Seroatlas · Human Serome Atlas

CPSF6

Cleavage and polyadenylation specificity factor subunit 6

Also known as: CFIM, CFIM68, CFIM72, CPSF6_HUMAN, HPBRII-4, HPBRII-7

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

Protein identityUniProt · HPA

UniProt accession: Q16630
Gene: CPSF6
Ensembl: ENSG00000111605
Chromosome: 12
Canonical length: 551 aa
Protein class: Plasma proteins, Predicted intracellular proteins
Subcellular location: Nucleoplasm,Nuclear speckles

OverviewNCBI Gene

The protein encoded by this gene is one subunit of a cleavage factor required for 3' RNA cleavage and polyadenylation processing. The interaction of the protein with the RNA is one of the earliest steps in the assembly of the 3' end processing complex and facilitates the recruitment of other processing factors. The cleavage factor complex is composed of four polypeptides. This gene encodes the 68kD subunit. It has a domain organization reminiscent of spliceosomal proteins. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

551 residues, UniProt reviewed canonical sequence.

>Q16630|CPSF6
     1  MADGVDHIDI YADVGEEFNQ EAEYGGHDQI DLYDDVISPS ANNGDAPEDR DYMDTLPPTV
    61  GDDVGKGAAP NVVYTYTGKR IALYIGNLTW WTTDEDLTEA VHSLGVNDIL EIKFFENRAN
   121  GQSKGFALVG VGSEASSKKL MDLLPKRELH GQNPVVTPCN KQFLSQFEMQ SRKTTQSGQM
   181  SGEGKAGPPG GSSRAAFPQG GRGRGRFPGA VPGGDRFPGP AGPGGPPPPF PAGQTPPRPP
   241  LGPPGPPGPP GPPPPGQVLP PPLAGPPNRG DRPPPPVLFP GQPFGQPPLG PLPPGPPPPV
   301  PGYGPPPGPP PPQQGPPPPP GPFPPRPPGP LGPPLTLAPP PHLPGPPPGA PPPAPHVNPA
   361  FFPPPTNSGM PTSDSRGPPP TDPYGRPPPY DRGDYGPPGR EMDTARTPLS EAEFEEIMNR
   421  NRAISSSAIS RAVSDASAGD YGSAIETLVT AISLIKQSKV SADDRCKVLI SSLQDCLHGI
   481  ESKSYGSGSR RERSRERDHS RSREKSRRHK SRSRDRHDDY YRERSRERER HRDRDRDRDR
   541  ERDREREYRH R

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against CPSF6 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): 0.59
Highest tissue expression: 68 nTPM

Expression across tissuesHPA

Tissue

bone marrow: 68 nTPM
lymph node: 44 nTPM
thymus: 41 nTPM
retina: 40 nTPM
tonsil: 38 nTPM
ovary: 37 nTPM

Single-cell type

lactotrophs: 266 nCPM
thyrotrophs: 227 nCPM
somatotrophs: 225 nCPM
neutrophil progenitors: 219 nCPM
corticotrophs: 211 nCPM
leydig cells: 197 nCPM

Immune cell

T-reg: 47 nTPM
basophil: 45 nTPM
myeloid DC: 39 nTPM
memory B-cell: 33 nTPM
intermediate monocyte: 33 nTPM
memory CD4 T-cell: 31 nTPM

Brain region

cerebellum: 108 nTPM
hypothalamus: 79 nTPM
cerebral cortex: 75 nTPM
hippocampal formation: 73 nTPM
amygdala: 72 nTPM
basal ganglia: 71 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): 0.16
gnomAD pLI: 1
gnomAD missense Z: 3.94
DepMap mean gene effect: -0.83
DepMap dependency class: common

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 7% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

mRNA binding
ribosomal large subunit binding
RNA binding
exon-exon junction complex binding

Cellular components

Protein domainsUniProt · Pfam · InterPro

RNA recognition motif domain
Nucleotide-binding alpha-beta plait domain superfamily
CPSF6/7
RNA-binding domain superfamily
CPSF6/7, RSLD domain, N-terminal region
RNA recognition motif
CPSF6-like, RSLD domain, N-terminal region
Cleavage and polyadenylation specificity factor subunit 6, RNA recognition motif

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of CPSF6 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads CPSF6 as an antibody target. Whether an autoantibody or antibody against CPSF6 could matter depends on whether native CPSF6 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

CPSF6 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 CPSF6 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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