PAIP2B

Summary

PAIP2B (poly(A) binding protein interacting protein 2B, HGNC:29200) is a protein-coding gene on chromosome 2p13.3, encoding Polyadenylate-binding protein-interacting protein 2B (Q9ULR5). Inhibits translation of capped and polyadenylated mRNAs by displacing PABPC1 from the poly(A) tail.

Most mRNAs, except for histones, contain a 3-prime poly(A) tail. Poly(A)-binding protein (PABP; see MIM 604679) enhances translation by circularizing mRNA through its interaction with the translation initiation factor EIF4G1 (MIM 600495) and the poly(A) tail. Various PABP-binding proteins regulate PABP activity, including PAIP1 (MIM 605184), a translational stimulator, and PAIP2A (MIM 605604) and PAIP2B, translational inhibitors (Derry et al., 2006 [PubMed 17381337]).

Source: NCBI Gene 400961 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 25 total
• MANE Select transcript: NM_020459

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29200
Approved symbol	PAIP2B
Name	poly(A) binding protein interacting protein 2B
Location	2p13.3
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1155
Ensembl gene	ENSG00000124374
Ensembl biotype	protein_coding
OMIM	611018
Entrez	400961

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 12 protein_coding

ENST00000244221, ENST00000890279, ENST00000890282, ENST00000890284, ENST00000890286, ENST00000890288, ENST00000890290, ENST00000890292, ENST00000890294, ENST00000921243, ENST00000921244, ENST00000961014

RefSeq mRNA: 1 — MANE Select: NM_020459 NM_020459

CCDS: CCDS46322

Canonical transcript exons

ENST00000244221 — 4 exons

Exon	Start	End
ENSE00000846584	71189845	71190021
ENSE00001201741	71182738	71188535
ENSE00001330891	71202452	71202600
ENSE00001546891	71226928	71227103

Expression profiles

Bgee: expression breadth ubiquitous, 277 present calls, max score 98.07.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.2212 / max 702.3679, expressed in 1221 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
29066	13.1230	1219
29065	0.0982	46

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
corpus callosum	UBERON:0002336	98.07	gold quality
medial globus pallidus	UBERON:0002477	98.06	gold quality
globus pallidus	UBERON:0001875	97.85	gold quality
inferior vagus X ganglion	UBERON:0005363	97.83	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	97.52	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	97.13	gold quality
subthalamic nucleus	UBERON:0001906	96.85	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	96.75	gold quality
spinal cord	UBERON:0002240	96.60	gold quality
middle frontal gyrus	UBERON:0002702	96.47	gold quality
substantia nigra	UBERON:0002038	96.30	gold quality
cranial nerve II	UBERON:0000941	96.22	gold quality
lateral globus pallidus	UBERON:0002476	96.16	gold quality
diaphragm	UBERON:0001103	96.14	gold quality
midbrain	UBERON:0001891	96.14	gold quality
inferior olivary complex	UBERON:0002127	96.02	gold quality
substantia nigra pars reticulata	UBERON:0001966	95.47	gold quality
amygdala	UBERON:0001876	95.35	gold quality
medulla oblongata	UBERON:0001896	95.23	gold quality
superior vestibular nucleus	UBERON:0007227	94.82	gold quality
left ventricle myocardium	UBERON:0006566	94.52	gold quality
dorsal plus ventral thalamus	UBERON:0001897	94.41	gold quality
body of pancreas	UBERON:0001150	94.32	gold quality
substantia nigra pars compacta	UBERON:0001965	94.02	gold quality
putamen	UBERON:0001874	93.90	gold quality
ventral tegmental area	UBERON:0002691	93.71	gold quality
biceps brachii	UBERON:0001507	93.70	gold quality
hypothalamus	UBERON:0001898	93.70	gold quality
triceps brachii	UBERON:0001509	93.60	gold quality
Ammon’s horn	UBERON:0001954	93.34	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-GEOD-81547	yes	19.11
E-HCAD-11	yes	16.99
E-ANND-3	yes	12.94

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

187 targeting PAIP2B, 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-3613-3P	100.00	76.36	7965
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-12118	100.00	65.88	1270
HSA-MIR-3120-5P	100.00	65.56	965
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-499A-5P	99.98	70.79	1323
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-22-3P	99.93	68.13	917
HSA-MIR-3143	99.93	71.96	3104

Literature-anchored findings (GeneRIF, showing 1)

• Study provides evidence that a low-frequency SNP of the translation inhibitor gene PAIP2B with a significant association with pancreatic cancer survival. (PMID:28470677)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	paip2b	ENSDARG00000008706
mus_musculus	Paip2b	ENSMUSG00000045896
rattus_norvegicus	Paip2b	ENSRNOG00000070386
drosophila_melanogaster	Paip2	FBGN0038100

Paralogs (1): PAIP2 (ENSG00000120727)

Protein

Protein identifiers

Polyadenylate-binding protein-interacting protein 2B — Q9ULR5 (reviewed: Q9ULR5)

All UniProt accessions (1): Q9ULR5

UniProt curated annotations — full annotation on UniProt →

Function. Inhibits translation of capped and polyadenylated mRNAs by displacing PABPC1 from the poly(A) tail.

Subunit / interactions. Interacts (via central acidic portion and C-terminus) with PABPC1 (via the second and third RRM domains and the C-terminus).

Tissue specificity. Expressed in brain, cervix, heart, liver, ovary, kidney, prostate and testis.

Post-translational modifications. Ubiquitinated in vitro.

Similarity. Belongs to the PAIP2 family.

RefSeq proteins (1): NP_065192* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009818	PAM2_motif	Conserved_site
IPR040396	PAIP2-like	Family

Pfam: PF07145

UniProt features (7 total): compositionally biased region 3, region of interest 2, chain 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9ULR5-F1	72.62	0.18

Functional residue map

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

Post-translational modifications (1): 1

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 123 (showing top): MORF_RAGE, GOBP_TRANSLATIONAL_INITIATION, GOBP_NEGATIVE_REGULATION_OF_TRANSLATION, GOBP_NEGATIVE_REGULATION_OF_TRANSLATIONAL_INITIATION, GOBP_TRANSLATION, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, GOMF_TRANSLATION_REGULATOR_ACTIVITY, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_METABOLIC_PROCESS, MORF_IKBKG, MARIADASON_REGULATED_BY_HISTONE_ACETYLATION_DN, NUYTTEN_EZH2_TARGETS_DN, MORF_ORC1L, GOBP_REGULATION_OF_TRANSLATION, GOBP_REGULATION_OF_TRANSLATIONAL_INITIATION, MARSON_BOUND_BY_FOXP3_UNSTIMULATED

GO Biological Process (3): negative regulation of translation (GO:0017148), negative regulation of translational initiation (GO:0045947), regulation of translation (GO:0006417)

GO Molecular Function (3): mRNA regulatory element binding translation repressor activity (GO:0000900), translation repressor activity (GO:0030371), protein binding (GO:0005515)

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
translation	2
negative regulation of translation	2
regulation of translation	1
negative regulation of gene expression	1
negative regulation of protein metabolic process	1
translational initiation	1
regulation of translational initiation	1
post-transcriptional regulation of gene expression	1
regulation of protein metabolic process	1
mRNA binding	1
translation repressor activity	1
translation regulator activity	1
binding	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

462 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PAIP2B	ATP1B3	P54709	810
PAIP2B	ADCY6	O43306	763
PAIP2B	SLC1A1	P43005	761
PAIP2B	PAIP1	Q9H074	668
PAIP2B	PABPC1	P11940	562
PAIP2B	EIF4G1	Q04637	519
PAIP2B	MITF	O75030	451
PAIP2B	OCM2	P0CE71	426
PAIP2B	OTX1	P32242	425
PAIP2B	OCM	P0CE72	404
PAIP2B	EBF1	Q9UH73	389
PAIP2B	SLC26A5	P58743	352
PAIP2B	CLEC18B	Q6UXF7	348
PAIP2B	RCAN3	Q9UKA8	348
PAIP2B	PITPNM1	O00562	344

IntAct

32 interactions, top by confidence:

A	B	Type	Score
RBM3	PRMT5	psi-mi:“MI:0914”(association)	0.530
CIRBP	PRMT5	psi-mi:“MI:0914”(association)	0.530
CELF5	CASC3	psi-mi:“MI:0914”(association)	0.530
SNIP1	CASC3	psi-mi:“MI:0914”(association)	0.530
ELAVL2	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
LUC7L2	CASC3	psi-mi:“MI:0914”(association)	0.530
PAIP2B	CASC3	psi-mi:“MI:0914”(association)	0.530
HNRNPA1	PTCD1	psi-mi:“MI:0914”(association)	0.530
RBM3	AARS2	psi-mi:“MI:0914”(association)	0.530
PRR3	MRPS14	psi-mi:“MI:0914”(association)	0.530
ELAVL2	IGF2BP3	psi-mi:“MI:0914”(association)	0.350
LUC7L2	CASC3	psi-mi:“MI:0914”(association)	0.350
HNRNPA1	HNRNPR	psi-mi:“MI:0914”(association)	0.350
DND1	ATXN3	psi-mi:“MI:0914”(association)	0.350
PABPC4	HNRNPR	psi-mi:“MI:0914”(association)	0.350
PURG	ZNF320	psi-mi:“MI:0914”(association)	0.350
FAM120A	GTPBP10	psi-mi:“MI:0914”(association)	0.350
PRR3	ZNF316	psi-mi:“MI:0914”(association)	0.350
PABPC5	APOBEC3DE	psi-mi:“MI:0914”(association)	0.350
LARP4B	IGF2BP3	psi-mi:“MI:0914”(association)	0.350
RBMS2	ZNF275	psi-mi:“MI:0914”(association)	0.350
HNRNPCL1	KPNA3	psi-mi:“MI:0914”(association)	0.350
ALYREF	CASC3	psi-mi:“MI:0914”(association)	0.350
PABPC5	IGF2BP3	psi-mi:“MI:0914”(association)	0.350
PAIP1	CASC3	psi-mi:“MI:0914”(association)	0.350

BioGRID (68): PAIP2B (Affinity Capture-MS), PAIP2B (Affinity Capture-MS), PAIP2B (Affinity Capture-MS), PAIP2B (Affinity Capture-MS), PAIP2B (Affinity Capture-MS), PAIP2B (Affinity Capture-MS), PAIP2B (Affinity Capture-MS), PAIP2B (Affinity Capture-MS), PAIP2B (Affinity Capture-MS), PAIP2B (Affinity Capture-MS), PAIP2B (Affinity Capture-MS), PAIP2B (Proximity Label-MS), PAIP2B (Proximity Label-MS), C17orf85 (Affinity Capture-MS), PAIP2B (Affinity Capture-MS)

ESM2 similar proteins: A4IGY3, A6H767, A8XLU5, O08585, O14140, O88271, O94742, P04973, P04975, P08081, P08082, P09496, P09497, P11845, P28656, P41236, P50411, P55209, P60896, P60897, P62499, Q28EB4, Q3SZX2, Q3ZBR6, Q4ADK4, Q4ADK7, Q4U0Y4, Q54K21, Q5H7N8, Q5I0B5, Q5R4D4, Q60FC2, Q6INR1, Q6IRU5, Q6NXS1, Q75UQ2, Q7SA04, Q7SXU0, Q7ZY81, Q803P1

Diamond homologs: Q3ZC67, Q5R596, Q5ZJS6, Q6AXZ0, Q91W45, Q9BPZ3, Q9D6V8, Q9ULR5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 32 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
mRNA Splicing - Major Pathway	5	19.5×	2e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	18
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

880 predictions. Top by Δscore:

Variant	Effect	Δscore
2:71188460:T:TA	donor_gain	1.0000
2:71189838:CTCTT:C	donor_loss	1.0000
2:71189839:TCTTA:T	donor_loss	1.0000
2:71189840:CTTA:C	donor_loss	1.0000
2:71189841:TTA:T	donor_loss	1.0000
2:71189842:TA:T	donor_loss	1.0000
2:71189843:A:AC	donor_gain	1.0000
2:71189843:A:AT	donor_loss	1.0000
2:71189844:C:CC	donor_gain	1.0000
2:71189844:C:CT	donor_loss	1.0000
2:71190018:CCAC:C	acceptor_gain	1.0000
2:71190019:CAC:C	acceptor_gain	1.0000
2:71190019:CACC:C	acceptor_gain	1.0000
2:71190022:C:CA	acceptor_loss	1.0000
2:71202446:CTTTA:C	donor_loss	1.0000
2:71202448:TTA:T	donor_loss	1.0000
2:71202449:TAC:T	donor_loss	1.0000
2:71202450:A:AT	donor_loss	1.0000
2:71202451:CCTGT:C	donor_gain	1.0000
2:71202596:GGAAC:G	acceptor_gain	1.0000
2:71202597:GAAC:G	acceptor_gain	1.0000
2:71202597:GAACC:G	acceptor_loss	1.0000
2:71202598:AAC:A	acceptor_gain	1.0000
2:71202598:AACCT:A	acceptor_loss	1.0000
2:71202599:AC:A	acceptor_gain	1.0000
2:71202599:ACC:A	acceptor_loss	1.0000
2:71202600:CC:C	acceptor_gain	1.0000
2:71202600:CCT:C	acceptor_loss	1.0000
2:71202601:C:CC	acceptor_gain	1.0000
2:71202601:C:T	acceptor_gain	1.0000

AlphaMissense

837 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:71202482:C:A	W36C	1.000
2:71202482:C:G	W36C	1.000
2:71202484:A:G	W36R	1.000
2:71202484:A:T	W36R	1.000
2:71188500:A:C	F117L	0.999
2:71188500:A:T	F117L	0.999
2:71188502:A:G	F117L	0.999
2:71202480:A:G	M37T	0.999
2:71189969:A:G	M64T	0.998
2:71190008:A:G	L51P	0.998
2:71202479:C:A	M37I	0.998
2:71202479:C:G	M37I	0.998
2:71202479:C:T	M37I	0.998
2:71202497:A:C	F31L	0.998
2:71202497:A:T	F31L	0.998
2:71202498:A:C	F31C	0.998
2:71202499:A:G	F31L	0.998
2:71188501:A:G	F117S	0.997
2:71189966:A:G	L65P	0.997
2:71202461:G:C	F43L	0.997
2:71202461:G:T	F43L	0.997
2:71202463:A:G	F43L	0.997
2:71202483:C:G	W36S	0.997
2:71202490:A:G	Y34H	0.997
2:71202498:A:G	F31S	0.997
2:71188501:A:C	F117C	0.996
2:71189969:A:C	M64R	0.996
2:71189978:A:G	F61S	0.996
2:71189982:A:G	C60R	0.996
2:71189993:A:G	F56S	0.996

dbSNP variants (sampled 300 via entrez): RS1000012521 (2:71188740 G>A), RS1000051067 (2:71216067 T>G), RS1000080458 (2:71216422 T>C), RS1000162436 (2:71215470 T>C), RS1000305403 (2:71223289 T>C), RS1000377472 (2:71209226 G>T), RS1000587571 (2:71194093 C>G,T), RS1000636193 (2:71223736 C>T), RS1000651550 (2:71186572 A>G), RS1000723421 (2:71228481 G>A), RS1000735217 (2:71200762 C>A,T), RS1000796952 (2:71228156 C>T), RS1000817432 (2:71188920 T>C), RS1001041434 (2:71221760 G>A), RS1001087658 (2:71187222 G>T)

Disease associations

OMIM: gene MIM:611018 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST004033_15	QRS interval (sulfonylurea treatment interaction)	4.000000e-08
GCST004485_1	Survival in pancreatic cancer	3.000000e-06
GCST007044_5	Extremely high intelligence	6.000000e-09
GCST007096_21	Pulse pressure	6.000000e-09
GCST009391_716	Metabolite levels	3.000000e-06

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0007922	response to sulfonylurea
EFO:0000638	overall survival
EFO:0004337	intelligence
EFO:0005763	pulse pressure measurement
EFO:0010532	salicylurate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

44 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, decreases expression	5
methylmercuric chloride	decreases expression	2
sodium arsenite	affects methylation, decreases expression	2
(+)-JQ1 compound	increases expression	2
Nickel	decreases expression	2
GSK-J4	increases expression	1
bisphenol F	affects cotreatment, increases expression	1
triphenyl phosphate	affects expression	1
uranyl acetate	affects expression	1
bisphenol A	affects cotreatment, increases expression	1
trichostatin A	affects expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
hydroquinone	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	increases expression, affects response to substance	1
perfluoro-n-nonanoic acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
jinfukang	decreases expression, affects cotreatment	1
Sunitinib	increases expression	1
Leflunomide	decreases expression	1
Air Pollutants	decreases expression	1
Benzo(a)pyrene	decreases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Diethylhexyl Phthalate	decreases expression	1
Dimethyl Sulfoxide	increases expression	1
Doxorubicin	decreases expression	1
Herbicides	increases expression	1
Indomethacin	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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