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

Gene ID: 363000, updated on 3-Apr-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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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

  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

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

  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

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

  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

  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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