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

Gene ID: 25766, updated on 2-Nov-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
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Genomic context

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See PRPF40B in Genome Data Viewer
Location:
12q13.12
Exon count:
30
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (49622646..49644665)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (49585655..49607675)
RS_2024_09 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

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

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. 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
  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. 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
  5. Huntingtin interacts with a family of WW domain proteins. Faber PW, et al. Hum Mol Genet, 1998 Sep. PMID 9700202

See all (22) 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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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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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_2024_08

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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