucleic Acids Res, 2017 Feb 17. PMID 28180295, Free PMC Article
  5. FRA2A is a CGG repeat expansion associated with silencing of AFF3. Metsu S, et al. PLoS Genet, 2014 Apr. PMID 24763282, Free PMC Article

See all (37) 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)
  • Transposon induced (1) 
  • Targeted (1) 
  • Endonuclease-mediated (6)  1 citation

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
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 ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in cytosol ISO
Inferred from Sequence Orthology
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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