U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Aff2 ALF transcription elongation factor 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 293922, updated on 13-Apr-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Aff2provided by RGD
    Official Full Name
    ALF transcription elongation factor 2provided by RGD
    Primary source
    RGD:1565592
    See related
    Ensembl:ENSRNOG00000052572 AllianceGenome:RGD:1565592
    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
    RGD1565592
    Summary
    Predicted to enable G-quadruplex RNA binding activity. Predicted to be involved in regulation of RNA splicing. Predicted to act upstream of or within learning or memory; negative regulation of gene expression; and nuclear speck organization. Predicted to be located in nucleus. Predicted to be active in nuclear speck. Human ortholog(s) of this gene implicated in X-linked intellectual developmental disorder 109. Orthologous to human AFF2 (AF4/FMR2 family member 2). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Brain (RPKM 28.4), Adrenal (RPKM 14.5) and 7 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Aff2 in Genome Data Viewer
    Location:
    Xq37
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) X NC_086039.1 (152972579..153477080)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) X NC_051356.1 (147928130..148432484)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) X NC_005120.4 (153539951..154051022, complement)

    Chromosome X - NC_086039.1Genomic Context describing neighboring genes Neighboring gene nucleolar pre-rRNA processing protein NIP7, pseudogene 14 Neighboring gene disks large homolog 5-like Neighboring gene eukaryotic translation elongation factor 1 alpha 1 like 1 Neighboring gene uncharacterized LOC134484104

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. FRAXE-associated mental retardation protein (FMR2) is an RNA-binding protein with high affinity for G-quartet RNA forming structure. Bensaid M, et al. Nucleic Acids Res, 2009 Mar. PMID 19136466, Free PMC Article
    2. Impaired conditioned fear and enhanced long-term potentiation in Fmr2 knock-out mice. Gu Y, et al. J Neurosci, 2002 Apr 1. PMID 11923441, Free PMC Article
    3. Special characteristics of the transcription and splicing machinery in photoreceptor cells of the mammalian retina. Derlig K, et al. Cell Tissue Res, 2015 Nov. PMID 26013685
    4. Loss of FMR2 further emphasizes the link between deregulation of immediate early response genes FOS and JUN and intellectual disability. Melko M, et al. Hum Mol Genet, 2013 Aug 1. PMID 23562910
    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

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables G-quadruplex RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables G-quadruplex RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    acts_upstream_of_or_within learning or memory ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within nuclear speck organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of RNA splicing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of RNA splicing ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nuclear speck IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nuclear speck ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    NOT part_of super elongation complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    AF4/FMR2 family member 2
    Names
    AF4/FMR2 family, member 2

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_001427288.1 → NP_001414217.1  AF4/FMR2 family member 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000021
      UniProtKB/TrEMBL
      A0A0G2K1Y9

    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_086039.1 Reference GRCr8

      Range
      152972579..153477080
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006229539.4 → XP_006229601.1  AF4/FMR2 family member 2 isoform X3

      See identical proteins and their annotated locations for XP_006229601.1

      UniProtKB/TrEMBL
      A6KQ91
      Conserved Domains (1) summary
      pfam05110
      Location:19 → 1274
      AF-4; AF-4 proto-oncoprotein

    2. XM_017602424.2 → XP_017457913.1  AF4/FMR2 family member 2 isoform X1

      UniProtKB/TrEMBL
      A6KQ91

    3. XM_006229538.3 → XP_006229600.1  AF4/FMR2 family member 2 isoform X2

      See identical proteins and their annotated locations for XP_006229600.1

      UniProtKB/TrEMBL
      A6KQ91
      Conserved Domains (1) summary
      pfam05110
      Location:19 → 1280
      AF-4; AF-4 proto-oncoprotein

    4. XM_039100404.2 → XP_038956332.1  AF4/FMR2 family member 2 isoform X4

      Conserved Domains (5) summary
      PTZ00449
      Location:173 → 565
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      pfam17380
      Location:130 → 270
      DUF5401; Family of unknown function (DUF5401)
      pfam05110
      Location:2 → 115
      AF-4; AF-4 proto-oncoprotein
      pfam18875
      Location:383 → 397
      AF4_int; AF4 interaction motif
      pfam18876
      Location:644 → 896
      AF-4_C; AF-4 proto-oncoprotein C-terminal region

    5. XM_039100405.2 → XP_038956333.1  AF4/FMR2 family member 2 isoform X5

      Conserved Domains (4) summary
      pfam17380
      Location:100 → 240
      DUF5401; Family of unknown function (DUF5401)
      pfam05110
      Location:4 → 85
      AF-4; AF-4 proto-oncoprotein
      pfam18875
      Location:353 → 367
      AF4_int; AF4 interaction motif
      pfam18876
      Location:614 → 866
      AF-4_C; AF-4 proto-oncoprotein C-terminal region
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.