POU5F1B

Summary

POU5F1B (POU class 5 homeobox 1B, HGNC:9223) is a protein-coding gene on chromosome 8q24.21, encoding POU domain, class 5, transcription factor 1B (Q06416). Shows weak transcriptional activator activity.

This intronless gene was thought to be a transcribed pseudogene of POU class 5 homeobox 1, however, it has been reported that this gene can encode a functional protein. The encoded protein is nearly the same length as and highly similar to the POU class 5 homeobox 1 transcription factor, has been shown to be a weak transcriptional activator and may play a role in carcinogenesis and eye development.

Source: NCBI Gene 5462 — RefSeq curated summary.

At a glance

• GWAS associations: 17
• Clinical variants (ClinVar): 2 total
• MANE Select transcript: NM_001159542

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:9223
Approved symbol	POU5F1B
Name	POU class 5 homeobox 1B
Location	8q24.21
Locus type	gene with protein product
Status	Approved
Aliases	OTF3C
Ensembl gene	ENSG00000212993
Ensembl biotype	protein_coding
OMIM	615739
Entrez	5462

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000465342, ENST00000645438, ENST00000696633

RefSeq mRNA: 2 — MANE Select: NM_001159542 NM_001159542, NM_001395745

CCDS: CCDS55274

Canonical transcript exons

ENST00000696633 — 1 exons

Exon	Start	End
ENSE00003967918	127415867	127416946

Expression profiles

Bgee: expression breadth ubiquitous, 103 present calls, max score 72.13.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 4.5957 / max 297.3958, expressed in 124 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
90645	4.5957	124

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	72.13	gold quality
endometrium	UBERON:0001295	64.31	gold quality
cortical plate	UBERON:0005343	60.08	gold quality
granulocyte	CL:0000094	57.42	gold quality
cortex of kidney	UBERON:0001225	56.36	gold quality
mucosa of transverse colon	UBERON:0004991	56.19	gold quality
metanephros cortex	UBERON:0010533	55.18	gold quality
adult mammalian kidney	UBERON:0000082	53.60	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	53.36	gold quality
saliva-secreting gland	UBERON:0001044	53.19	gold quality
kidney	UBERON:0002113	53.06	gold quality
hindlimb stylopod muscle	UBERON:0004252	52.96	gold quality
ventricular zone	UBERON:0003053	52.72	gold quality
right uterine tube	UBERON:0001302	52.68	gold quality
tonsil	UBERON:0002372	52.42	silver quality
thoracic mammary gland	UBERON:0005200	52.16	gold quality
minor salivary gland	UBERON:0001830	52.06	gold quality
skin of leg	UBERON:0001511	51.36	gold quality
omental fat pad	UBERON:0010414	50.96	gold quality
prostate gland	UBERON:0002367	50.71	gold quality
zone of skin	UBERON:0000014	50.69	gold quality
lymph node	UBERON:0000029	50.64	gold quality
left lobe of thyroid gland	UBERON:0001120	50.29	gold quality
fallopian tube	UBERON:0003889	50.14	gold quality
thyroid gland	UBERON:0002046	50.08	gold quality
adipose tissue	UBERON:0001013	49.89	gold quality
lower esophagus mucosa	UBERON:0035834	49.82	gold quality
blood	UBERON:0000178	49.80	silver quality
skin of abdomen	UBERON:0001416	49.73	gold quality
body of uterus	UBERON:0009853	49.70	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.22

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA0792.1	POU5F1B	POU domain factors

JASPAR matrix evidence (PMIDs): PMID:2350782

miRNA regulators (miRDB)

15 targeting POU5F1B, 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-3667-3P	99.99	67.17	1636
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-548AZ-5P	99.83	69.94	3230
HSA-MIR-548T-5P	99.83	69.91	3220
HSA-MIR-6752-3P	99.72	66.71	1587
HSA-MIR-3609	99.52	69.89	2587
HSA-MIR-548AH-5P	99.52	69.73	2626
HSA-MIR-103A-2-5P	99.39	67.72	1577
HSA-MIR-3606-5P	99.31	69.67	1168
HSA-MIR-6734-3P	99.15	66.27	1627
HSA-MIR-6815-3P	99.13	68.98	1530
HSA-MIR-299-3P	97.73	66.67	773
HSA-MIR-335-5P	97.10	68.12	1022
HSA-MIR-4654	95.86	65.72	751
HSA-MIR-4769-5P	95.37	66.09	570

Literature-anchored findings (GeneRIF, showing 14)

• that a putative POU5F1P1 protein is localized in the nucleus, acts as a transcriptional activator and regulates the expression in a similar way to the POU5F1 isoform 1 (PMID:18949397)
• Over-expression of POU5F1P1 in prostatic carcinoma in addition to its genomic location and the putative function of its gene product render POU5F1P1 a good candidate to harbour functional genetic variants which modulate prostatic cancer susceptibility. (PMID:20017164)
• Data suggest that expression of Oct4 and NANOG (Nanog homeobox protein) is up-regulated in visceral adipose tissue stem cells in type 2 diabetes as compared to control; expression is also up-regulated in hyperglycemic conditions. (PMID:23064289)
• Association of rs7014346 in POU5F1P1, rs989902 in PTPN13, and rs7003146 in TCF7L2 with variations in the risk of breast cancer in a Chinese Han population. (PMID:24338422)
• The POU5F1B pseudogene is amplified and expressed at a high level in, as well as confers an aggressive phenotype on, GC, and that POU5F1B amplification is associated with a poor prognosis in GC patients. (PMID:24362523)
• POU5F1P1 rs10505477 is correlated with survival of gastric cancer patients who receving cisplatin-based chemotherapy after gastrectomy. (PMID:25046748)
• We identified eight specific CpG sites at 8q24, including six correlated sites in the POU5F1B gene, as well as two CpG sites in intergenic regions, whose DNA methylation levels were associated with prostate cancer risk. (PMID:28463958)
• POU5F1B promotes hepatocellular carcinoma cell proliferation by activating AKT protein. (PMID:29454285)
• Study shows that irrespective of tumor type or clinicopathological status, breast cancer cells expressed high levels of Oct3/4 at mRNA and protein levels. Further sequencing analysis show that breast tumors and MCF-7 cell line predominantly expressed transcripts of POU5F1B, an Oct4-like gene from chromosome 8 which possess 94% similitude with oct-4. (PMID:29620155)
• POU5F1B was upregulated in cervical cancer and down-regulation inhibited cell proliferation and migration and induced apoptosis in cervical cancer cell lines by modulating OCT4. (PMID:30762028)
• Radiotherapy contributed to the decline in the expression level of POU5F1B in plasma, which was upregulated in ECA109, ECA9706, KYSE410, and KYSE510, but not in HEEPIC. The knockdown of POU5F1B increased the radiosensitivity of esophageal cancer cell lines. (PMID:30763293)
• POU5F1B was underexpressed in AML compared with controls (P<0.001). The receiver operating characteristic (ROC) curve revealed that the POU5F1B transcript level was able to differentiate AML patients from healthy individuals (AUC=0.682). In non-APL AML patients. (PMID:31271156)
• Recurrent Superenhancer of the Oncogene POU5F1B in Colorectal Cancers. (PMID:34934770)
• Transposon-activated POU5F1B promotes colorectal cancer growth and metastasis. (PMID:35987910)

Cross-species orthologs

8 orthologs

Organism	Symbol	Gene ID
danio_rerio	pou3f1	ENSDARG00000009823
danio_rerio	pou5f3	ENSDARG00000044774
mus_musculus	Pou5f1	ENSMUSG00000024406
rattus_norvegicus	Pou5f1	ENSRNOG00000046487
drosophila_melanogaster	acj6	FBGN0000028
drosophila_melanogaster	vvl	FBGN0086680
caenorhabditis_elegans		WBGENE00000441
caenorhabditis_elegans		WBGENE00006818

Paralogs (17): POU2F2 (ENSG00000028277), POU1F1 (ENSG00000064835), POU4F3 (ENSG00000091010), POU6F2 (ENSG00000106536), POU2F3 (ENSG00000137709), POU2F1 (ENSG00000143190), POU4F2 (ENSG00000151615), POU4F1 (ENSG00000152192), HDX (ENSG00000165259), POU6F1 (ENSG00000184271), POU3F2 (ENSG00000184486), POU3F1 (ENSG00000185668), POU3F4 (ENSG00000196767), POU3F3 (ENSG00000198914), CCDC160 (ENSG00000203952), POU5F1 (ENSG00000204531), POU5F2 (ENSG00000248483)

Protein

Protein identifiers

POU domain, class 5, transcription factor 1B — Q06416 (reviewed: Q06416)

Alternative names: Oct4-pg1, Octamer-binding protein 3-like, Octamer-binding transcription factor 3-like

All UniProt accessions (1): Q06416

UniProt curated annotations — full annotation on UniProt →

Function. Shows weak transcriptional activator activity.

Subcellular location. Nucleus. Cytoplasm.

Tissue specificity. Detected in epithelial cells of the prostate (at protein level). Detected at the mRNA level in several cancer tissues (breast, uterine cervix, lung, thyroid gland, esophagus, colon, urinary bladder, and glioma).

Similarity. Belongs to the POU transcription factor family. Class-5 subfamily.

RefSeq proteins (2): NP_001153014, NP_001382674 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000327	POU_dom	Domain
IPR001356	HD	Domain
IPR009057	Homeodomain-like_sf	Homologous_superfamily
IPR010982	Lambda_DNA-bd_dom_sf	Homologous_superfamily
IPR013847	POU	Domain
IPR017970	Homeobox_CS	Conserved_site
IPR050255	POU_domain_TF	Family

Pfam: PF00046, PF00157

UniProt features (69 total): sequence conflict 49, sequence variant 7, modified residue 6, region of interest 3, chain 1, domain 1, DNA-binding region 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q06416-F1	65.97	0.32

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 (6): 288, 289, 354, 111, 235, 236

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 30 (showing top): GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, KRIEG_HYPOXIA_NOT_VIA_KDM3A, chr8q24, ZWANG_CLASS_1_TRANSIENTLY_INDUCED_BY_EGF, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, MIR3658, MIR548AZ_5P, MIR548T_5P, MIR335_5P, MIR4654, MIR4769_5P, HARALAMBIEVA_PBMC_M_M_R_II_AGE_11_22YO_VACCINATED_VS_UNVACCINATED_7YR_UP, GOMF_DNA_BINDING_TRANSCRIPTION_FACTOR_ACTIVITY, GOMF_CIS_REGULATORY_REGION_SEQUENCE_SPECIFIC_DNA_BINDING, GSE29617_CTRL_VS_TIV_FLU_VACCINE_PBMC_2008_DN

GO Biological Process (2): regulation of DNA-templated transcription (GO:0006355), regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (4): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription factor activity (GO:0003700), DNA binding (GO:0003677)

GO Cellular Component (6): chromatin (GO:0000785), nucleoplasm (GO:0005654), mitochondrion (GO:0005739), cytosol (GO:0005829), nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
regulation of DNA-templated transcription	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
cytoplasm	2
intracellular membrane-bounded organelle	2
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
transcription by RNA polymerase II	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
transcription cis-regulatory region binding	1
transcription regulator activity	1
nucleic acid binding	1
chromosome	1
nuclear lumen	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

814 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
POU5F1B	LRATD2	Q96KN1	642
POU5F1B	MYC	P01106	628
POU5F1B	NANOGP8	Q6NSW7	589
POU5F1B	TCF7L2	Q9NQB0	563
POU5F1B	NANOG	Q9H9S0	509
POU5F1B	PRDM14	Q9GZV8	498
POU5F1B	PGA4	P00790	479
POU5F1B	HLA-C	P04222	424
POU5F1B	HLA-A	P01891	390
POU5F1B	KLF12	Q9Y4X4	388
POU5F1B	FOXD3	Q9UJU5	378
POU5F1B	CCHCR1	Q8TD31	374
POU5F1B	P3H2	Q8IVL5	370
POU5F1B	WWP2	O00308	356
POU5F1B	PRKAA1	Q13131	353
POU5F1B	CDSN	Q15517	353

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A5PK23, A5PKW4, A6NKF2, A6PWV5, A7X8B3, A7X8B5, A7X8B7, A7X8B9, A7X8C2, A7X8C4, A7X8C7, A7X8C9, A7X8D2, A7X8D4, A7XW16, A7XW20, A7XW25, F1MUS9, O14512, O95402, O97552, P06186, P20263, P52946, P52947, P52954, P52955, P70118, Q00175, Q00417, Q06416, Q14209, Q1XID0, Q3B8N7, Q5DTT2, Q64731, Q6U8D7, Q7TN02, Q80YF9, Q8IVH2

Diamond homologs: A0A1L8FFY5, A1L0Z1, A7Y7W2, B3DM23, B3DM25, B7ZQA9, D3ZTL1, G3V7L5, O97552, P09086, P10036, P10037, P13528, P14859, P15143, P16143, P16241, P17208, P20263, P20264, P20265, P20266, P20267, P20268, P20912, P20913, P20914, P21952, P24350, P25425, P28069, P31360, P31361, P31362, P31363, P31364, P31365, P31367, P31368, P31369

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	2
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

229 predictions. Top by Δscore:

Variant	Effect	Δscore
8:127414329:G:GT	donor_gain	0.9600
8:127415023:G:GG	donor_gain	0.9500
8:127416761:GCTGC:G	donor_gain	0.9400
8:127415018:GCCAA:G	donor_gain	0.9200
8:127414330:A:T	donor_gain	0.9100
8:127415141:T:G	donor_gain	0.9100
8:127416752:GATTT:G	donor_gain	0.8600
8:127414558:GGT:G	donor_gain	0.8200
8:127415019:CCAAG:C	donor_loss	0.7800
8:127415020:CAAG:C	donor_loss	0.7800
8:127415022:AG:A	donor_loss	0.7800
8:127415023:G:GA	donor_loss	0.7800
8:127415024:T:TC	donor_loss	0.7800
8:127415025:A:AT	donor_loss	0.7800
8:127415026:A:AC	donor_loss	0.7700
8:127415027:G:C	donor_loss	0.7700
8:127414392:T:TA	donor_gain	0.7600
8:127414393:A:AA	donor_gain	0.7600
8:127416223:T:TA	acceptor_gain	0.7500
8:127414317:G:GT	donor_gain	0.7400
8:127414311:G:GT	donor_gain	0.7300
8:127416677:G:GT	donor_gain	0.7100
8:127415026:A:AG	donor_gain	0.7000
8:127415027:G:GG	donor_gain	0.7000
8:127414312:A:T	donor_gain	0.6800
8:127414559:GT:G	donor_gain	0.6800
8:127414560:T:G	donor_gain	0.6800
8:127414560:TT:T	donor_gain	0.6800
8:127415434:A:AG	acceptor_gain	0.6800
8:127416718:C:T	donor_gain	0.6500

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000588781 (8:127412381 T>C,G), RS1001366074 (8:127413223 T>C), RS1001668645 (8:127415202 C>T), RS1002209669 (8:127417480 G>T), RS1002261884 (8:127417703 T>A), RS1002743416 (8:127414082 G>C), RS1003096032 (8:127413830 C>T), RS1004129057 (8:127412873 A>G), RS1005047433 (8:127414927 G>C), RS1006045588 (8:127413581 A>T), RS1006245059 (8:127413801 A>C,G), RS1007207196 (8:127413734 C>A,G,T), RS1007671599 (8:127414002 T>C), RS1008005645 (8:127413221 A>G), RS1008932347 (8:127415526 G>A)

Disease associations

OMIM: gene MIM:615739 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

17 associations (top):

Study	Trait	p-value
GCST001308_2	Response to anti-depressant treatment in major depressive disorder	3.000000e-07
GCST002299_12	Chronic lymphocytic leukemia	3.000000e-06
GCST002421_1	Prostate cancer	4.000000e-15
GCST002421_5	Prostate cancer	5.000000e-12
GCST002460_1	Urinary bladder cancer	2.000000e-07
GCST003148_10	Prostate cancer	1.000000e-16
GCST003148_11	Prostate cancer	4.000000e-23
GCST004136_6	Methadone dose in opioid dependence	3.000000e-06
GCST004146_12	Chronic lymphocytic leukemia	7.000000e-16
GCST005591_8	Colorectal cancer	1.000000e-19
GCST007552_18	Colorectal cancer	1.000000e-31
GCST007798_87	Asthma	2.000000e-11
GCST007800_5	Asthma (childhood onset)	1.000000e-23
GCST009869_55	Colorectal cancer	3.000000e-33
GCST010396_8	Gut microbiota (bacterial taxa, hurdle binary method)	9.000000e-06
GCST90011898_108	Alanine aminotransferase levels	2.000000e-75
GCST90011899_192	Aspartate aminotransferase levels	3.000000e-23

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0006320	antidepressant-induced side effect
EFO:0007907	methadone dose measurement
EFO:0007874	gut microbiome measurement
EFO:0004736	aspartate aminotransferase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, decreases methylation	3
trichostatin A	affects cotreatment, increases expression	2
entinostat	decreases expression, increases expression, affects cotreatment	2
belinostat	increases expression, affects cotreatment	2
Panobinostat	affects cotreatment, increases expression	2
Phenylmercuric Acetate	decreases expression, affects cotreatment	2
sotorasib	affects cotreatment, decreases expression	1
methylmercuric chloride	increases expression	1
potassium chromate(VI)	affects cotreatment, increases expression	1
S-(1,2-dichlorovinyl)cysteine	increases expression, affects response to substance	1
epigallocatechin gallate	affects cotreatment, increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression, decreases expression	1
dorsomorphin	affects cotreatment, increases expression, decreases expression	1
trametinib	decreases expression, affects cotreatment	1
NVP-BKM120	affects cotreatment, decreases expression	1
Benzo(a)pyrene	increases methylation	1
Lipopolysaccharides	affects response to substance, increases expression	1
Oxygen	increases expression	1
Tretinoin	decreases expression	1
Antirheumatic Agents	decreases expression	1

Clinical trials (associated diseases)

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