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

Gene ID: 170791, updated on 8-Jan-2023

Summary

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
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Genomic context

See Rbm39 in Genome Data Viewer
Location:
2; 2 H1
Exon count:
22
Annotation release Status Assembly Chr Location
109 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 RNA binding motif protein 12 Neighboring gene nitrogen fixation gene 1 (S. cerevisiae) Neighboring gene reactive oxygen species modulator 1 Neighboring gene PHD finger protein 20 Neighboring gene SCAN domain-containing 1 Neighboring gene cyclic nucleotide binding domain containing 2

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Gene trapped (1)  1 citation
  • Endonuclease-mediated (3) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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
PubMed 
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

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_001291114.1NP_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/Swiss-Prot
    Q8VH51
    UniProtKB/TrEMBL
    A0A6P5P9Y1, Q3U313, Q3UXT6
    Related
    ENSMUSP00000029149.7, ENSMUST00000029149.13
    Conserved Domains (1) summary
    TIGR01622
    Location:46512
    SF-CC1; splicing factor, CC1-like family
  2. NM_001291115.1NP_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/Swiss-Prot
    Q8VH51
    UniProtKB/TrEMBL
    A0A6P5P9Y1, Q3U313, Q3UXT6
    Related
    ENSMUSP00000119298.2, ENSMUST00000146297.8
    Conserved Domains (1) summary
    TIGR01622
    Location:46512
    SF-CC1; splicing factor, CC1-like family
  3. NM_001362763.1NP_001349692.1  RNA-binding protein 39 isoform c

    Status: VALIDATED

    Source sequence(s)
    AL929404, BX649640
    UniProtKB/TrEMBL
    A0A6P5PFN4
    Conserved Domains (1) summary
    TIGR01622
    Location:46517
    SF-CC1; splicing factor, CC1-like family
  4. NM_001362764.1NP_001349693.1  RNA-binding protein 39 isoform d

    Status: VALIDATED

    Source sequence(s)
    AL929404, BX649640
    UniProtKB/TrEMBL
    A0A6P7QUJ7
    Conserved Domains (1) summary
    TIGR01622
    Location:46511
    SF-CC1; splicing factor, CC1-like family
  5. NM_001362765.1NP_001349694.1  RNA-binding protein 39 isoform e

    Status: VALIDATED

    Source sequence(s)
    AL929404, BX649640
    Conserved Domains (1) summary
    TIGR01622
    Location:37509
    SF-CC1; splicing factor, CC1-like family
  6. NM_001362766.1NP_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
    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  7. NM_001362767.1NP_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
    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  8. NM_001362768.1NP_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
    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  9. NM_001362769.1NP_001349698.1  RNA-binding protein 39 isoform g

    Status: VALIDATED

    Source sequence(s)
    AL929404, BX649640
    UniProtKB/TrEMBL
    A0A6P7QXI5, Q0VGU9
    Conserved Domains (1) summary
    TIGR01622
    Location:1355
    SF-CC1; splicing factor, CC1-like family
  10. NM_133242.3NP_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
    Q8VH51, Q99KV0
    UniProtKB/TrEMBL
    A0A6P5P5V6, A0A8C6GGC8
    Related
    ENSMUSP00000105216.3, ENSMUST00000109587.9
    Conserved Domains (1) summary
    TIGR01622
    Location:46518
    SF-CC1; splicing factor, CC1-like family

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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_017316005.3XP_017171494.1  RNA-binding protein 39 isoform X2

    UniProtKB/Swiss-Prot
    Q8VH51
    UniProtKB/TrEMBL
    A0A6P7QXI5, Q0VGU9
    Conserved Domains (1) summary
    TIGR01622
    Location:1355
    SF-CC1; splicing factor, CC1-like family
  2. XM_036158987.1XP_036014880.1  RNA-binding protein 39 isoform X1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  3. XM_011239327.4XP_011237629.1  RNA-binding protein 39 isoform X2

    See identical proteins and their annotated locations for XP_011237629.1

    UniProtKB/Swiss-Prot
    Q8VH51
    UniProtKB/TrEMBL
    A0A6P7QXI5, Q0VGU9
    Conserved Domains (1) summary
    TIGR01622
    Location:1355
    SF-CC1; splicing factor, CC1-like family
  4. XM_011239323.3XP_011237625.1  RNA-binding protein 39 isoform X1

    See identical proteins and their annotated locations for XP_011237625.1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  5. XM_017315994.3XP_017171483.1  RNA-binding protein 39 isoform X2

    UniProtKB/Swiss-Prot
    Q8VH51
    UniProtKB/TrEMBL
    A0A6P7QXI5, Q0VGU9
    Conserved Domains (1) summary
    TIGR01622
    Location:1355
    SF-CC1; splicing factor, CC1-like family
  6. XM_011239324.3XP_011237626.1  RNA-binding protein 39 isoform X1

    See identical proteins and their annotated locations for XP_011237626.1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  7. XM_036158984.1XP_036014877.1  RNA-binding protein 39 isoform X1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  8. XM_011239322.3XP_011237624.1  RNA-binding protein 39 isoform X1

    See identical proteins and their annotated locations for XP_011237624.1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  9. XM_017315991.3XP_017171480.1  RNA-binding protein 39 isoform X1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  10. XM_017315976.2XP_017171465.1  RNA-binding protein 39 isoform X1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  11. XM_036158991.1XP_036014884.1  RNA-binding protein 39 isoform X2

    UniProtKB/TrEMBL
    A0A6P7QXI5, Q0VGU9
    Conserved Domains (1) summary
    TIGR01622
    Location:1355
    SF-CC1; splicing factor, CC1-like family
  12. XM_036158986.1XP_036014879.1  RNA-binding protein 39 isoform X1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  13. XM_030248017.2XP_030103877.1  RNA-binding protein 39 isoform X2

    UniProtKB/TrEMBL
    A0A6P7QXI5, Q0VGU9
    Conserved Domains (1) summary
    TIGR01622
    Location:1355
    SF-CC1; splicing factor, CC1-like family
  14. XM_030247972.2XP_030103832.1  RNA-binding protein 39 isoform X1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  15. XM_036158990.1XP_036014883.1  RNA-binding protein 39 isoform X2

    UniProtKB/TrEMBL
    A0A6P7QXI5, Q0VGU9
    Conserved Domains (1) summary
    TIGR01622
    Location:1355
    SF-CC1; splicing factor, CC1-like family
  16. XM_030248031.2XP_030103891.1  RNA-binding protein 39 isoform X2

    UniProtKB/TrEMBL
    A0A6P7QXI5, Q0VGU9
    Conserved Domains (1) summary
    TIGR01622
    Location:1355
    SF-CC1; splicing factor, CC1-like family
  17. XM_030248002.2XP_030103862.1  RNA-binding protein 39 isoform X1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  18. XM_030248011.2XP_030103871.1  RNA-binding protein 39 isoform X2

    UniProtKB/TrEMBL
    A0A6P7QXI5, Q0VGU9
    Conserved Domains (1) summary
    TIGR01622
    Location:1355
    SF-CC1; splicing factor, CC1-like family
  19. XM_030247970.2XP_030103830.1  RNA-binding protein 39 isoform X1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  20. XM_036158989.1XP_036014882.1  RNA-binding protein 39 isoform X2

    UniProtKB/TrEMBL
    A0A6P7QXI5, Q0VGU9
    Conserved Domains (1) summary
    TIGR01622
    Location:1355
    SF-CC1; splicing factor, CC1-like family
  21. XM_036158983.1XP_036014876.1  RNA-binding protein 39 isoform X1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  22. XM_030248020.2XP_030103880.1  RNA-binding protein 39 isoform X2

    UniProtKB/TrEMBL
    A0A6P7QXI5, Q0VGU9
    Conserved Domains (1) summary
    TIGR01622
    Location:1355
    SF-CC1; splicing factor, CC1-like family
  23. XM_006498849.4XP_006498912.1  RNA-binding protein 39 isoform X1

    See identical proteins and their annotated locations for XP_006498912.1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  24. XM_011239325.3XP_011237627.1  RNA-binding protein 39 isoform X1

    See identical proteins and their annotated locations for XP_011237627.1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  25. XM_030247991.2XP_030103851.1  RNA-binding protein 39 isoform X1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  26. XM_006498844.4XP_006498907.1  RNA-binding protein 39 isoform X1

    See identical proteins and their annotated locations for XP_006498907.1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  27. XM_036158988.1XP_036014881.1  RNA-binding protein 39 isoform X2

    UniProtKB/TrEMBL
    A0A6P7QXI5, Q0VGU9
    Conserved Domains (1) summary
    TIGR01622
    Location:1355
    SF-CC1; splicing factor, CC1-like family
  28. XM_030247989.2XP_030103849.1  RNA-binding protein 39 isoform X1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  29. XM_030247975.2XP_030103835.1  RNA-binding protein 39 isoform X1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  30. XM_030247987.2XP_030103847.1  RNA-binding protein 39 isoform X1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  31. XM_030247986.2XP_030103846.1  RNA-binding protein 39 isoform X1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  32. XM_030247973.2XP_030103833.1  RNA-binding protein 39 isoform X1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  33. XM_036158985.1XP_036014878.1  RNA-binding protein 39 isoform X1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  34. XM_017315989.3XP_017171478.1  RNA-binding protein 39 isoform X1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  35. XM_030248000.2XP_030103860.1  RNA-binding protein 39 isoform X1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  36. XM_036158977.1XP_036014870.1  RNA-binding protein 39 isoform X1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  37. XM_030247976.2XP_030103836.1  RNA-binding protein 39 isoform X1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  38. XM_036158981.1XP_036014874.1  RNA-binding protein 39 isoform X1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  39. XM_036158975.1XP_036014868.1  RNA-binding protein 39 isoform X1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family
  40. XM_030248021.2XP_030103881.1  RNA-binding protein 39 isoform X2

    UniProtKB/TrEMBL
    A0A6P7QXI5, Q0VGU9
    Conserved Domains (1) summary
    TIGR01622
    Location:1355
    SF-CC1; splicing factor, CC1-like family
  41. XM_030248028.2XP_030103888.1  RNA-binding protein 39 isoform X2

    UniProtKB/TrEMBL
    A0A6P7QXI5, Q0VGU9
    Conserved Domains (1) summary
    TIGR01622
    Location:1355
    SF-CC1; splicing factor, CC1-like family
  42. XM_036158976.1XP_036014869.1  RNA-binding protein 39 isoform X1

    UniProtKB/TrEMBL
    A0A6P5PC43
    Conserved Domains (1) summary
    TIGR01622
    Location:1361
    SF-CC1; splicing factor, CC1-like family