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    Prpf40b pre-mRNA processing factor 40 homolog B [ Rattus norvegicus (Norway rat) ]

    Gene ID: 363000, updated on 6-Jun-2024

    Summary

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    Symbol
    Prpf40bprovided by RGD
    Full Name
    pre-mRNA processing factor 40 homolog Bprovided by RGD
    Primary source
    RGD:1565411
    See related
    Ensembl:ENSRNOG00000052539 AllianceGenome:RGD:1565411
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1565411
    Summary
    Predicted to enable RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be part of U1 snRNP and U2-type prespliceosome. Orthologous to human PRPF40B (pre-mRNA processing factor 40 homolog B). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Adrenal (RPKM 82.1), Testes (RPKM 79.2) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Prpf40b in Genome Data Viewer
    Location:
    7q36
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 7 NC_086025.1 (132271469..132332913)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 7 NC_051342.1 (130392611..130454053)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 7 NC_005106.4 (140958952..140981588)

    Chromosome 7 - NC_086025.1Genomic Context describing neighboring genes Neighboring gene spermatogenesis associated, serine-rich 2 Neighboring gene U1 spliceosomal RNA Neighboring gene potassium voltage-gated channel subfamily H member 3 Neighboring gene small nucleolar RNA SNORA70 Neighboring gene microspherule protein 1 Neighboring gene family with sequence similarity 186, member B Neighboring gene formin-like 3 Neighboring gene transmembrane BAX inhibitor motif containing 6

    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. 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 RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in mRNA cis splicing, via spliceosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of U1 snRNP IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U2-type prespliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    pre-mRNA-processing factor 40 homolog B
    Names
    PRP40 homolog, pre-mRNA processing factor B
    PRP40 pre-mRNA processing factor 40 homolog B

    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_001134583.1 → NP_001128055.1  pre-mRNA-processing factor 40 homolog B

      See identical proteins and their annotated locations for NP_001128055.1

      Status: PROVISIONAL

      Source sequence(s)
      CH474035
      UniProtKB/TrEMBL
      A6KCE7, F1LTJ8
      Related
      ENSRNOP00000071841.2, ENSRNOT00000091306.2
      Conserved Domains (6) summary
      smart00441
      Location:631 → 679
      FF; Contains two conserved F residues
      COG5104
      Location:84 → 579
      PRP40; Splicing factor [RNA processing and modification]
      cd00201
      Location:137 → 166
      WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...
      pfam00397
      Location:98 → 123
      WW; WW domain
      pfam01846
      Location:276 → 325
      FF; FF domain
      cl21455
      Location:398 → 456
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    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_086025.1 Reference GRCr8

      Range
      132271469..132332913
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039079642.2 → XP_038935570.1  pre-mRNA-processing factor 40 homolog B isoform X15

      UniProtKB/TrEMBL
      A0A8I6ALK3
      Conserved Domains (2) summary
      smart00441
      Location:625 → 673
      FF; Contains two conserved F residues
      COG5104
      Location:78 → 573
      PRP40; Splicing factor [RNA processing and modification]

    2. XM_039079641.1 → XP_038935569.1  pre-mRNA-processing factor 40 homolog B isoform X12

      UniProtKB/TrEMBL
      F1LTJ8
      Conserved Domains (2) summary
      smart00441
      Location:631 → 679
      FF; Contains two conserved F residues
      COG5104
      Location:84 → 579
      PRP40; Splicing factor [RNA processing and modification]

    3. XM_063263960.1 → XP_063120030.1  pre-mRNA-processing factor 40 homolog B isoform X13

      UniProtKB/TrEMBL
      F1LTJ8

    4. XM_006257369.5 → XP_006257431.1  pre-mRNA-processing factor 40 homolog B isoform X7

      UniProtKB/TrEMBL
      A0A8I6ALK3
      Related
      ENSRNOP00000080666.1
      Conserved Domains (6) summary
      smart00441
      Location:653 → 701
      FF; Contains two conserved F residues
      COG5104
      Location:106 → 601
      PRP40; Splicing factor [RNA processing and modification]
      cd00201
      Location:159 → 188
      WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...
      pfam00397
      Location:120 → 145
      WW; WW domain
      pfam01846
      Location:298 → 347
      FF; FF domain
      cl21455
      Location:420 → 478
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    5. XM_006257371.5 → XP_006257433.1  pre-mRNA-processing factor 40 homolog B isoform X14

      UniProtKB/TrEMBL
      A0A8I6ALK3
      Conserved Domains (6) summary
      smart00441
      Location:626 → 674
      FF; Contains two conserved F residues
      COG5104
      Location:79 → 574
      PRP40; Splicing factor [RNA processing and modification]
      cd00201
      Location:132 → 161
      WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...
      pfam00397
      Location:93 → 118
      WW; WW domain
      pfam01846
      Location:271 → 320
      FF; FF domain
      cl21455
      Location:393 → 451
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    6. XM_063263957.1 → XP_063120027.1  pre-mRNA-processing factor 40 homolog B isoform X8

      UniProtKB/TrEMBL
      A0A8I5ZQT3, A0A8I6ALK3

    7. XM_063263958.1 → XP_063120028.1  pre-mRNA-processing factor 40 homolog B isoform X9

      UniProtKB/TrEMBL
      F1LTJ8

    8. XM_006257370.5 → XP_006257432.1  pre-mRNA-processing factor 40 homolog B isoform X12

      UniProtKB/TrEMBL
      F1LTJ8
      Conserved Domains (2) summary
      smart00441
      Location:631 → 679
      FF; Contains two conserved F residues
      COG5104
      Location:84 → 579
      PRP40; Splicing factor [RNA processing and modification]

    9. XM_008765768.4 → XP_008763990.1  pre-mRNA-processing factor 40 homolog B isoform X15

      UniProtKB/TrEMBL
      A0A8I6ALK3
      Conserved Domains (2) summary
      smart00441
      Location:625 → 673
      FF; Contains two conserved F residues
      COG5104
      Location:78 → 573
      PRP40; Splicing factor [RNA processing and modification]

    10. XM_008765767.4 → XP_008763989.1  pre-mRNA-processing factor 40 homolog B isoform X10

      UniProtKB/TrEMBL
      A0A8I6ALK3
      Conserved Domains (6) summary
      smart00441
      Location:693 → 741
      FF; Contains two conserved F residues
      COG5104
      Location:146 → 641
      PRP40; Splicing factor [RNA processing and modification]
      cd00201
      Location:199 → 228
      WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...
      pfam00397
      Location:160 → 185
      WW; WW domain
      pfam01846
      Location:338 → 387
      FF; FF domain
      cl21455
      Location:460 → 518
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    11. XM_006257367.5 → XP_006257429.1  pre-mRNA-processing factor 40 homolog B isoform X4

      UniProtKB/TrEMBL
      A0A8I6ALK3
      Conserved Domains (6) summary
      smart00441
      Location:693 → 741
      FF; Contains two conserved F residues
      COG5104
      Location:146 → 641
      PRP40; Splicing factor [RNA processing and modification]
      cd00201
      Location:199 → 228
      WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...
      pfam00397
      Location:160 → 185
      WW; WW domain
      pfam01846
      Location:338 → 387
      FF; FF domain
      cl21455
      Location:460 → 518
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    12. XM_006257372.5 → XP_006257434.1  pre-mRNA-processing factor 40 homolog B isoform X16

      Conserved Domains (6) summary
      smart00441
      Location:693 → 741
      FF; Contains two conserved F residues
      COG5104
      Location:146 → 641
      PRP40; Splicing factor [RNA processing and modification]
      cd00201
      Location:199 → 228
      WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...
      pfam00397
      Location:160 → 185
      WW; WW domain
      pfam01846
      Location:338 → 387
      FF; FF domain
      cl21455
      Location:460 → 518
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    13. XM_063263955.1 → XP_063120025.1  pre-mRNA-processing factor 40 homolog B isoform X5

      UniProtKB/TrEMBL
      A0A8I6ALK3

    14. XM_063263959.1 → XP_063120029.1  pre-mRNA-processing factor 40 homolog B isoform X11

      UniProtKB/TrEMBL
      F1LTJ8

    15. XM_039079643.2 → XP_038935571.1  pre-mRNA-processing factor 40 homolog B isoform X17

      Conserved Domains (2) summary
      smart00441
      Location:693 → 741
      FF; Contains two conserved F residues
      COG5104
      Location:146 → 641
      PRP40; Splicing factor [RNA processing and modification]

    16. XM_006257364.5 → XP_006257426.1  pre-mRNA-processing factor 40 homolog B isoform X1

      UniProtKB/TrEMBL
      A0A8I6ALK3
      Conserved Domains (6) summary
      smart00441
      Location:693 → 741
      FF; Contains two conserved F residues
      COG5104
      Location:146 → 641
      PRP40; Splicing factor [RNA processing and modification]
      cd00201
      Location:199 → 228
      WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...
      pfam00397
      Location:160 → 185
      WW; WW domain
      pfam01846
      Location:338 → 387
      FF; FF domain
      cl21455
      Location:460 → 518
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    17. XM_006257365.5 → XP_006257427.1  pre-mRNA-processing factor 40 homolog B isoform X2

      UniProtKB/TrEMBL
      F1LTJ8
      Conserved Domains (6) summary
      smart00441
      Location:693 → 741
      FF; Contains two conserved F residues
      COG5104
      Location:146 → 641
      PRP40; Splicing factor [RNA processing and modification]
      cd00201
      Location:199 → 228
      WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...
      pfam00397
      Location:160 → 185
      WW; WW domain
      pfam01846
      Location:338 → 387
      FF; FF domain
      cl21455
      Location:460 → 518
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    18. XM_063263956.1 → XP_063120026.1  pre-mRNA-processing factor 40 homolog B isoform X6

      UniProtKB/TrEMBL
      F1LTJ8

    19. XM_006257366.5 → XP_006257428.1  pre-mRNA-processing factor 40 homolog B isoform X3

      UniProtKB/TrEMBL
      A0A8I6ALK3
      Related
      ENSRNOP00000094837.1
      Conserved Domains (6) summary
      smart00441
      Location:693 → 741
      FF; Contains two conserved F residues
      COG5104
      Location:146 → 641
      PRP40; Splicing factor [RNA processing and modification]
      cd00201
      Location:199 → 228
      WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...
      pfam00397
      Location:160 → 185
      WW; WW domain
      pfam01846
      Location:338 → 387
      FF; FF domain
      cl21455
      Location:460 → 518
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    RNA

    1. XR_010053022.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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