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    Celf3 CUGBP, Elav-like family member 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 499669, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Celf3provided by RGD
    Official Full Name
    CUGBP, Elav-like family member 3provided by RGD
    Primary source
    RGD:1563168
    See related
    EnsemblRapid:ENSRNOG00000020875 AllianceGenome:RGD:1563168
    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
    Tnrc4; RGD1563168
    Summary
    Predicted to enable 7SK snRNA binding activity and mRNA binding activity. Predicted to be involved in mRNA splice site recognition; positive regulation of mRNA splicing, via spliceosome; and regulation of alternative mRNA splicing, via spliceosome. Predicted to act upstream of or within several processes, including flagellated sperm motility; lncRNA transcription; and nuclear body organization. Predicted to be located in nuclear body. Predicted to be part of ribonucleoprotein complex. Predicted to be active in cytoplasm and nucleus. Orthologous to human CELF3 (CUGBP Elav-like family member 3). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Brain (RPKM 32.8), Adrenal (RPKM 20.3) and 8 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Celf3 in Genome Data Viewer
    Location:
    2q34
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (184805078..184819189)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (182116034..182130163)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (195716373..195732872)

    Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102556390 Neighboring gene mitochondrial ribosomal protein L9 Neighboring gene regulatory subunit of type II PKA R-subunit domain containing 1 Neighboring gene sorting nexin 27 Neighboring gene uncharacterized LOC134485647 Neighboring gene nuclear receptor binding factor 2 like 1

    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. Expression, localization and tau exon 10 splicing activity of the brain RNA-binding protein TNRC4. Chapple JP, et al. Hum Mol Genet, 2007 Nov 15. PMID 17725984
    2. Mice deficient for RNA-binding protein brunol1 show reduction of spermatogenesis but are fertile. Dev A, et al. Mol Reprod Dev, 2007 Nov. PMID 17393433
    3. The CELF family of RNA binding proteins is implicated in cell-specific and developmentally regulated alternative splicing. Ladd AN, et al. Mol Cell Biol, 2001 Feb. PMID 11158314, Free PMC Article
    4. Tau exon 10, whose missplicing causes frontotemporal dementia, is regulated by an intricate interplay of cis elements and trans factors. Wang J, et al. J Neurochem, 2004 Mar. PMID 15009664
    5. Formation of nuclear bodies by the lncRNA Gomafu-associating proteins Celf3 and SF1. Ishizuka A, et al. Genes Cells, 2014 Sep. PMID 25145264, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables 7SK snRNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in RNA splicing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    acts_upstream_of_or_within flagellated sperm motility ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within lncRNA transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in mRNA splice site recognition IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within nuclear body organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of mRNA splicing, via spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of alternative mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of alternative mRNA splicing, via spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within spermatogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear body ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of ribonucleoprotein complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    CUGBP Elav-like family member 3
    Names
    CUG-BP- and ETR-3-like factor 3
    trinucleotide repeat containing 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_001109190.2 → NP_001102660.1  CUGBP Elav-like family member 3

      See identical proteins and their annotated locations for NP_001102660.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000002
      UniProtKB/TrEMBL
      A6K2R6
      Conserved Domains (4) summary
      PRK12323
      Location:214 → 351
      PRK12323; DNA polymerase III subunit gamma/tau
      cd12639
      Location:384 → 462
      RRM3_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins
      cd12632
      Location:2 → 88
      RRM1_CELF3_4_5_6; RNA recognition motif 1 (RRM1) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins
      cd12635
      Location:94 → 174
      RRM2_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

    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_086020.1 Reference GRCr8

      Range
      184805078..184819189
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063282393.1 → XP_063138463.1  CUGBP Elav-like family member 3 isoform X21

    2. XM_063282398.1 → XP_063138468.1  CUGBP Elav-like family member 3 isoform X25

    3. XM_063282388.1 → XP_063138458.1  CUGBP Elav-like family member 3 isoform X19

    4. XM_063282399.1 → XP_063138469.1  CUGBP Elav-like family member 3 isoform X26

    5. XM_063282390.1 → XP_063138460.1  CUGBP Elav-like family member 3 isoform X20

    6. XM_008761322.4 → XP_008759544.1  CUGBP Elav-like family member 3 isoform X1

      See identical proteins and their annotated locations for XP_008759544.1

      UniProtKB/TrEMBL
      A0A8I6AGJ7
      Related
      ENSRNOP00000092441.1, ENSRNOT00000115671.2
      Conserved Domains (4) summary
      TIGR01645
      Location:8 → 491
      half-pint; poly-U binding splicing factor, half-pint family
      cd12639
      Location:412 → 490
      RRM3_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins
      cd12632
      Location:2 → 88
      RRM1_CELF3_4_5_6; RNA recognition motif 1 (RRM1) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins
      cd12635
      Location:94 → 174
      RRM2_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

    7. XM_006232904.5 → XP_006232966.1  CUGBP Elav-like family member 3 isoform X8

      See identical proteins and their annotated locations for XP_006232966.1

      UniProtKB/TrEMBL
      D4A916
      Conserved Domains (4) summary
      TIGR01628
      Location:21 → 225
      PABP-1234; polyadenylate binding protein, human types 1, 2, 3, 4 family
      PRK14951
      Location:174 → 300
      PRK14951; DNA polymerase III subunits gamma and tau; Provisional
      cd12639
      Location:336 → 414
      RRM3_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins
      cd12635
      Location:18 → 98
      RRM2_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

    8. XM_063282394.1 → XP_063138464.1  CUGBP Elav-like family member 3 isoform X22

    9. XM_039102932.2 → XP_038958860.1  CUGBP Elav-like family member 3 isoform X9

      UniProtKB/TrEMBL
      D4A916
      Conserved Domains (4) summary
      TIGR01628
      Location:30 → 224
      PABP-1234; polyadenylate binding protein, human types 1, 2, 3, 4 family
      PRK14951
      Location:173 → 299
      PRK14951; DNA polymerase III subunits gamma and tau; Provisional
      cd12639
      Location:335 → 413
      RRM3_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins
      cd12635
      Location:17 → 97
      RRM2_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

    10. XM_063282401.1 → XP_063138471.1  CUGBP Elav-like family member 3 isoform X27

    11. XM_063282380.1 → XP_063138450.1  CUGBP Elav-like family member 3 isoform X11

      Related
      ENSRNOP00000028324.7, ENSRNOT00000028324.9

    12. XM_063282395.1 → XP_063138465.1  CUGBP Elav-like family member 3 isoform X23

    13. XM_063282383.1 → XP_063138453.1  CUGBP Elav-like family member 3 isoform X14

    14. XM_063282384.1 → XP_063138454.1  CUGBP Elav-like family member 3 isoform X15

    15. XM_063282387.1 → XP_063138457.1  CUGBP Elav-like family member 3 isoform X18

    16. XM_063282386.1 → XP_063138456.1  CUGBP Elav-like family member 3 isoform X17

    17. XM_063282376.1 → XP_063138446.1  CUGBP Elav-like family member 3 isoform X3

    18. XM_039102915.2 → XP_038958843.1  CUGBP Elav-like family member 3 isoform X5

    19. XM_063282377.1 → XP_063138447.1  CUGBP Elav-like family member 3 isoform X6

      Related
      ENSRNOP00000111046.1, ENSRNOT00000145844.1

    20. XM_063282381.1 → XP_063138451.1  CUGBP Elav-like family member 3 isoform X12

    21. XM_006232898.5 → XP_006232960.1  CUGBP Elav-like family member 3 isoform X2

      Conserved Domains (4) summary
      TIGR01645
      Location:8 → 490
      half-pint; poly-U binding splicing factor, half-pint family
      cd12639
      Location:411 → 489
      RRM3_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins
      cd12632
      Location:2 → 88
      RRM1_CELF3_4_5_6; RNA recognition motif 1 (RRM1) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins
      cd12635
      Location:93 → 173
      RRM2_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

    22. XM_006232900.5 → XP_006232962.1  CUGBP Elav-like family member 3 isoform X4

      Conserved Domains (4) summary
      PRK12323
      Location:213 → 350
      PRK12323; DNA polymerase III subunit gamma/tau
      cd12639
      Location:383 → 461
      RRM3_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins
      cd12632
      Location:2 → 88
      RRM1_CELF3_4_5_6; RNA recognition motif 1 (RRM1) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins
      cd12635
      Location:93 → 173
      RRM2_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

    23. XM_063282378.1 → XP_063138448.1  CUGBP Elav-like family member 3 isoform X7

    24. XM_063282382.1 → XP_063138452.1  CUGBP Elav-like family member 3 isoform X13

    25. XM_063282385.1 → XP_063138455.1  CUGBP Elav-like family member 3 isoform X16

    26. XM_006232908.5 → XP_006232970.1  CUGBP Elav-like family member 3 isoform X10

      See identical proteins and their annotated locations for XP_006232970.1

      Conserved Domains (3) summary
      cd12639
      Location:334 → 412
      RRM3_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins
      cd12632
      Location:2 → 88
      RRM1_CELF3_4_5_6; RNA recognition motif 1 (RRM1) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins
      cd12635
      Location:94 → 174
      RRM2_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

    27. XM_063282379.1 → XP_063138449.1  CUGBP Elav-like family member 3 isoform X8

    28. XM_063282389.1 → XP_063138459.1  CUGBP Elav-like family member 3 isoform X19

    29. XM_063282392.1 → XP_063138462.1  CUGBP Elav-like family member 3 isoform X21

    30. XM_063282397.1 → XP_063138467.1  CUGBP Elav-like family member 3 isoform X25

    31. XM_063282391.1 → XP_063138461.1  CUGBP Elav-like family member 3 isoform X20

    32. XM_063282396.1 → XP_063138466.1  CUGBP Elav-like family member 3 isoform X24

    RNA

    1. XR_010063651.1 RNA Sequence

    2. XR_010063652.1 RNA Sequence

    3. XR_010063649.1 RNA Sequence

    4. XR_010063644.1 RNA Sequence

    5. XR_010063646.1 RNA Sequence

    6. XR_010063645.1 RNA Sequence

    7. XR_010063647.1 RNA Sequence

    8. XR_010063648.1 RNA Sequence

    9. XR_010063653.1 RNA Sequence

    10. XR_010063650.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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