POLR2J3

Summary

POLR2J3 (RNA polymerase II subunit J3, HGNC:33853) is a protein-coding gene on chromosome 7q22.1, encoding DNA-directed RNA polymerase II subunit RPB11-b2 (Q9H1A7). DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.

This gene is a member of the RNA polymerase II subunit 11 gene family, which includes three genes in a cluster on chromosome 7q22.1 and a pseudogene on chromosome 7p13. The founding member of this family, DNA directed RNA polymerase II polypeptide J, has been shown to encode a subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. This locus produces multiple, alternatively spliced transcripts that potentially express isoforms with distinct C-termini compared to DNA directed RNA polymerase II polypeptide J. Most or all variants are spliced to include additional non-coding exons at the 3’ end which makes them candidates for nonsense-mediated decay (NMD). Consequently, it is not known if this locus expresses a protein or proteins in vivo.

Source: NCBI Gene 548644 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 8 total

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33853
Approved symbol	POLR2J3
Name	RNA polymerase II subunit J3
Location	7q22.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000168255
Ensembl biotype	protein_coding
Entrez	548644

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 6 nonsense_mediated_decay, 5 protein_coding_CDS_not_defined, 1 protein_coding

ENST00000379340, ENST00000464525, ENST00000486319, ENST00000489144, ENST00000502415, ENST00000503564, ENST00000504677, ENST00000506060, ENST00000507355, ENST00000508848, ENST00000511773, ENST00000513506

RefSeq mRNA: 0 — MANE Select: None

CCDS: CCDS47673

Canonical transcript exons

ENST00000379340 — 9 exons

Exon	Start	End
ENSE00001707267	102572472	102572539
ENSE00003544024	102541501	102541662
ENSE00003574676	102539606	102539726
ENSE00003582097	102540015	102540091
ENSE00003656273	102537919	102538525
ENSE00003689559	102541093	102541303
ENSE00003819153	102566997	102567083
ENSE00003822796	102568010	102568184
ENSE00003824147	102569835	102569924

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 96.39.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lower esophagus mucosa	UBERON:0035834	96.39	gold quality
granulocyte	CL:0000094	96.17	gold quality
stromal cell of endometrium	CL:0002255	95.66	gold quality
mucosa of stomach	UBERON:0001199	94.50	gold quality
right ovary	UBERON:0002118	94.45	gold quality
right uterine tube	UBERON:0001302	94.06	gold quality
tonsil	UBERON:0002372	93.92	gold quality
primary visual cortex	UBERON:0002436	93.90	gold quality
hindlimb stylopod muscle	UBERON:0004252	93.75	gold quality
superior frontal gyrus	UBERON:0002661	93.74	gold quality
blood	UBERON:0000178	93.56	gold quality
right lobe of thyroid gland	UBERON:0001119	93.40	gold quality
vagina	UBERON:0000996	93.38	gold quality
uterine cervix	UBERON:0000002	93.36	gold quality
right coronary artery	UBERON:0001625	93.29	gold quality
endocervix	UBERON:0000458	93.15	gold quality
fundus of stomach	UBERON:0001160	93.09	gold quality
ganglionic eminence	UBERON:0004023	92.69	gold quality
thyroid gland	UBERON:0002046	92.68	gold quality
cortical plate	UBERON:0005343	92.67	gold quality
right hemisphere of cerebellum	UBERON:0014890	92.60	gold quality
cerebellum	UBERON:0002037	92.58	gold quality
left lobe of thyroid gland	UBERON:0001120	92.55	gold quality
spleen	UBERON:0002106	92.54	gold quality
cerebellar cortex	UBERON:0002129	92.51	gold quality
ovary	UBERON:0000992	92.47	gold quality
sural nerve	UBERON:0015488	92.42	gold quality
cerebellar hemisphere	UBERON:0002245	92.38	gold quality
fallopian tube	UBERON:0003889	92.38	gold quality
ectocervix	UBERON:0012249	92.17	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

63 targeting POLR2J3, 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-7110-3P	100.00	73.18	2486
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4487	99.96	64.58	1252
HSA-MIR-4302	99.89	67.94	1187
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-3151-5P	99.86	63.83	1069
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-3934-5P	99.67	64.04	846
HSA-MIR-6762-3P	99.66	66.94	1188
HSA-MIR-10394-5P	99.65	66.83	1852
HSA-MIR-1205	99.65	66.76	1826
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-4756-3P	99.62	66.30	1319
HSA-MIR-1249-5P	99.61	66.55	2049
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-4762-3P	99.43	69.72	2363
HSA-MIR-128-1-5P	99.33	60.46	332
HSA-MIR-128-2-5P	99.33	60.83	311
HSA-MIR-3176	99.25	64.35	954
HSA-MIR-3922-3P	99.25	64.96	1136
HSA-MIR-330-5P	98.73	67.63	1788
HSA-MIR-12114	98.70	63.45	730
HSA-MIR-7977	98.65	66.18	2590
HSA-MIR-7155-5P	98.65	66.14	1290
HSA-MIR-1301-3P	98.64	68.27	1071
HSA-MIR-5047	98.64	68.62	1035

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

DNA-directed RNA polymerase II subunit RPB11-b2 — Q9H1A7 (reviewed: Q9H1A7)

Alternative names: DNA-directed RNA polymerase II subunit J3

All UniProt accessions (7): A0A0B4J1Z8, A0A0B4J2F8, E2QRJ6, E7EP90, Q9H1A7, E7EWC6, F8WF84

UniProt curated annotations — full annotation on UniProt →

Function. DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB11 is part of the core element with the central large cleft.

Subunit / interactions. Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits.

Subcellular location. Nucleus.

Similarity. Belongs to the archaeal Rpo11/eukaryotic RPB11/RPC19 RNA polymerase subunit family.

RefSeq proteins (0): (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR008193	RNA_pol_Rpb11_13-16kDa_CS	Conserved_site
IPR009025	RBP11-like_dimer	Domain
IPR022905	Rpo11-like	Family
IPR036603	RBP11-like	Homologous_superfamily
IPR037685	RBP11	Family

Pfam: PF13656

UniProt features (2 total): chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H1A7-F1	92.86	0.79

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 60 (showing top): KEGG_HUNTINGTONS_DISEASE, KEGG_PURINE_METABOLISM, GOCC_RNA_POLYMERASE_COMPLEX, ACEVEDO_LIVER_CANCER_UP, GOCC_TRANSFERASE_COMPLEX_TRANSFERRING_PHOSPHORUS_CONTAINING_GROUPS, GOCC_TRANSFERASE_COMPLEX, KEGG_RNA_POLYMERASE, GOMF_PROTEIN_DIMERIZATION_ACTIVITY, GOCC_RNA_POLYMERASE_II_CORE_COMPLEX, GOMF_RNA_POLYMERASE_ACTIVITY, GOMF_TRANSFERASE_ACTIVITY_TRANSFERRING_PHOSPHORUS_CONTAINING_GROUPS, PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_UP, GOMF_CATALYTIC_ACTIVITY_ACTING_ON_RNA, DIDO1_TARGET_GENES, SKIL_TARGET_GENES

GO Biological Process (2): transcription by RNA polymerase II (GO:0006366), DNA-templated transcription (GO:0006351)

GO Molecular Function (4): DNA binding (GO:0003677), DNA-directed RNA polymerase activity (GO:0003899), protein dimerization activity (GO:0046983), protein binding (GO:0005515)

GO Cellular Component (4): RNA polymerase II, core complex (GO:0005665), DNA-directed RNA polymerase complex (GO:0000428), nucleus (GO:0005634), nuclear DNA-directed RNA polymerase complex (GO:0055029)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA biosynthetic process	2
DNA-templated transcription	1
gene expression	1
nucleic acid binding	1
5’-3’ RNA polymerase activity	1
protein binding	1
binding	1
RNA polymerase II, holoenzyme	1
nuclear DNA-directed RNA polymerase complex	1
RNA polymerase complex	1
intracellular membrane-bounded organelle	1
DNA-directed RNA polymerase complex	1
nucleoplasm	1
nuclear protein-containing complex	1

Protein interactions and networks

STRING

1094 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
POLR2J3	POLR2L	P52436	783
POLR2J3	POLR2D	O15514	777
POLR2J3	POLR2C	P19387	760
POLR2J3	POLR2G	P52433	748
POLR2J3	POLR2F	P41584	675
POLR2J3	POLR2E	P19388	671
POLR2J3	POLR2B	P30876	619
POLR2J3	SPDYE2	Q495Y8	583
POLR2J3	A0A087WWV3	A0A087WWV3	570
POLR2J3	POLR2A	P24928	539
POLR2J3	POLR2H	P52434	408
POLR2J3	POLR3K	Q9Y2Y1	357
POLR2J3	UQCRHL	A0A096LP55	354
POLR2J3	MLLT1	Q03111	350
POLR2J3	PRKRIP1	Q9H875	338

IntAct

20 interactions, top by confidence:

A	B	Type	Score
TRAF4	POLR2J3	psi-mi:“MI:0915”(physical association)	0.560
POLR2J3	SATB2	psi-mi:“MI:0915”(physical association)	0.560
TTC23	POLR2J3	psi-mi:“MI:0915”(physical association)	0.560
ATPAF2	POLR2J3	psi-mi:“MI:0915”(physical association)	0.560
POLR1C	POLR2J3	psi-mi:“MI:0915”(physical association)	0.560
VPS37C	POLR2J3	psi-mi:“MI:0915”(physical association)	0.560
LIN28A	AGPS	psi-mi:“MI:0914”(association)	0.350
TRAF4	POLR2J3	psi-mi:“MI:0915”(physical association)	0.000
ATPAF2	POLR2J3	psi-mi:“MI:0915”(physical association)	0.000
POLR1C	POLR2J3	psi-mi:“MI:0915”(physical association)	0.000
VPS37C	POLR2J3	psi-mi:“MI:0915”(physical association)	0.000
SATB2	POLR2J3	psi-mi:“MI:0915”(physical association)	0.000
TTC23	POLR2J3	psi-mi:“MI:0915”(physical association)	0.000
POLR2J3	POLR1C	psi-mi:“MI:0915”(physical association)	0.000

ESM2 similar proteins: A1D5Z0, A6QLJ3, A9S3D3, B0XZZ2, B3RXR7, B6QW35, B9RUN8, C5DWG7, C5Z3W1, F4JWP9, O08740, O42130, O42131, O46374, P0DPB6, P11388, P15348, P28000, P34617, P38902, P41515, P41516, P52435, P87123, P97304, Q01320, Q02880, Q09177, Q1RMG8, Q23670, Q32P79, Q38859, Q4WYV0, Q54HL6, Q60SM4, Q64399, Q64511, Q6DRI4, Q7PVQ9, Q86JJ5

Diamond homologs: A0B533, A4FZS6, A4YHV0, A6URP9, A6VIQ1, A9A836, B0R4B1, B1L7Q7, B6YTH7, B8YB62, C3MRD1, C3MXM0, C3MZG6, C3N7I8, C3NFY8, C4KIP6, C5A5J3, C6A1R5, O08740, O30032, P28000, P34476, P38902, P46217, P52435, P57671, P87123, Q32P79, Q38859, Q3INY0, Q46C10, Q5JE88, Q5UQD9, Q60SM4, Q61IX2, Q6M0K9, Q74MN9, Q7PVQ9, Q86JJ5, Q8PVT0

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
POLR2J3	“form complex”	“RNA Polymerase II”	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

3325 predictions. Top by Δscore:

Variant	Effect	Δscore
7:102539747:C:CT	acceptor_gain	1.0000
7:102539749:C:CT	acceptor_gain	1.0000
7:102539751:C:CT	acceptor_gain	1.0000
7:102540010:CCTAC:C	donor_loss	1.0000
7:102540012:TA:T	donor_loss	1.0000
7:102540013:A:C	donor_loss	1.0000
7:102540014:C:CA	donor_loss	1.0000
7:102540014:CCTTG:C	donor_gain	1.0000
7:102540090:CC:C	acceptor_gain	1.0000
7:102540091:CC:C	acceptor_gain	1.0000
7:102540092:C:CC	acceptor_gain	1.0000
7:102541301:TGG:T	acceptor_gain	1.0000
7:102541304:C:CC	acceptor_gain	1.0000
7:102541498:CAC:C	donor_loss	1.0000
7:102541499:A:AC	donor_gain	1.0000
7:102541499:A:T	donor_loss	1.0000
7:102541500:C:CC	donor_gain	1.0000
7:102541500:C:CG	donor_loss	1.0000
7:102541516:C:CT	donor_gain	1.0000
7:102541517:C:CT	donor_gain	1.0000
7:102541658:GGCAG:G	acceptor_gain	1.0000
7:102541659:GCAG:G	acceptor_gain	1.0000
7:102541660:CAG:C	acceptor_gain	1.0000
7:102541660:CAGC:C	acceptor_gain	1.0000
7:102541661:AG:A	acceptor_gain	1.0000
7:102541663:C:CC	acceptor_gain	1.0000
7:102543519:ACTC:A	donor_loss	1.0000
7:102543523:A:AC	donor_gain	1.0000
7:102543523:AC:A	donor_gain	1.0000
7:102543524:C:CA	donor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1013944486 (7:102572748 A>C,G,T), RS1019491181 (7:102572879 C>G,T), RS10248669 (7:102572697 A>C,T), RS1043384212 (7:102571972 A>G), RS1055533022 (7:102566765 C>G,T), RS111641325 (7:102571865 T>C), RS111789112 (7:102572587 A>C,G), RS112662161 (7:102572292 G>A), RS113657563 (7:102574164 C>T), RS11487073 (7:102572565 C>T), RS11557255 (7:102569885 A>G,T), RS1156253523 (7:102573084 G>A,T), RS1156642132 (7:102570031 T>C), RS1156662993 (7:102568478 G>A), RS1156800279 (7:102572396 G>C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sotorasib	affects cotreatment, increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
methacrylaldehyde	affects cotreatment, increases expression	1
di-n-butylphosphoric acid	affects expression	1
2-palmitoylglycerol	increases expression	1
trametinib	affects cotreatment, increases expression	1
MT19c compound	decreases expression	1
NVP-BKM120	affects cotreatment, increases expression	1
Temozolomide	decreases expression	1
Acrolein	affects cotreatment, increases expression	1
Cisplatin	decreases expression	1
Niclosamide	decreases expression	1
Ozone	increases expression, affects cotreatment	1
Smoke	decreases expression	1
Cadmium Chloride	increases expression	1

Clinical trials (associated diseases)

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