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    PRPF40B pre-mRNA processing factor 40 homolog B [ Homo sapiens (human) ]

    Gene ID: 25766, updated on 3-Apr-2024

    Summary

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    Official Symbol
    PRPF40Bprovided by HGNC
    Official Full Name
    pre-mRNA processing factor 40 homolog Bprovided by HGNC
    Primary source
    HGNC:HGNC:25031
    See related
    Ensembl:ENSG00000110844 AllianceGenome:HGNC:25031
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    HYPC
    Summary
    This gene encodes a WW-domain containing protein similar to yeast splicing factor PRP40. This protein has been shown to interact with Huntingtin and methyl CpG binding protein 2 (MeCP2). Alternative splicing results in different transcript variants. [provided by RefSeq, Aug 2014]
    Expression
    Broad expression in testis (RPKM 13.2), thyroid (RPKM 7.6) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    12q13.12
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (49622646..49644665)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (49585655..49607675)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (50017344..50038448)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 186 member B Neighboring gene PARK7 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6320 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4441 Neighboring gene HIG1 hypoxia inducible domain family member 1A pseudogene 9 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:50041399-50042391 Neighboring gene formin like 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:50052522-50052699 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:50056671-50057609 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:50067301-50067999 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6322 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6323 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:50090751-50091252 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6324 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6325 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6326 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6327 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6328 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4442 Neighboring gene uncharacterized LOC124902929 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6329 Neighboring gene cytochrome c oxidase subunit 5B pseudogene 5 Neighboring gene MPRA-validated peak1727 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:50134965-50135656 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6332 Neighboring gene transmembrane BAX inhibitor motif containing 6

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Human PRPF40B regulates hundreds of alternative splicing targets and represses a hypoxia expression signature. Lorenzini PA, et al. RNA, 2019 Aug. PMID 31088860, Free PMC Article
    2. Prp40 pre-mRNA processing factor 40 homolog B (PRPF40B) associates with SF1 and U2AF65 and modulates alternative pre-mRNA splicing in vivo. Becerra S, et al. RNA, 2015 Mar. PMID 25605964, Free PMC Article
    3. A WW domain binding region in methyl-CpG-binding protein MeCP2: impact on Rett syndrome. Buschdorf JP, et al. J Mol Med (Berl), 2004 Feb. PMID 14618241
    4. Huntingtin's WW domain partners in Huntington's disease post-mortem brain fulfill genetic criteria for direct involvement in Huntington's disease pathogenesis. Passani LA, et al. Hum Mol Genet, 2000 Sep 1. PMID 10958656
    5. Huntingtin interacts with a family of WW domain proteins. Faber PW, et al. Hum Mol Genet, 1998 Sep. PMID 9700202

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Study characterizes the transcriptomic regulation of PRPF40B in K562 cells upon knockout (KO) and rescue with MDS mutations, to reveal a set of targets with weak splice sites and A-rich motifs. Importantly, PRPF40B KO up-regulated a hypoxia signature which, together with its low expression in AML, suggests a role of PRPF40B in myeloid leukemias.
      Title: Human PRPF40B regulates hundreds of alternative splicing targets and represses a hypoxia expression signature.
    2. Placing our data in a functional context, we also show that PRPF40B depletion increased Fas/CD95 receptor number and cell apoptosis, which suggests the ability of PRPF40B to alter the alternative splicing of key apoptotic genes to regulate cell survival
      Title: Prp40 pre-mRNA processing factor 40 homolog B (PRPF40B) associates with SF1 and U2AF65 and modulates alternative pre-mRNA splicing in vivo.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    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 GOA

    Function Evidence Code Pubs
    enables RNA 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 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
    		  
    located_in nuclear speck IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    pre-mRNA-processing factor 40 homolog B
    Names
    Huntingtin interacting protein C
    PRP40 pre-mRNA processing factor 40 homolog B
    huntingtin yeast partner C

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_032901.2 RefSeqGene

      Range
      60197..81452
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_625

    mRNA and Protein(s)

    1. NM_001031698.3 → NP_001026868.2  pre-mRNA-processing factor 40 homolog B isoform 1

      See identical proteins and their annotated locations for NP_001026868.2

      Status: REVIEWED

      Source sequence(s)
      AC020612
      Consensus CDS
      CCDS31796.2
      UniProtKB/Swiss-Prot
      O75401, Q6NWY9, Q6PI09, Q6ZWB3, Q8NCZ1, Q9H5G4, Q9NT95
      UniProtKB/TrEMBL
      F8VU11
      Related
      ENSP00000448073.2, ENST00000548825.7
      Conserved Domains (6) summary
      smart00441
      Location:655 → 703
      FF; Contains two conserved F residues
      COG5104
      Location:111 → 603
      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:300 → 349
      FF; FF domain
      cl21455
      Location:422 → 480
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    2. NM_001363607.2 → NP_001350536.2  pre-mRNA-processing factor 40 homolog B isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC020612
      Consensus CDS
      CCDS86298.2
      UniProtKB/Swiss-Prot
      O75401, Q6NWY9, Q6PI09, Q6ZWB3, Q8NCZ1, Q9H5G4, Q9NT95
      UniProtKB/TrEMBL
      A0A8Z5ADK7
      Related
      ENSP00000369634.2, ENST00000380281.6
      Conserved Domains (2) summary
      smart00441
      Location:655 → 703
      FF; Contains two conserved F residues
      COG5104
      Location:111 → 603
      PRP40; Splicing factor [RNA processing and modification]

    3. NM_001379030.1 → NP_001365959.1  pre-mRNA-processing factor 40 homolog B isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC020612
      UniProtKB/Swiss-Prot
      O75401, Q6NWY9, Q6PI09, Q6ZWB3, Q8NCZ1, Q9H5G4, Q9NT95
      Conserved Domains (2) summary
      smart00441
      Location:645 → 693
      FF; Contains two conserved F residues
      COG5104
      Location:111 → 593
      PRP40; Splicing factor [RNA processing and modification]

    4. NM_001379031.1 → NP_001365960.1  pre-mRNA-processing factor 40 homolog B isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC020612
      UniProtKB/Swiss-Prot
      O75401, Q6NWY9, Q6PI09, Q6ZWB3, Q8NCZ1, Q9H5G4, Q9NT95
      Conserved Domains (2) summary
      smart00441
      Location:628 → 676
      FF; Contains two conserved F residues
      COG5104
      Location:84 → 576
      PRP40; Splicing factor [RNA processing and modification]

    5. NM_001379032.1 → NP_001365961.1  pre-mRNA-processing factor 40 homolog B isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC020612
      UniProtKB/Swiss-Prot
      O75401, Q6NWY9, Q6PI09, Q6ZWB3, Q8NCZ1, Q9H5G4, Q9NT95
      Conserved Domains (2) summary
      smart00441
      Location:628 → 676
      FF; Contains two conserved F residues
      COG5104
      Location:84 → 576
      PRP40; Splicing factor [RNA processing and modification]

    6. NM_001379033.1 → NP_001365962.1  pre-mRNA-processing factor 40 homolog B isoform 7

      Status: REVIEWED

      Source sequence(s)
      AC020612
      UniProtKB/Swiss-Prot
      O75401, Q6NWY9, Q6PI09, Q6ZWB3, Q8NCZ1, Q9H5G4, Q9NT95
      Conserved Domains (2) summary
      smart00441
      Location:618 → 666
      FF; Contains two conserved F residues
      COG5104
      Location:117 → 566
      PRP40; Splicing factor [RNA processing and modification]

    7. NM_001379034.1 → NP_001365963.1  pre-mRNA-processing factor 40 homolog B isoform 8

      Status: REVIEWED

      Source sequence(s)
      AC020612
      UniProtKB/Swiss-Prot
      O75401, Q6NWY9, Q6PI09, Q6ZWB3, Q8NCZ1, Q9H5G4, Q9NT95
      Conserved Domains (2) summary
      smart00441
      Location:618 → 666
      FF; Contains two conserved F residues
      COG5104
      Location:117 → 566
      PRP40; Splicing factor [RNA processing and modification]

    8. NM_001379035.1 → NP_001365964.1  pre-mRNA-processing factor 40 homolog B isoform 9

      Status: REVIEWED

      Source sequence(s)
      AC020612
      UniProtKB/Swiss-Prot
      O75401, Q6NWY9, Q6PI09, Q6ZWB3, Q8NCZ1, Q9H5G4, Q9NT95
      Conserved Domains (2) summary
      smart00441
      Location:591 → 639
      FF; Contains two conserved F residues
      COG5104
      Location:90 → 539
      PRP40; Splicing factor [RNA processing and modification]

    9. NM_001379036.1 → NP_001365965.1  pre-mRNA-processing factor 40 homolog B isoform 10

      Status: REVIEWED

      Source sequence(s)
      AC020612
      UniProtKB/Swiss-Prot
      O75401, Q6NWY9, Q6PI09, Q6ZWB3, Q8NCZ1, Q9H5G4, Q9NT95
      Conserved Domains (2) summary
      smart00441
      Location:591 → 639
      FF; Contains two conserved F residues
      COG5104
      Location:90 → 539
      PRP40; Splicing factor [RNA processing and modification]

    10. NM_001379037.1 → NP_001365966.1  pre-mRNA-processing factor 40 homolog B isoform 11

      Status: REVIEWED

      Source sequence(s)
      AC020612
      UniProtKB/Swiss-Prot
      O75401, Q6NWY9, Q6PI09, Q6ZWB3, Q8NCZ1, Q9H5G4, Q9NT95
      Conserved Domains (2) summary
      smart00441
      Location:536 → 584
      FF; Contains two conserved F residues
      COG5104
      Location:90 → 484
      PRP40; Splicing factor [RNA processing and modification]

    11. NM_012272.3 → NP_036404.1  pre-mRNA-processing factor 40 homolog B isoform 2

      See identical proteins and their annotated locations for NP_036404.1

      Status: REVIEWED

      Source sequence(s)
      AC020612
      UniProtKB/Swiss-Prot
      O75401, Q6NWY9, Q6PI09, Q6ZWB3, Q8NCZ1, Q9H5G4, Q9NT95
      Related
      ENSP00000261897.1, ENST00000261897.5
      Conserved Domains (6) summary
      smart00441
      Location:620 → 668
      FF; Contains two conserved F residues
      COG5104
      Location:83 → 568
      PRP40; Splicing factor [RNA processing and modification]
      cd00201
      Location:131 → 160
      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:92 → 117
      WW; WW domain
      pfam01846
      Location:272 → 321
      FF; FF domain
      cl21455
      Location:394 → 452
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      49622646..49644665
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047428678.1 → XP_047284634.1  pre-mRNA-processing factor 40 homolog B isoform X11

    2. XM_017019135.3 → XP_016874624.1  pre-mRNA-processing factor 40 homolog B isoform X10

      UniProtKB/Swiss-Prot
      O75401, Q6NWY9, Q6PI09, Q6ZWB3, Q8NCZ1, Q9H5G4, Q9NT95

    3. XM_011538139.4 → XP_011536441.1  pre-mRNA-processing factor 40 homolog B isoform X4

      UniProtKB/Swiss-Prot
      O75401, Q6NWY9, Q6PI09, Q6ZWB3, Q8NCZ1, Q9H5G4, Q9NT95
      Conserved Domains (6) summary
      smart00441
      Location:655 → 703
      FF; Contains two conserved F residues
      COG5104
      Location:111 → 603
      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:300 → 349
      FF; FF domain
      cl21455
      Location:422 → 480
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    4. XM_011538140.4 → XP_011536442.1  pre-mRNA-processing factor 40 homolog B isoform X5

      UniProtKB/Swiss-Prot
      O75401, Q6NWY9, Q6PI09, Q6ZWB3, Q8NCZ1, Q9H5G4, Q9NT95
      Conserved Domains (6) summary
      smart00441
      Location:655 → 703
      FF; Contains two conserved F residues
      COG5104
      Location:111 → 603
      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:300 → 349
      FF; FF domain
      cl21455
      Location:422 → 480
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    5. XM_011538143.4 → XP_011536445.1  pre-mRNA-processing factor 40 homolog B isoform X8

      UniProtKB/Swiss-Prot
      O75401, Q6NWY9, Q6PI09, Q6ZWB3, Q8NCZ1, Q9H5G4, Q9NT95
      Conserved Domains (6) summary
      smart00441
      Location:628 → 676
      FF; Contains two conserved F residues
      COG5104
      Location:84 → 576
      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:273 → 322
      FF; FF domain
      cl21455
      Location:395 → 453
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    6. XM_047428677.1 → XP_047284633.1  pre-mRNA-processing factor 40 homolog B isoform X9

    7. XM_047428674.1 → XP_047284630.1  pre-mRNA-processing factor 40 homolog B isoform X3

    8. XM_047428676.1 → XP_047284632.1  pre-mRNA-processing factor 40 homolog B isoform X7

    9. XM_047428675.1 → XP_047284631.1  pre-mRNA-processing factor 40 homolog B isoform X6

    10. XM_047428679.1 → XP_047284635.1  pre-mRNA-processing factor 40 homolog B isoform X13

    11. XM_017019138.2 → XP_016874627.1  pre-mRNA-processing factor 40 homolog B isoform X12

    12. XM_006719324.5 → XP_006719387.1  pre-mRNA-processing factor 40 homolog B isoform X1

      UniProtKB/Swiss-Prot
      O75401, Q6NWY9, Q6PI09, Q6ZWB3, Q8NCZ1, Q9H5G4, Q9NT95
      Conserved Domains (6) summary
      smart00441
      Location:717 → 765
      FF; Contains two conserved F residues
      COG5104
      Location:173 → 665
      PRP40; Splicing factor [RNA processing and modification]
      cd00201
      Location:221 → 250
      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:182 → 207
      WW; WW domain
      pfam01846
      Location:362 → 411
      FF; FF domain
      cl21455
      Location:484 → 542
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    13. XM_006719325.5 → XP_006719388.1  pre-mRNA-processing factor 40 homolog B isoform X2

      UniProtKB/Swiss-Prot
      O75401, Q6NWY9, Q6PI09, Q6ZWB3, Q8NCZ1, Q9H5G4, Q9NT95
      Conserved Domains (6) summary
      smart00441
      Location:717 → 765
      FF; Contains two conserved F residues
      COG5104
      Location:173 → 665
      PRP40; Splicing factor [RNA processing and modification]
      cd00201
      Location:221 → 250
      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:182 → 207
      WW; WW domain
      pfam01846
      Location:362 → 411
      FF; FF domain
      cl21455
      Location:484 → 542
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      49585655..49607675
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054371695.1 → XP_054227670.1  pre-mRNA-processing factor 40 homolog B isoform X11

    2. XM_054371694.1 → XP_054227669.1  pre-mRNA-processing factor 40 homolog B isoform X10

    3. XM_054371688.1 → XP_054227663.1  pre-mRNA-processing factor 40 homolog B isoform X4

    4. XM_054371689.1 → XP_054227664.1  pre-mRNA-processing factor 40 homolog B isoform X5

    5. XM_054371692.1 → XP_054227667.1  pre-mRNA-processing factor 40 homolog B isoform X8

    6. XM_054371693.1 → XP_054227668.1  pre-mRNA-processing factor 40 homolog B isoform X9

    7. XM_054371687.1 → XP_054227662.1  pre-mRNA-processing factor 40 homolog B isoform X3

    8. XM_054371691.1 → XP_054227666.1  pre-mRNA-processing factor 40 homolog B isoform X7

    9. XM_054371690.1 → XP_054227665.1  pre-mRNA-processing factor 40 homolog B isoform X6

    10. XM_054371697.1 → XP_054227672.1  pre-mRNA-processing factor 40 homolog B isoform X13

    11. XM_054371696.1 → XP_054227671.1  pre-mRNA-processing factor 40 homolog B isoform X12

    12. XM_054371685.1 → XP_054227660.1  pre-mRNA-processing factor 40 homolog B isoform X1

    13. XM_054371686.1 → XP_054227661.1  pre-mRNA-processing factor 40 homolog B isoform X2

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NR_052006.1: Suppressed sequence

      Description
      NR_052006.1: This RefSeq was permanently suppressed because it is now thought that this transcript does encode a protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6NWY9.1 GenPept UniProtKB/Swiss-Prot:Q6NWY9

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