Seroatlas · Human Serome Atlas

PRPF39

Pre-mRNA-processing factor 39

Also known as: FLJ11128, FLJ20666, PRP39_HUMAN

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: Q86UA1
Gene: PRPF39
Ensembl: ENSG00000185246
Chromosome: 14
Canonical length: 669 aa
Protein class: Predicted intracellular proteins
Subcellular location: Nucleoplasm

OverviewNCBI Gene

Predicted to contribute to pre-mRNA 5'-splice site binding activity. Predicted to be involved in mRNA 5'-splice site recognition. Predicted to be located in nucleus. Predicted to be part of U1 snRNP; U2-type prespliceosome; and commitment complex. [provided by Alliance of Genome Resources, Jul 2025]

Canonical amino-acid sequenceUniProt

669 residues, UniProt reviewed canonical sequence.

>Q86UA1|PRPF39
     1  MQNSHMDEYR NSSNGSTGNS SEVVVEHPTD FSTEIMNVTE MEQSPDDSPN VNASTEETEM
    61  ASAVDLPVTL TETEANFPPE YEKFWKTVEN NPQDFTGWVY LLQYVEQENH LMAARKAFDR
   121  FFIHYPYCYG YWKKYADLEK RHDNIKPSDE VYRRGLQAIP LSVDLWIHYI NFLKETLDPG
   181  DPETNNTIRG TFEHAVLAAG TDFRSDRLWE MYINWENEQG NLREVTAIYD RILGIPTQLY
   241  SHHFQRFKEH VQNNLPRDLL TGEQFIQLRR ELASVNGHSG DDGPPGDDLP SGIEDITDPA
   301  KLITEIENMR HRIIEIHQEM FNYNEHEVSK RWTFEEGIKR PYFHVKPLEK AQLKNWKEYL
   361  EFEIENGTHE RVVVLFERCV ISCALYEEFW IKYAKYMENH SIEGVRHVFS RACTIHLPKK
   421  PMVHMLWAAF EEQQGNINEA RNILKTFEEC VLGLAMVRLR RVSLERRHGN LEEAEHLLQD
   481  AIKNAKSNNE SSFYAVKLAR HLFKIQKNLP KSRKVLLEAI ERDKENTKLY LNLLEMEYSG
   541  DLKQNEENIL NCFDKAVHGS LPIKMRITFS QRKVEFLEDF GSDVNKLLNA YDEHQTLLKE
   601  QDSLKRKAEN GSEEPEEKKA HTEDTTSSST QMIDGDLQAN QAVYNYSAWY QYNYQNPWNY
   661  GQYYPPPPT

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PRPF39 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Intracellular
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.34
Highest tissue expression: 3.1 nTPM

Expression across tissuesHPA

Tissue

skeletal muscle: 3.1 nTPM
bone marrow: 2.6 nTPM
colon: 2.3 nTPM
prostate: 2.2 nTPM
spleen: 2.1 nTPM
blood vessel: 1.9 nTPM

Single-cell type

myonuclei: 99 nCPM
cardiomyocytes: 83 nCPM
oligodendrocytes: 72 nCPM
rod photoreceptor cells: 72 nCPM
suprabasal keratinocytes: 70 nCPM
lactotrophs: 67 nCPM

Immune cell

MAIT T-cell: 6.4 nTPM
naive CD8 T-cell: 6.1 nTPM
memory B-cell: 5.6 nTPM
T-reg: 5.4 nTPM
naive CD4 T-cell: 5.3 nTPM
basophil: 5.2 nTPM

Brain region

white matter: 7.7 nTPM
cerebral cortex: 7.6 nTPM
basal ganglia: 7 nTPM
pons: 6.8 nTPM
amygdala: 6.4 nTPM
cerebellum: 6.3 nTPM

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.24
gnomAD pLI: 1
gnomAD missense Z: 2.69
DepMap mean gene effect: -0.5
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

mRNA 5'-splice site recognition

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads PRPF39 as an antibody target. Whether an autoantibody or antibody against PRPF39 could matter depends on whether native PRPF39 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PRPF39 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label PRPF39 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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