POLR2B (RNA polymerase II subunit B)

Gene

• Entrez ID: 5431
• Gene name: RNA polymerase II subunit B
• Gene symbol: POLR2B
• Synonyms (NCBI Gene): POL2RB, RPB2, hRPB140
• Chromosome: 4
• Chromosome location: 4q12
• Summary: This gene encodes the second largest subunit of RNA polymerase II (Pol II), a DNA-dependent RNA polymerase that catalyzes the transcription of DNA into precursors of mRNA, snRNA and microRNA. This subunit and the largest subunit form opposite sides of the

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT023207	hsa-miR-124-3p	Proteomics;Microarray	18668037
MIRT028617	hsa-miR-30a-5p	Proteomics	18668040
MIRT040387	hsa-miR-615-3p	CLASH	23622248
MIRT037880	hsa-miR-455-3p	CLASH	23622248
MIRT2073335	hsa-miR-101	CLIP-seq
MIRT2073336	hsa-miR-3145-3p	CLIP-seq
MIRT2073337	hsa-miR-616	CLIP-seq
MIRT2073335	hsa-miR-101	CLIP-seq
MIRT2073337	hsa-miR-616	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000428	Component	DNA-directed RNA polymerase complex	IEA
GO:0000781	Component	Chromosome, telomeric region	IDA	24270157
GO:0001172	Process	RNA-templated transcription	IEA
GO:0003677	Function	DNA binding	IEA
GO:0003677	Function	DNA binding	TAS	1518060
GO:0003682	Function	Chromatin binding	IEA
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0003899	Function	DNA-directed RNA polymerase activity	IDA	9852112, 23748380
GO:0003899	Function	DNA-directed RNA polymerase activity	IEA
GO:0003899	Function	DNA-directed RNA polymerase activity	ISS
GO:0003968	Function	RNA-directed RNA polymerase activity	IDA	23395899
GO:0003968	Function	RNA-directed RNA polymerase activity	IEA
GO:0005515	Function	Protein binding	IPI	17998332
GO:0005634	Component	Nucleus	IDA	9852112
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005665	Component	RNA polymerase II, core complex	IBA
GO:0005665	Component	RNA polymerase II, core complex	IDA	9852112
GO:0006351	Process	DNA-templated transcription	IEA
GO:0006366	Process	Transcription by RNA polymerase II	IDA	9852112
GO:0008270	Function	Zinc ion binding	IEA
GO:0016020	Component	Membrane	HDA
GO:0016740	Function	Transferase activity	IEA
GO:0016779	Function	Nucleotidyltransferase activity	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0032549	Function	Ribonucleoside binding	IEA
GO:0034062	Function	5'-3' RNA polymerase activity	IEA
GO:0046872	Function	Metal ion binding	IEA

Other IDs

• MIM: 180661
• HGNC: 9188
• e!Ensembl: ENSG00000047315

Protein

• UniProt ID: P30876
• Protein name: DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) (3'-5' exoribonuclease) (EC 3.1.13.-) (DNA-directed RNA polymerase II 140 kDa polypeptide) (DNA-directed RNA polymerase II subunit B) (RNA polymerase II subunit 2) (RNA polymerase II subunit B2) (RN
• Protein function: Catalytic core component of RNA polymerase II (Pol II), a DNA-dependent RNA polymerase which synthesizes mRNA precursors and many functional non-coding RNAs using the four ribonucleoside triphosphates as substrates (By similarity) (PubMed:271936
• PDB: 5IY6, 5IY7, 5IY8, 5IY9, 5IYA, 5IYB, 5IYC, 5IYD, 6DRD, 6O9L, 6XRE, 7LBM, 9EHZ, 9EI1, 9EI3, 9EI4
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF04563	RNA_pol_Rpb2_1	38 → 442	RNA polymerase beta subunit	Family
  PF04561	RNA_pol_Rpb2_2	201 → 394	RNA polymerase Rpb2, domain 2	Domain
  PF04565	RNA_pol_Rpb2_3	468 → 532	RNA polymerase Rpb2, domain 3	Domain
  PF04566	RNA_pol_Rpb2_4	567 → 629	RNA polymerase Rpb2, domain 4	Domain
  PF04567	RNA_pol_Rpb2_5	653 → 700	RNA polymerase Rpb2, domain 5	Domain
  PF00562	RNA_pol_Rpb2_6	707 → 1080	RNA polymerase Rpb2, domain 6	Domain
  PF04560	RNA_pol_Rpb2_7	1082 → 1174	RNA polymerase Rpb2, domain 7	Domain

• Sequence:

  MYDADEDMQYDEDDDEITPDLWQEACWIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVE
  DAPPIDLQAEAQHASGEVEEPPRYLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRNLTY
  SAPLYVDITKTVIKEGEEQLQTQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLD
  PGGYFIINGSEKVLIAQEKMATNTVYVFAKKDSKYAYTGECRSCLENSSRPTSTIWVSML
  ARGGQGAKKSAIGQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEM
  VKPSLDEAFVIQEQNVALNFIGSRGAKPGVTKEKRIKYAKEVLQKEMLPHVGVSDFCETK
  KAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQ
  KFIDRGKDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLS
  HLRRLNSPIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSP
  ILEFLEEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSE
  VSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNNYSWQDLVASG
  VVEYIDTLEEETVMLAMTPDDLQEKEVAYCSTYTHCEIHPSMILGVCASIIPFPDHNQSP
  RNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIV
  AIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVFEKPTRETCQGM
  RHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELESTNRRYTKRDCSTFLRTSE
  TGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEG
  ITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDAVNVQKISNLLSDYGY
  HLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSR
  DGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANTRTHTYECRGC
  RNKTQISLVRMPYACKLLFQELMSMSIAPRMMSV

• Sequence length: 1174

Pathways

KEGG:

RNA polymerase
Nucleotide excision repair
Huntington disease

Reactome:

Formation of RNA Pol II elongation complex
Formation of the Early Elongation Complex
Formation of HIV-1 elongation complex containing HIV-1 Tat
Viral Messenger RNA Synthesis
MicroRNA (miRNA) biogenesis
Transcriptional regulation by small RNAs
RNA Polymerase II Pre-transcription Events
Formation of TC-NER Pre-Incision Complex
Transcription-Coupled Nucleotide Excision Repair (TC-NER)
Dual incision in TC-NER
Gap-filling DNA repair synthesis and ligation in TC-NER
TP53 Regulates Transcription of DNA Repair Genes
FGFR2 alternative splicing
RNA polymerase II transcribes snRNA genes
mRNA Capping
mRNA Splicing - Major Pathway
mRNA Splicing - Minor Pathway
Processing of Capped Intron-Containing Pre-mRNA
RNA Polymerase II Promoter Escape
RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
RNA Polymerase II Transcription Initiation
RNA Polymerase II Transcription Elongation
RNA Polymerase II Transcription Initiation And Promoter Clearance
RNA Pol II CTD phosphorylation and interaction with CE
Estrogen-dependent gene expression

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Esophageal atresia/tracheoesophageal fistula	Likely pathogenic	rs1723396043	RCV001172299	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
BREAST CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BREAST CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL HEART DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Age related macular degeneration	Age-related macular degeneration	BEFREE	23868022, 24235014		★☆☆☆☆ Found in Text Mining only
Asthma	Asthma	Pubtator	39217320	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	36367018	Associate	★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	27111221		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	27111221	Associate	★☆☆☆☆ Found in Text Mining only
Diabetic Nephropathies	Diabetic neuropathy	Pubtator	36482994	Associate	★☆☆☆☆ Found in Text Mining only
Keratitis	Keratitis	BEFREE	17507522		★☆☆☆☆ Found in Text Mining only