Human Gene POLR1B (ENST00000263331.10_4) from GENCODE V47lift37
  Description: RNA polymerase I subunit B, transcript variant 1 (from RefSeq NM_019014.6)
Gencode Transcript: ENST00000263331.10_4
Gencode Gene: ENSG00000125630.16_14
Transcript (Including UTRs)
   Position: hg19 chr2:113,300,042-113,337,395 Size: 37,354 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr2:113,300,072-113,333,306 Size: 33,235 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:113,300,042-113,337,395)mRNA (may differ from genome)Protein (1135 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RPA2_HUMAN
DESCRIPTION: RecName: Full=DNA-directed RNA polymerase I subunit RPA2; Short=RNA polymerase I subunit 2; EC=2.7.7.6; AltName: Full=DNA-directed RNA polymerase I 135 kDa polypeptide; Short=RPA135;
FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest core component of RNA polymerase I which synthesizes ribosomal RNA precursors. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol I is composed of mobile elements and RPA2 is part of the core element with the central large cleft and probably a clamp element that moves to open and close the cleft (By similarity).
CATALYTIC ACTIVITY: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).
SUBUNIT: Component of the RNA polymerase I (Pol I) complex consisting of at least 13 subunits (By similarity).
SUBCELLULAR LOCATION: Nucleus, nucleolus.
SIMILARITY: Belongs to the RNA polymerase beta chain family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 10.81 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 142.27 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -7.7030-0.257 Picture PostScript Text
3' UTR -1170.204089-0.286 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR015712 - DNA-dir_RNA_pol_su2
IPR007120 - DNA-dir_RNA_pol_su2_6
IPR007121 - RNA_pol_bsu_CS
IPR007644 - RNA_pol_bsu_protrusion
IPR009674 - RNA_pol_Rpa2-specific
IPR007642 - RNA_pol_Rpb2_2
IPR007645 - RNA_pol_Rpb2_3
IPR007647 - RNA_pol_Rpb2_5
IPR007641 - RNA_pol_Rpb2_7

Pfam Domains:
PF00562 - RNA polymerase Rpb2, domain 6
PF04560 - RNA polymerase Rpb2, domain 7
PF04561 - RNA polymerase Rpb2, domain 2
PF04563 - RNA polymerase beta subunit
PF04565 - RNA polymerase Rpb2, domain 3
PF06883 - RNA polymerase I, Rpa2 specific domain

SCOP Domains:
81296 - E set domains
64484 - beta and beta-prime subunits of DNA dependent RNA-polymerase
82919 - Zn-finger domain of Sec23/24

ModBase Predicted Comparative 3D Structure on Q9H9Y6
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details  Gene Details 
Gene SorterGene Sorter  Gene Sorter 
 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0016779 nucleotidyltransferase activity
GO:0032549 ribonucleoside binding
GO:0046872 metal ion binding
GO:0001054 RNA polymerase I activity

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006361 transcription initiation from RNA polymerase I promoter
GO:0006363 termination of RNA polymerase I transcription
GO:0007566 embryo implantation
GO:0009303 rRNA transcription
GO:0017126 nucleologenesis
GO:0045815 positive regulation of gene expression, epigenetic

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005736 DNA-directed RNA polymerase I complex
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AK128044 - Homo sapiens cDNA FLJ46164 fis, clone TESTI4002799, highly similar to DNA-directed RNA polymerase I 135 kDa polypeptide (EC 2.7.7.6).
AK302814 - Homo sapiens cDNA FLJ58985 complete cds, highly similar to DNA-directed RNA polymerase I 135 kDa polypeptide (EC 2.7.7.6).
BX647360 - Homo sapiens mRNA; cDNA DKFZp686M1462 (from clone DKFZp686M1462).
BC110833 - Homo sapiens polymerase (RNA) I polypeptide B, 128kDa, mRNA (cDNA clone MGC:131780 IMAGE:6053210), complete cds.
BC150139 - Homo sapiens cDNA clone IMAGE:40108504.
LF205888 - JP 2014500723-A/13391: Polycomb-Associated Non-Coding RNAs.
AK294027 - Homo sapiens cDNA FLJ61223 complete cds, highly similar to DNA-directed RNA polymerase I 135 kDa polypeptide (EC 2.7.7.6).
AK301178 - Homo sapiens cDNA FLJ53412 complete cds, highly similar to DNA-directed RNA polymerase I 135 kDa polypeptide (EC 2.7.7.6).
AK001678 - Homo sapiens cDNA FLJ10816 fis, clone NT2RP4000997, highly similar to DNA-DIRECTED RNA POLYMERASE I 135 KD POLYPEPTIDE (EC 2.7.7.6).
AK022533 - Homo sapiens cDNA FLJ12471 fis, clone NT2RM1000894, highly similar to DNA-DIRECTED RNA POLYMERASE I 135 KD POLYPEPTIDE (EC 2.7.7.6).
BX647683 - Homo sapiens mRNA; cDNA DKFZp686N05112 (from clone DKFZp686N05112).
KJ904911 - Synthetic construct Homo sapiens clone ccsbBroadEn_14305 POLR1B gene, encodes complete protein.
LF349421 - JP 2014500723-A/156924: Polycomb-Associated Non-Coding RNAs.
LF349428 - JP 2014500723-A/156931: Polycomb-Associated Non-Coding RNAs.
LF349429 - JP 2014500723-A/156932: Polycomb-Associated Non-Coding RNAs.
LF349430 - JP 2014500723-A/156933: Polycomb-Associated Non-Coding RNAs.
JD404329 - Sequence 385353 from Patent EP1572962.
JD559752 - Sequence 540776 from Patent EP1572962.
JD334103 - Sequence 315127 from Patent EP1572962.
JD219481 - Sequence 200505 from Patent EP1572962.
JD463363 - Sequence 444387 from Patent EP1572962.
AK022890 - Homo sapiens cDNA FLJ12828 fis, clone NT2RP2002993, highly similar to DNA-DIRECTED RNA POLYMERASE I 135 KD POLYPEPTIDE (EC 2.7.7.6).
JD164305 - Sequence 145329 from Patent EP1572962.
BC096748 - Homo sapiens polymerase (RNA) I polypeptide B, 128kDa, mRNA (cDNA clone IMAGE:5295769), partial cds.
BC004882 - Homo sapiens polymerase (RNA) I polypeptide B, 128kDa, mRNA (cDNA clone IMAGE:3833619), partial cds.
BC073857 - Homo sapiens polymerase (RNA) I polypeptide B, 128kDa, mRNA (cDNA clone IMAGE:3867133), partial cds.
JD328062 - Sequence 309086 from Patent EP1572962.
JD063440 - Sequence 44464 from Patent EP1572962.
JD136733 - Sequence 117757 from Patent EP1572962.
AK025574 - Homo sapiens cDNA: FLJ21921 fis, clone HEP04058.
JD087750 - Sequence 68774 from Patent EP1572962.
LF349435 - JP 2014500723-A/156938: Polycomb-Associated Non-Coding RNAs.
JD494394 - Sequence 475418 from Patent EP1572962.
JD221525 - Sequence 202549 from Patent EP1572962.
JD378598 - Sequence 359622 from Patent EP1572962.
LF349436 - JP 2014500723-A/156939: Polycomb-Associated Non-Coding RNAs.
LF349437 - JP 2014500723-A/156940: Polycomb-Associated Non-Coding RNAs.
LF349438 - JP 2014500723-A/156941: Polycomb-Associated Non-Coding RNAs.
AK172817 - Homo sapiens cDNA FLJ23978 fis, clone HEP20708, highly similar to DNA-directed RNA polymerase I 135 kDa polypeptide (EC 2.7.7.6).
LF349439 - JP 2014500723-A/156942: Polycomb-Associated Non-Coding RNAs.
JD101325 - Sequence 82349 from Patent EP1572962.
JD351514 - Sequence 332538 from Patent EP1572962.
JD046463 - Sequence 27487 from Patent EP1572962.
JD302535 - Sequence 283559 from Patent EP1572962.
JD124003 - Sequence 105027 from Patent EP1572962.
LF349440 - JP 2014500723-A/156943: Polycomb-Associated Non-Coding RNAs.
JD564801 - Sequence 545825 from Patent EP1572962.
JD260216 - Sequence 241240 from Patent EP1572962.
JD082627 - Sequence 63651 from Patent EP1572962.
JD268955 - Sequence 249979 from Patent EP1572962.
JD243331 - Sequence 224355 from Patent EP1572962.
JD358788 - Sequence 339812 from Patent EP1572962.
JD266481 - Sequence 247505 from Patent EP1572962.
JD358825 - Sequence 339849 from Patent EP1572962.
JD266846 - Sequence 247870 from Patent EP1572962.
JD044249 - Sequence 25273 from Patent EP1572962.
JD135266 - Sequence 116290 from Patent EP1572962.
JD043215 - Sequence 24239 from Patent EP1572962.
JD055900 - Sequence 36924 from Patent EP1572962.
JD362692 - Sequence 343716 from Patent EP1572962.
JD476981 - Sequence 458005 from Patent EP1572962.
JD549050 - Sequence 530074 from Patent EP1572962.
JD202044 - Sequence 183068 from Patent EP1572962.
JD501496 - Sequence 482520 from Patent EP1572962.
JD449247 - Sequence 430271 from Patent EP1572962.
JD254936 - Sequence 235960 from Patent EP1572962.
JD454102 - Sequence 435126 from Patent EP1572962.
JD376025 - Sequence 357049 from Patent EP1572962.
JD497719 - Sequence 478743 from Patent EP1572962.
JD542660 - Sequence 523684 from Patent EP1572962.
JD246645 - Sequence 227669 from Patent EP1572962.
JD323785 - Sequence 304809 from Patent EP1572962.
JD496938 - Sequence 477962 from Patent EP1572962.
JD274588 - Sequence 255612 from Patent EP1572962.
JD274589 - Sequence 255613 from Patent EP1572962.
JD178815 - Sequence 159839 from Patent EP1572962.
JD092488 - Sequence 73512 from Patent EP1572962.
JD559647 - Sequence 540671 from Patent EP1572962.
JD201249 - Sequence 182273 from Patent EP1572962.
JD430105 - Sequence 411129 from Patent EP1572962.
JD557288 - Sequence 538312 from Patent EP1572962.
JD169112 - Sequence 150136 from Patent EP1572962.
JD041127 - Sequence 22151 from Patent EP1572962.
JD320598 - Sequence 301622 from Patent EP1572962.
JD517900 - Sequence 498924 from Patent EP1572962.
JD219962 - Sequence 200986 from Patent EP1572962.
JD283343 - Sequence 264367 from Patent EP1572962.
JD279083 - Sequence 260107 from Patent EP1572962.
JD222856 - Sequence 203880 from Patent EP1572962.
JD375983 - Sequence 357007 from Patent EP1572962.
JD497643 - Sequence 478667 from Patent EP1572962.
JD542520 - Sequence 523544 from Patent EP1572962.
JD412650 - Sequence 393674 from Patent EP1572962.
JD512572 - Sequence 493596 from Patent EP1572962.
JD118065 - Sequence 99089 from Patent EP1572962.
JD287028 - Sequence 268052 from Patent EP1572962.
JD251147 - Sequence 232171 from Patent EP1572962.
JD114431 - Sequence 95455 from Patent EP1572962.
JD363245 - Sequence 344269 from Patent EP1572962.
JD425377 - Sequence 406401 from Patent EP1572962.
JD482702 - Sequence 463726 from Patent EP1572962.
JD493394 - Sequence 474418 from Patent EP1572962.
JD366479 - Sequence 347503 from Patent EP1572962.
JD517640 - Sequence 498664 from Patent EP1572962.
AL355692 - Homo sapiens EST from clone 937911, 5' end.
MA584998 - JP 2018138019-A/156924: Polycomb-Associated Non-Coding RNAs.
MA585005 - JP 2018138019-A/156931: Polycomb-Associated Non-Coding RNAs.
MA585006 - JP 2018138019-A/156932: Polycomb-Associated Non-Coding RNAs.
MA585007 - JP 2018138019-A/156933: Polycomb-Associated Non-Coding RNAs.
MA585012 - JP 2018138019-A/156938: Polycomb-Associated Non-Coding RNAs.
MA585013 - JP 2018138019-A/156939: Polycomb-Associated Non-Coding RNAs.
MA585014 - JP 2018138019-A/156940: Polycomb-Associated Non-Coding RNAs.
MA585015 - JP 2018138019-A/156941: Polycomb-Associated Non-Coding RNAs.
MA585016 - JP 2018138019-A/156942: Polycomb-Associated Non-Coding RNAs.
MA585017 - JP 2018138019-A/156943: Polycomb-Associated Non-Coding RNAs.
MA441465 - JP 2018138019-A/13391: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_arfPathway - Tumor Suppressor Arf Inhibits Ribosomal Biogenesis

Reactome (by CSHL, EBI, and GO)

Protein Q9H9Y6 (Reactome details) participates in the following event(s):

R-HSA-73865 Assembly of RNA Polymerase I Holoenzyme (human)
R-HSA-73757 Binding of RRN3 to RNA Polymerase I
R-HSA-5250947 B-WICH complex binds rDNA promoter
R-HSA-73758 Recruitment of Active RNA Polymerase I to SL1:phos.UBF-1:rDNA Promoter
R-HSA-74994 Polymerase I Transcription Complex/Nascent Pre rRNA Complex pauses at the TTF-I:Sal Box
R-HSA-73769 Loss of Rrn3 from RNA Polymerase I promoter escape complex
R-HSA-74992 Dissociation of PTRF:Polymerase I/Nascent Pre rRNA Complex:TTF-I:Sal Box
R-HSA-5250930 B-WICH recruits histone acetyltransferases
R-HSA-74993 PTRF Binds the Polymerase I Transcription Complex/Nascent Pre rRNA Complex paused at the TTF-I:Sal Box
R-HSA-74986 Elongation of pre-rRNA transcript
R-HSA-427366 Transcription of intergenic spacer of the rRNA gene
R-HSA-5250938 B-WICH:histone acetyltransferase acetylates histone H3 at lysine-9
R-HSA-73762 RNA Polymerase I Transcription Initiation
R-HSA-5250924 B-WICH complex positively regulates rRNA expression
R-HSA-73854 RNA Polymerase I Promoter Clearance
R-HSA-73863 RNA Polymerase I Transcription Termination
R-HSA-73772 RNA Polymerase I Promoter Escape
R-HSA-5250913 Positive epigenetic regulation of rRNA expression
R-HSA-73864 RNA Polymerase I Transcription
R-HSA-73777 RNA Polymerase I Chain Elongation
R-HSA-427413 NoRC negatively regulates rRNA expression
R-HSA-212165 Epigenetic regulation of gene expression
R-HSA-74160 Gene expression (Transcription)
R-HSA-5250941 Negative epigenetic regulation of rRNA expression

-  Other Names for This Gene
  Alternate Gene Symbols: B7Z6Y7, B7Z823, ENST00000263331.1, ENST00000263331.2, ENST00000263331.3, ENST00000263331.4, ENST00000263331.5, ENST00000263331.6, ENST00000263331.7, ENST00000263331.8, ENST00000263331.9, F5GZX4, F8W898, NM_019014, Q2TAM4, Q585T5, Q6ZRR2, Q9H9D3, Q9H9Y6, RPA2_HUMAN, uc317hir.1, uc317hir.2
UCSC ID: ENST00000263331.10_4
RefSeq Accession: NM_019014.6
Protein: Q9H9Y6 (aka RPA2_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene POLR1B:
tcs (Treacher Collins Syndrome)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.