POLR2J2

Summary

POLR2J2 (RNA polymerase II subunit J2, HGNC:23208) is a protein-coding gene on chromosome 7q22.1, encoding DNA-directed RNA polymerase II subunit RPB11-b1 (Q9GZM3). 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 246721 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 11 total
• MANE Select transcript: NM_032959

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23208
Approved symbol	POLR2J2
Name	RNA polymerase II subunit J2
Location	7q22.1
Locus type	gene with protein product
Status	Approved
Aliases	RPB11b1
Ensembl gene	ENSG00000228049
Ensembl biotype	protein_coding
OMIM	609881
Entrez	246721

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000333432, ENST00000358438

RefSeq mRNA: 1 — MANE Select: NM_032959 NM_032959

CCDS: CCDS43627

Canonical transcript exons

ENST00000333432 — 4 exons

Exon	Start	End
ENSE00003655614	102668915	102669004
ENSE00003779240	102667090	102667264
ENSE00003978326	102671552	102671663
ENSE00003978327	102666046	102666163

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 86.52.

FANTOM5 (CAGE): breadth broad, TPM avg 1.4502 / max 24.2459, expressed in 756 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
85358	1.4502	756

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.52	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	79.84	gold quality
blood	UBERON:0000178	79.70	gold quality
stromal cell of endometrium	CL:0002255	76.93	gold quality
mucosa of transverse colon	UBERON:0004991	74.08	gold quality
sural nerve	UBERON:0015488	73.54	gold quality
monocyte	CL:0000576	73.47	gold quality
bone marrow cell	CL:0002092	73.05	gold quality
leukocyte	CL:0000738	72.99	gold quality
granulocyte	CL:0000094	72.67	gold quality
spleen	UBERON:0002106	72.41	gold quality
mucosa of stomach	UBERON:0001199	72.10	gold quality
calcaneal tendon	UBERON:0003701	71.44	gold quality
duodenum	UBERON:0002114	71.19	gold quality
small intestine Peyer’s patch	UBERON:0003454	70.82	gold quality
right lobe of thyroid gland	UBERON:0001119	70.79	gold quality
metanephros cortex	UBERON:0010533	70.36	gold quality
adrenal tissue	UBERON:0018303	70.29	gold quality
ventricular zone	UBERON:0003053	70.00	gold quality
vermiform appendix	UBERON:0001154	69.91	gold quality
cortex of kidney	UBERON:0001225	69.85	gold quality
small intestine	UBERON:0002108	69.81	gold quality
esophagus mucosa	UBERON:0002469	69.80	gold quality
left lobe of thyroid gland	UBERON:0001120	69.71	gold quality
liver	UBERON:0002107	69.71	gold quality
bone marrow	UBERON:0002371	69.27	gold quality
thyroid gland	UBERON:0002046	68.96	gold quality
transverse colon	UBERON:0001157	68.95	gold quality
lower esophagus mucosa	UBERON:0035834	68.92	gold quality
right adrenal gland cortex	UBERON:0035827	68.70	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.64

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

58 targeting POLR2J2, 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-6759-5P	99.99	66.54	785
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-6793-5P	99.97	65.95	758
HSA-MIR-4487	99.96	64.58	1252
HSA-MIR-4302	99.89	67.94	1187
HSA-MIR-7845-5P	99.88	64.88	771
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-1207-5P	99.49	69.11	2983
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-4763-3P	99.10	67.83	2649
HSA-MIR-6814-5P	99.03	66.68	1273
HSA-MIR-873-5P	98.84	66.90	1348
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

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	polr2j	ENSDARG00000035146
mus_musculus	Polr2j	ENSMUSG00000039771
rattus_norvegicus	Polr2j	ENSRNOG00000001430
drosophila_melanogaster	Polr2J	FBGN0032634
caenorhabditis_elegans		WBGENE00012187

Paralogs (3): POLR2J (ENSG00000005075), POLR1D (ENSG00000186184), POLR2J3 (ENSG00000285437)

Protein

Protein identifiers

DNA-directed RNA polymerase II subunit RPB11-b1 — Q9GZM3 (reviewed: Q9GZM3)

Alternative names: DNA-directed RNA polymerase II subunit J2

All UniProt accessions (2): Q9GZM3, A6NFM0

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.

Tissue specificity. Ubiquitously expressed.

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

Isoforms (2)

UniProt ID	Names	Canonical?
Q9GZM3-1	1, RPB11b1-alpha	yes
Q9GZM3-2	2, RPB11b1-beta

RefSeq proteins (1): NP_116581* (*=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 (3 total): chain 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9GZM3-F1	93.38	0.84

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 48 (showing top): LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, KEGG_HUNTINGTONS_DISEASE, KEGG_PURINE_METABOLISM, GOCC_RNA_POLYMERASE_COMPLEX, CAFFAREL_RESPONSE_TO_THC_24HR_5_DN, 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, GOMF_CATALYTIC_ACTIVITY_ACTING_ON_RNA, STK33_NOMO_DN, MIR616_5P

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

GO Molecular Function (3): DNA binding (GO:0003677), DNA-directed RNA polymerase activity (GO:0003899), protein dimerization activity (GO:0046983)

GO Cellular Component (3): RNA polymerase II, core complex (GO:0005665), DNA-directed RNA polymerase complex (GO:0000428), nucleus (GO:0005634)

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
RNA polymerase II, holoenzyme	1
nuclear DNA-directed RNA polymerase complex	1
RNA polymerase complex	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

982 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
POLR2J2	POLR2C	P19387	794
POLR2J2	POLR2L	P52436	790
POLR2J2	POLR2D	O15514	786
POLR2J2	POLR2G	P52433	754
POLR2J2	POLR2E	P19388	722
POLR2J2	POLR2F	P41584	702
POLR2J2	POLR2B	P30876	634
POLR2J2	SPDYE2	Q495Y8	582
POLR2J2	POLR2A	P24928	547
POLR2J2	A0A087WWV3	A0A087WWV3	544
POLR2J2	POLR2H	P52434	428
POLR2J2	POLR3K	Q9Y2Y1	353
POLR2J2	MLLT1	Q03111	350
POLR2J2	UQCRHL	A0A096LP55	349
POLR2J2	SPDYE1	Q8NFV5	348

IntAct

6 interactions, top by confidence:

A	B	Type	Score
POLR2J	POLR1C	psi-mi:“MI:0914”(association)	0.830
POLR2J	POLR2D	psi-mi:“MI:0914”(association)	0.730
LIN28A	AGPS	psi-mi:“MI:0914”(association)	0.350
POLR2J2	POLR2D	psi-mi:“MI:0914”(association)	0.350

BioGRID (27): POLR2J2 (Affinity Capture-RNA), POLR2J3 (Affinity Capture-RNA), POLR2J2 (Affinity Capture-RNA), POLR2J3 (Two-hybrid), POLR2J3 (Two-hybrid), POLR2J3 (Two-hybrid), POLR2J3 (Two-hybrid), POLR1C (Two-hybrid), ATPAF2 (Two-hybrid), POLR2J3 (Affinity Capture-RNA), POLR2J3 (Proximity Label-MS), RPAP2 (Affinity Capture-MS), POLR2M (Affinity Capture-MS), RPAP1 (Affinity Capture-MS), POLR2D (Affinity Capture-MS)

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
POLR2J2	“form complex”	“RNA Polymerase II”	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	8
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1069 predictions. Top by Δscore:

Variant	Effect	Δscore
7:102666169:CA:C	acceptor_gain	1.0000
7:102666170:A:AC	acceptor_gain	1.0000
7:102666170:A:C	acceptor_gain	1.0000
7:102666173:T:C	acceptor_gain	1.0000
7:102666173:T:TC	acceptor_gain	1.0000
7:102667273:C:CT	acceptor_gain	1.0000
7:102668908:AACTT:A	donor_loss	1.0000
7:102668909:ACTTA:A	donor_loss	1.0000
7:102668910:CTT:C	donor_loss	1.0000
7:102668911:TTA:T	donor_loss	1.0000
7:102668912:TA:T	donor_loss	1.0000
7:102668913:A:AC	donor_gain	1.0000
7:102668914:C:A	donor_loss	1.0000
7:102668914:C:CA	donor_gain	1.0000
7:102668914:C:CG	donor_gain	1.0000
7:102668914:CG:C	donor_gain	1.0000
7:102668914:CGA:C	donor_gain	1.0000
7:102668914:CGAT:C	donor_gain	1.0000
7:102668914:CGATT:C	donor_gain	1.0000
7:102669000:TGATC:T	acceptor_gain	1.0000
7:102669001:GATC:G	acceptor_gain	1.0000
7:102669002:ATC:A	acceptor_gain	1.0000
7:102669003:TC:T	acceptor_gain	1.0000
7:102669003:TCCTA:T	acceptor_loss	1.0000
7:102669004:CC:C	acceptor_gain	1.0000
7:102669004:CCT:C	acceptor_loss	1.0000
7:102669004:CCTAG:C	acceptor_loss	1.0000
7:102669005:C:CC	acceptor_gain	1.0000
7:102669006:T:G	acceptor_loss	1.0000
7:102671550:A:AC	donor_gain	1.0000

AlphaMissense

746 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:102667234:A:C	F57L	0.994
7:102667234:A:T	F57L	0.994
7:102667236:A:G	F57L	0.994
7:102667127:A:G	L93P	0.993
7:102667140:C:G	A89P	0.991
7:102667232:G:T	A58D	0.989
7:102667190:A:T	I72N	0.986
7:102668930:C:T	G42E	0.986
7:102668960:A:G	F32S	0.985
7:102667184:A:T	V74E	0.984
7:102667259:A:G	L49P	0.984
7:102667213:G:C	H64Q	0.982
7:102667213:G:T	H64Q	0.982
7:102671581:G:C	F7L	0.982
7:102671581:G:T	F7L	0.982
7:102671583:A:G	F7L	0.982
7:102667139:G:T	A89D	0.981
7:102667187:C:G	R73P	0.981
7:102667259:A:T	L49H	0.981
7:102667241:A:T	V55E	0.980
7:102668930:C:A	G42V	0.979
7:102667115:A:G	L97P	0.978
7:102668921:A:T	I45N	0.977
7:102668947:T:A	K36N	0.977
7:102668947:T:G	K36N	0.977
7:102667229:C:T	G59D	0.976
7:102667151:G:T	A85D	0.974
7:102667190:A:C	I72S	0.974
7:102668931:C:G	G42R	0.974
7:102668931:C:T	G42R	0.974

dbSNP variants (sampled 300 via entrez): RS1006631316 (7:102666314 C>G,T), RS1017049229 (7:102666375 C>T), RS10275702 (7:102671888 A>G,T), RS111627599 (7:102667500 T>C,G), RS111903153 (7:102671727 C>A,G,T), RS112146944 (7:102667797 GA>G), RS112553034 (7:102672741 T>G), RS113237397 (7:102671391 G>T), RS1156428702 (7:102673548 A>T), RS1156818658 (7:102672228 G>A), RS1157081514 (7:102667926 C>G,T), RS1157197534 (7:102671750 A>T), RS1157578893 (7:102669665 T>C), RS1157617644 (7:102665617 G>A), RS1157812084 (7:102666448 C>A)

Disease associations

OMIM: gene MIM:609881 | 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

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
GSK-J4	decreases expression	1
bisphenol F	affects cotreatment, increases expression	1
urushiol	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, increases expression	1
arsenite	decreases expression, increases abundance	1
sodium arsenite	increases abundance, decreases expression	1
cobaltous chloride	decreases expression	1
butyraldehyde	increases expression	1
avobenzone	decreases expression	1
antimonite	decreases expression, increases abundance	1
bisphenol S	increases expression, affects cotreatment	1
Temozolomide	decreases expression	1
Arsenic Trioxide	increases expression	1
Antimony Potassium Tartrate	increases abundance, decreases expression	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Endosulfan	increases expression	1
Hydralazine	affects cotreatment, increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Smoke	decreases expression	1
Dronabinol	decreases expression	1
Valproic Acid	affects cotreatment, increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Sodium Selenite	increases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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