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    Rbm39 RNA binding motif protein 39 [ Mus musculus (house mouse) ]

    Gene ID: 170791, updated on 4-Jan-2025

    Summary

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    Official Symbol
    Rbm39provided by MGI
    Official Full Name
    RNA binding motif protein 39provided by MGI
    Primary source
    MGI:MGI:2157953
    See related
    Ensembl:ENSMUSG00000027620 AllianceGenome:MGI:2157953
    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
    Rnpc2; caper; 1500012C14Rik; 2310040E03Rik; B330012G18Rik
    Summary
    Enables RS domain binding activity. Predicted to be involved in regulation of mRNA splicing, via spliceosome. Predicted to be located in centriolar satellite and nuclear speck. Predicted to be part of protein-containing complex. Is expressed in several structures, including central nervous system; genitourinary system; limb; olfactory epithelium; and retina. Orthologous to human RBM39 (RNA binding motif protein 39). [provided by Alliance of Genome Resources, Jan 2025]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 25.2), limb E14.5 (RPKM 24.7) and 27 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Rbm39 in Genome Data Viewer
    Location:
    2 H1; 2 77.36 cM
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (155989159..156022649, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (156147239..156180238, complement)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene copine I Neighboring gene STARR-seq mESC enhancer starr_06153 Neighboring gene STARR-positive B cell enhancer ABC_E3414 Neighboring gene RNA binding motif protein 12 Neighboring gene nitrogen fixation gene 1 (S. cerevisiae) Neighboring gene reactive oxygen species modulator 1 Neighboring gene CapStarr-seq enhancer MGSCv37_chr2:156005117-156005304 Neighboring gene STARR-positive B cell enhancer ABC_E817 Neighboring gene STARR-seq mESC enhancer starr_06156 Neighboring gene STARR-positive B cell enhancer ABC_E9537 Neighboring gene STARR-seq mESC enhancer starr_06157 Neighboring gene PHD finger protein 20 Neighboring gene STARR-seq mESC enhancer starr_06159 Neighboring gene CapStarr-seq enhancer MGSCv37_chr2:156104477-156104678 Neighboring gene CapStarr-seq enhancer MGSCv37_chr2:156113998-156114107 Neighboring gene SCAN domain-containing 1 Neighboring gene cyclic nucleotide binding domain containing 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. CAPER is vital for energy and redox homeostasis by integrating glucose-induced mitochondrial functions via ERR-α-Gabpa and stress-induced adaptive responses via NF-κB-cMYC. Kang YK, et al. PLoS Genet, 2015 Apr. PMID 25830341, Free PMC Article
    2. Negative autoregulation of BMP dependent transcription by SIN3B splicing reveals a role for RBM39. Faherty N, et al. Sci Rep, 2016 Jun 21. PMID 27324164, Free PMC Article
    3. Molecular cloning and characterization of CAPER, a novel coactivator of activating protein-1 and estrogen receptors. Jung DJ, et al. J Biol Chem, 2002 Jan 11. PMID 11704680
    4. Coordinated control of senescence by lncRNA and a novel T-box3 co-repressor complex. Kumar P P, et al. Elife, 2014 May 29. PMID 24876127, Free PMC Article
    5. Severe muscle wasting and denervation in mice lacking the RNA-binding protein ZFP106. Anderson DM, et al. Proc Natl Acad Sci U S A, 2016 Aug 2. PMID 27418600, Free PMC Article

    See all (52) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. this study shows that negative autoregulation of BMP4 dependent transcription by SIN3B splicing reveals a role for RBM39
      Title: Negative autoregulation of BMP dependent transcription by SIN3B splicing reveals a role for RBM39.
    2. CAPER integrates mitochondrial energy metabolism by coactivating ERR-alpha-Gabpa and stress-induced adaptive metabolic responses via NF- kappaB/c-Myc.
      Title: CAPER is vital for energy and redox homeostasis by integrating glucose-induced mitochondrial functions via ERR-α-Gabpa and stress-induced adaptive responses via NF-κB-cMYC.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (4) 
    • Gene trapped (1)  1 citation

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RS domain binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables U1 snRNP binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of mRNA splicing, via spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of mRNA splicing, via spliceosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in centriolar satellite IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in centriolar satellite ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in microtubule cytoskeleton ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear speck IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear speck ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of protein-containing complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of protein-containing complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    RNA-binding protein 39
    Names
    Caper alpha
    RNA-binding region (RNP1, RRM) containing 2
    RNA-binding region-containing protein 2
    coactivator of AP-1 and ERs
    coactivator of activating protein-1 and estrogen receptors
    transcription coactivator CAPER

    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_001291114.1 → NP_001278043.1  RNA-binding protein 39 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a. Both variants 2 and 3 encode isoform b.
      Source sequence(s)
      AK135289, AK147076, AL929404, BF465342
      Consensus CDS
      CCDS71168.1
      UniProtKB/TrEMBL
      Q3U313, Q3UXT6
      Related
      ENSMUSP00000029149.7, ENSMUST00000029149.13
      Conserved Domains (1) summary
      TIGR01622
      Location:46 → 512
      SF-CC1; splicing factor, CC1-like family

    2. NM_001291115.1 → NP_001278044.1  RNA-binding protein 39 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a. Both variants 2 and 3 encode isoform b.
      Source sequence(s)
      AK135289, AK146046, AK147076, AL929404, BF465342
      Consensus CDS
      CCDS71168.1
      UniProtKB/TrEMBL
      Q3U313, Q3UXT6
      Related
      ENSMUSP00000119298.2, ENSMUST00000146297.8
      Conserved Domains (1) summary
      TIGR01622
      Location:46 → 512
      SF-CC1; splicing factor, CC1-like family

    3. NM_001362763.1 → NP_001349692.1  RNA-binding protein 39 isoform c

      Status: VALIDATED

      Source sequence(s)
      AL929404, BX649640
      UniProtKB/TrEMBL
      Q3UXT6
      Conserved Domains (1) summary
      TIGR01622
      Location:46 → 517
      SF-CC1; splicing factor, CC1-like family

    4. NM_001362764.1 → NP_001349693.1  RNA-binding protein 39 isoform d

      Status: VALIDATED

      Source sequence(s)
      AL929404, BX649640
      UniProtKB/TrEMBL
      Q3UXT6
      Conserved Domains (1) summary
      TIGR01622
      Location:46 → 511
      SF-CC1; splicing factor, CC1-like family

    5. NM_001362765.1 → NP_001349694.1  RNA-binding protein 39 isoform e

      Status: VALIDATED

      Source sequence(s)
      AL929404, BX649640
      UniProtKB/TrEMBL
      Q3UXT6
      Conserved Domains (1) summary
      TIGR01622
      Location:37 → 509
      SF-CC1; splicing factor, CC1-like family

    6. NM_001362766.1 → NP_001349695.1  RNA-binding protein 39 isoform f

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7), as well as variants 8 and 9, encodes isoform f.
      Source sequence(s)
      AL929404, BX649640
      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    7. NM_001362767.1 → NP_001349696.1  RNA-binding protein 39 isoform f

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8), as well as variants 7 and 9, encodes isoform f.
      Source sequence(s)
      AL929404, BX649640
      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    8. NM_001362768.1 → NP_001349697.1  RNA-binding protein 39 isoform f

      Status: VALIDATED

      Description
      Transcript Variant: This variant (9), as well as variants 7 and 8, encodes isoform f.
      Source sequence(s)
      AL929404, BX649640
      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    9. NM_001362769.1 → NP_001349698.1  RNA-binding protein 39 isoform g

      Status: VALIDATED

      Source sequence(s)
      AL929404, BX649640
      UniProtKB/TrEMBL
      Q0VGU9
      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 355
      SF-CC1; splicing factor, CC1-like family

    10. NM_133242.3 → NP_573505.2  RNA-binding protein 39 isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).
      Source sequence(s)
      AK147076, AL929404, BF465342
      Consensus CDS
      CCDS16964.1
      UniProtKB/Swiss-Prot
      Q5RJI0, Q8VH51, Q99KV0
      UniProtKB/TrEMBL
      Q3UXT6
      Related
      ENSMUSP00000105216.3, ENSMUST00000109587.9
      Conserved Domains (1) summary
      TIGR01622
      Location:46 → 518
      SF-CC1; splicing factor, CC1-like family

    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_000068.8 Reference GRCm39 C57BL/6J

      Range
      155989159..156022649 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017316005.3 → XP_017171494.1  RNA-binding protein 39 isoform X2

      UniProtKB/TrEMBL
      Q0VGU9
      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 355
      SF-CC1; splicing factor, CC1-like family

    2. XM_036158987.1 → XP_036014880.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    3. XM_011239327.4 → XP_011237629.1  RNA-binding protein 39 isoform X2

      UniProtKB/TrEMBL
      Q0VGU9
      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 355
      SF-CC1; splicing factor, CC1-like family

    4. XM_011239323.3 → XP_011237625.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    5. XM_017315994.3 → XP_017171483.1  RNA-binding protein 39 isoform X2

      UniProtKB/TrEMBL
      Q0VGU9
      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 355
      SF-CC1; splicing factor, CC1-like family

    6. XM_011239324.3 → XP_011237626.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    7. XM_036158984.1 → XP_036014877.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    8. XM_011239322.3 → XP_011237624.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    9. XM_017315991.3 → XP_017171480.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    10. XM_017315976.2 → XP_017171465.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    11. XM_036158991.1 → XP_036014884.1  RNA-binding protein 39 isoform X2

      UniProtKB/TrEMBL
      Q0VGU9
      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 355
      SF-CC1; splicing factor, CC1-like family

    12. XM_036158986.1 → XP_036014879.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    13. XM_030248017.2 → XP_030103877.1  RNA-binding protein 39 isoform X2

      UniProtKB/TrEMBL
      Q0VGU9
      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 355
      SF-CC1; splicing factor, CC1-like family

    14. XM_030247972.2 → XP_030103832.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    15. XM_036158990.1 → XP_036014883.1  RNA-binding protein 39 isoform X2

      UniProtKB/TrEMBL
      Q0VGU9
      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 355
      SF-CC1; splicing factor, CC1-like family

    16. XM_030248031.2 → XP_030103891.1  RNA-binding protein 39 isoform X2

      UniProtKB/TrEMBL
      Q0VGU9
      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 355
      SF-CC1; splicing factor, CC1-like family

    17. XM_030248002.2 → XP_030103862.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    18. XM_030248011.2 → XP_030103871.1  RNA-binding protein 39 isoform X2

      UniProtKB/TrEMBL
      Q0VGU9
      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 355
      SF-CC1; splicing factor, CC1-like family

    19. XM_030247970.2 → XP_030103830.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    20. XM_036158989.1 → XP_036014882.1  RNA-binding protein 39 isoform X2

      UniProtKB/TrEMBL
      Q0VGU9
      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 355
      SF-CC1; splicing factor, CC1-like family

    21. XM_036158983.1 → XP_036014876.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    22. XM_030248020.2 → XP_030103880.1  RNA-binding protein 39 isoform X2

      UniProtKB/TrEMBL
      Q0VGU9
      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 355
      SF-CC1; splicing factor, CC1-like family

    23. XM_006498849.4 → XP_006498912.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    24. XM_011239325.3 → XP_011237627.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    25. XM_030247991.2 → XP_030103851.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    26. XM_006498844.4 → XP_006498907.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    27. XM_036158988.1 → XP_036014881.1  RNA-binding protein 39 isoform X2

      UniProtKB/TrEMBL
      Q0VGU9
      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 355
      SF-CC1; splicing factor, CC1-like family

    28. XM_030247989.2 → XP_030103849.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    29. XM_030247975.2 → XP_030103835.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    30. XM_030247987.2 → XP_030103847.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    31. XM_030247986.2 → XP_030103846.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    32. XM_030247973.2 → XP_030103833.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    33. XM_036158985.1 → XP_036014878.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    34. XM_017315989.3 → XP_017171478.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    35. XM_030248000.2 → XP_030103860.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    36. XM_036158977.1 → XP_036014870.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    37. XM_030247976.2 → XP_030103836.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    38. XM_036158981.1 → XP_036014874.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    39. XM_036158975.1 → XP_036014868.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family

    40. XM_030248021.2 → XP_030103881.1  RNA-binding protein 39 isoform X2

      UniProtKB/TrEMBL
      Q0VGU9
      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 355
      SF-CC1; splicing factor, CC1-like family

    41. XM_030248028.2 → XP_030103888.1  RNA-binding protein 39 isoform X2

      UniProtKB/TrEMBL
      Q0VGU9
      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 355
      SF-CC1; splicing factor, CC1-like family

    42. XM_036158976.1 → XP_036014869.1  RNA-binding protein 39 isoform X1

      Conserved Domains (1) summary
      TIGR01622
      Location:1 → 361
      SF-CC1; splicing factor, CC1-like family
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8VH51.2 GenPept UniProtKB/Swiss-Prot:Q8VH51

    Gene LinkOut

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