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

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

Summary

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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
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Genomic context

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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

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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
  • 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. 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

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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

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Preferred Names
AF4/FMR2 family member 2
Names
AF4/FMR2 family, member 2

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_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

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