PAPOLB

Summary

PAPOLB (poly(A) polymerase beta, HGNC:15970) is a protein-coding gene on chromosome 7p22.1, encoding Poly(A) polymerase beta (Q9NRJ5).

Predicted to enable poly(A) RNA polymerase activity. Predicted to be involved in RNA 3’-end processing and mRNA processing. Predicted to be located in endoplasmic reticulum. Predicted to be active in nucleus.

Source: NCBI Gene 56903 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 103 total
• MANE Select transcript: NM_020144

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:15970
Approved symbol	PAPOLB
Name	poly(A) polymerase beta
Location	7p22.1
Locus type	gene with protein product
Status	Approved
Aliases	PAPT
Ensembl gene	ENSG00000218823
Ensembl biotype	protein_coding
OMIM	607436
Entrez	56903

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000404991

RefSeq mRNA: 1 — MANE Select: NM_020144 NM_020144

CCDS: CCDS78202

Canonical transcript exons

ENST00000404991 — 1 exons

Exon	Start	End
ENSE00001558102	4857738	4862030

Expression profiles

Bgee: expression breadth broad, 17 present calls, max score 93.06.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0640 / max 46.0107, expressed in 8 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
82550	0.0545	7
82549	0.0095	4

Top tissues by expression

258 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	93.06	gold quality
male germ cell	CL:0000015	89.34	gold quality
right testis	UBERON:0004534	79.84	gold quality
left testis	UBERON:0004533	79.77	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.71	gold quality
testis	UBERON:0000473	78.42	gold quality
adult organism	UBERON:0007023	61.97	gold quality
buccal mucosa cell	CL:0002336	56.12	silver quality
deltoid	UBERON:0001476	52.89	gold quality
cerebellar vermis	UBERON:0004720	52.80	gold quality
myocardium	UBERON:0002349	51.72	gold quality
sural nerve	UBERON:0015488	51.50	gold quality
left ventricle myocardium	UBERON:0006566	51.17	gold quality
cardiac muscle of right atrium	UBERON:0003379	51.07	gold quality
quadriceps femoris	UBERON:0001377	50.94	gold quality
upper arm skin	UBERON:0004263	50.47	gold quality
colonic epithelium	UBERON:0000397	50.37	gold quality
epithelial cell of pancreas	CL:0000083	49.96	gold quality
ileal mucosa	UBERON:0000331	49.78	silver quality
vastus lateralis	UBERON:0001379	49.69	gold quality
Brodmann (1909) area 46	UBERON:0006483	49.30	gold quality
nasal cavity epithelium	UBERON:0005384	49.21	gold quality
cervix squamous epithelium	UBERON:0006922	49.20	gold quality
hair follicle	UBERON:0002073	49.18	gold quality
thymus	UBERON:0002370	49.07	gold quality
tendon of biceps brachii	UBERON:0008188	48.97	silver quality
olfactory bulb	UBERON:0002264	48.92	gold quality
kidney epithelium	UBERON:0004819	48.92	gold quality
type B pancreatic cell	CL:0000169	48.83	gold quality
CA1 field of hippocampus	UBERON:0003881	48.50	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.94

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

149 targeting PAPOLB, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-8075	99.97	67.20	962
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-9718	99.94	68.91	918
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-539-5P	99.93	70.30	2855

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
mus_musculus	Papolb	ENSMUSG00000074817
rattus_norvegicus	Papolb	ENSRNOG00000082193
drosophila_melanogaster	hrg	FBGN0015949
caenorhabditis_elegans		WBGENE00009658
caenorhabditis_elegans		WBGENE00011791
caenorhabditis_elegans		WBGENE00012528

Paralogs (2): PAPOLA (ENSG00000090060), PAPOLG (ENSG00000115421)

Protein

Protein identifiers

Poly(A) polymerase beta — Q9NRJ5 (reviewed: Q9NRJ5)

Alternative names: Polynucleotide adenylyltransferase beta, Testis-specific poly(A) polymerase

All UniProt accessions (2): Q9NRJ5, A4D1Z6

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Interacts with GSG1.

Subcellular location. Nucleus.

Tissue specificity. Testis specific.

Cofactor. Binds 2 magnesium ions. Also active with manganese.

Similarity. Belongs to the poly(A) polymerase family.

RefSeq proteins (1): NP_064529* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007010	PolA_pol_RNA-bd_dom	Domain
IPR007012	PolA_pol_cen_dom	Domain
IPR011068	NuclTrfase_I-like_C	Homologous_superfamily
IPR014492	PolyA_polymerase	Family
IPR043519	NT_sf	Homologous_superfamily
IPR048840	PolA_pol_NTPase	Domain

Pfam: PF04926, PF04928, PF20750

Catalyzed reactions (Rhea), 1 shown:

• RNA(n) + ATP = RNA(n)-3’-adenine ribonucleotide + diphosphate (RHEA:11332)

UniProt features (24 total): binding site 12, site 5, sequence conflict 3, region of interest 2, chain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NRJ5-F1	80.47	0.69

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (5): 154 (interaction with rna); 159 (interaction with rna); 329 (interaction with rna); 400 (interaction with rna); 525 (interaction with rna)

Ligand- & substrate-binding residues (12): 116; 168; 168; 229; 238; 247–248; 101–103; 110; 114–116; 114; 114; 116

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 88 (showing top): SHEPARD_BMYB_MORPHOLINO_UP, AAGTCCA_MIR422B_MIR422A, chr7p22, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, ACTTTAT_MIR1425P, NIKOLSKY_BREAST_CANCER_7P22_AMPLICON, WEBER_METHYLATED_HCP_IN_FIBROBLAST_DN, GCCATNTTG_YY1_Q6, GOMF_ADENYLYLTRANSFERASE_ACTIVITY, WEBER_METHYLATED_HCP_IN_SPERM_DN, GOMF_ADENYL_NUCLEOTIDE_BINDING, GOMF_TRANSFERASE_ACTIVITY_TRANSFERRING_PHOSPHORUS_CONTAINING_GROUPS, MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED, MEISSNER_BRAIN_HCP_WITH_H3_UNMETHYLATED, HATADA_METHYLATED_IN_LUNG_CANCER_UP

GO Biological Process (2): mRNA processing (GO:0006397), RNA 3’-end processing (GO:0031123)

GO Molecular Function (7): RNA binding (GO:0003723), ATP binding (GO:0005524), metal ion binding (GO:0046872), poly(A) RNA polymerase activity (GO:1990817), nucleotide binding (GO:0000166), transferase activity (GO:0016740), nucleotidyltransferase activity (GO:0016779)

GO Cellular Component (3): nucleus (GO:0005634), endoplasmic reticulum (GO:0005783), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
intracellular membrane-bounded organelle	2
mRNA metabolic process	1
nucleic acid binding	1
adenyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
cation binding	1
adenylyltransferase activity	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
catalytic activity	1
transferase activity, transferring phosphorus-containing groups	1
cytoplasm	1
endomembrane system	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1300 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PAPOLB	ZCCHC7	Q8N3Z6	995
PAPOLB	MTREX	P42285	994
PAPOLB	SNRNP70	P08621	985
PAPOLB	SYMPK	Q92797	976
PAPOLB	MTPAP	Q9NVV4	934
PAPOLB	TUT1	Q9H6E5	913
PAPOLB	PABPN1	Q86U42	892
PAPOLB	PARN	O95453	886
PAPOLB	U2AF2	P26368	869
PAPOLB	TENT2	Q6PIY7	867
PAPOLB	TUT4	Q5TAX3	864
PAPOLB	CPEB1	Q9BZB8	862
PAPOLB	CPSF6	Q16630	846
PAPOLB	CPSF3	Q9UKF6	843
PAPOLB	PCF11	O94913	830

IntAct

2 interactions, top by confidence:

A	B	Type	Score
ATG16L1	ESYT2	psi-mi:“MI:0914”(association)	0.350

BioGRID (7): PAPOLB (Co-fractionation), PAPOLB (Co-fractionation), PAPOLB (Co-fractionation), PAPOLB (Co-fractionation), TTC38 (Co-fractionation), PAPOLB (Affinity Capture-MS), PAPOLB (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: F4I507, F4JIU4, F4JWR0, F4K0A6, K7U9N8, O14977, O23617, O35484, O82387, O95568, P0C5K5, P17706, P93115, Q08891, Q0DV28, Q1EBV6, Q29122, Q2KIJ2, Q569U0, Q5R7K3, Q5W736, Q62774, Q63764, Q6H7U5, Q75L42, Q84ND9, Q8GXF0, Q8L870, Q8LJW3, Q8RWC9, Q8W032, Q8W4F0, Q94AH8, Q94C40, Q96EF0, Q99P81, Q9FJ55, Q9FZL3, Q9LGV5, Q9LH02

Diamond homologs: O42617, O82312, P25500, P29468, P51003, P51004, P51005, P51006, Q10295, Q51D88, Q54J73, Q56XM9, Q61183, Q6PCL9, Q8VYW1, Q9BWT3, Q9LMT2, Q9NRJ5, Q9UW26, Q9WVP6

SIGNOR signaling

5 interactions.

A	Effect	B	Mechanism
“CPSF complex”	“up-regulates activity”	PAPOLB	relocalization
PAPOLB	up-regulates	mRNA_polyadenylation
PAPOLB	“up-regulates quantity by stabilization”	“messenger RNA”	“chemical modification”
AHCYL1	“down-regulates activity”	PAPOLB	binding
AHCYL2	“down-regulates activity”	PAPOLB	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

103 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	97
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

109 predictions. Top by Δscore:

Variant	Effect	Δscore
7:4861383:T:TA	donor_gain	0.9400
7:4859600:T:TA	donor_gain	0.8800
7:4861644:T:TA	donor_gain	0.8800
7:4861621:AAAT:A	donor_gain	0.8700
7:4861523:T:A	donor_gain	0.7600
7:4861356:T:TA	donor_gain	0.7500
7:4861624:T:TA	donor_gain	0.7500
7:4861386:T:TA	donor_gain	0.7400
7:4861588:CCT:C	donor_gain	0.7300
7:4861714:TGGGG:T	donor_gain	0.7200
7:4861853:G:GT	donor_gain	0.6900
7:4861939:C:CA	donor_gain	0.6700
7:4861683:AG:A	donor_gain	0.6600
7:4861589:CT:C	donor_gain	0.6500
7:4861590:TT:T	donor_gain	0.6500
7:4861591:TT:T	donor_gain	0.6500
7:4861638:T:TA	donor_gain	0.6400
7:4861846:C:CT	donor_gain	0.6400
7:4861620:AAAAT:A	donor_gain	0.6100
7:4859813:T:C	donor_gain	0.5900
7:4859672:TTCA:T	donor_gain	0.5700
7:4861543:CAGA:C	donor_gain	0.5700
7:4859673:TCA:T	donor_gain	0.5600
7:4859675:A:AT	donor_gain	0.5600
7:4861847:C:CT	donor_gain	0.5400
7:4859809:CTTGT:C	donor_gain	0.5300
7:4861796:C:CT	acceptor_gain	0.5300
7:4861797:G:T	acceptor_gain	0.5300
7:4859756:C:A	donor_gain	0.5200
7:4861341:A:C	donor_gain	0.5100

AlphaMissense

4206 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000439646 (7:4860007 C>T), RS1000655169 (7:4862107 C>A,T), RS1000684883 (7:4862335 C>A,T), RS1001199431 (7:4857301 G>A,T), RS1001933311 (7:4862724 C>A,G), RS1002305817 (7:4862549 C>A), RS1002376972 (7:4861547 C>G), RS1002692978 (7:4859922 T>C,G), RS1003502101 (7:4862556 T>A), RS1003571933 (7:4863682 A>G), RS1003574228 (7:4863524 C>G), RS1003701663 (7:4858883 A>G), RS1003951522 (7:4857389 C>T), RS1003974354 (7:4858104 A>C), RS1004058339 (7:4862370 C>T)

Disease associations

OMIM: gene MIM:607436 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST010796_5292	Electrocardiogram morphology (amplitude at temporal datapoints)	4.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004327	electrocardiography

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression	1
CGP 52608	affects binding, increases reaction	1
Sunitinib	increases expression	1
Benzo(a)pyrene	affects methylation	1
Rotenone	decreases expression	1
Copper Sulfate	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.