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

Gene ID: 170791, updated on 5-Mar-2024

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 and transcription coactivator activity. Acts upstream of or within regulation of transcription by RNA polymerase II. 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; limb; olfactory epithelium; retina; and thymus. Orthologous to human RBM39 (RNA binding motif protein 39). [provided by Alliance of Genome Resources, Apr 2022]
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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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 (50) 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)
  • Gene trapped (1)  1 citation
  • Endonuclease-mediated (4) 

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 nucleic acid binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within RNA splicing IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of mRNA splicing, via spliceosome ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
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 ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus 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

    See identical proteins and their annotated locations for NP_001278043.1

    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

    See identical proteins and their annotated locations for NP_001278044.1

    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

    See identical proteins and their annotated locations for NP_573505.2

    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

    See identical proteins and their annotated locations for XP_011237629.1

    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

    See identical proteins and their annotated locations for XP_011237625.1

    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

    See identical proteins and their annotated locations for XP_011237626.1

    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

    See identical proteins and their annotated locations for XP_011237624.1

    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

    See identical proteins and their annotated locations for XP_006498912.1

    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

    See identical proteins and their annotated locations for XP_011237627.1

    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

    See identical proteins and their annotated locations for XP_006498907.1

    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

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