ID:RPB4_HUMAN DESCRIPTION: RecName: Full=DNA-directed RNA polymerase II subunit RPB4; Short=RNA polymerase II subunit B4; AltName: Full=DNA-directed RNA polymerase II subunit D; AltName: Full=RNA polymerase II 16 kDa subunit; Short=RPB16; 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. RPB4 is part of a subcomplex with RPB7 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA (By similarity). SUBUNIT: Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits. RPB4 and RPB7 form a subcomplex that protrudes from the 10-subunit Pol II core complex. SUBCELLULAR LOCATION: Nucleus. SIMILARITY: Belongs to the eukaryotic RPB4 RNA polymerase subunit family.
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.
ModBase Predicted Comparative 3D Structure on O15514
Front
Top
Side
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.
BC031919 - Homo sapiens cDNA clone IMAGE:4778940, partial cds. AK095788 - Homo sapiens cDNA FLJ38469 fis, clone FEBRA2021892. DQ589777 - Homo sapiens piRNA piR-56889, complete sequence. DQ583232 - Homo sapiens piRNA piR-50344, complete sequence. DQ590887 - Homo sapiens piRNA piR-57999, complete sequence. DQ592664 - Homo sapiens piRNA piR-59776, complete sequence. DQ586191 - Homo sapiens piRNA piR-53303, complete sequence. DQ600485 - Homo sapiens piRNA piR-38551, complete sequence. DQ582694 - Homo sapiens piRNA piR-32806, complete sequence. JD225368 - Sequence 206392 from Patent EP1572962. JD345683 - Sequence 326707 from Patent EP1572962. BC002958 - Homo sapiens, clone IMAGE:3543781, mRNA. BC010427 - Homo sapiens polymerase (RNA) II (DNA directed) polypeptide D, mRNA (cDNA clone IMAGE:2989498), complete cds. BC017205 - Homo sapiens polymerase (RNA) II (DNA directed) polypeptide D, mRNA (cDNA clone MGC:3610 IMAGE:3617979), complete cds. U85510 - Human RNA polymerase II subunit hsRPB4 mRNA, complete cds, and ribosomal protein S26 pseudogene, complete sequence. JD181525 - Sequence 162549 from Patent EP1572962. JD224801 - Sequence 205825 from Patent EP1572962. JD402946 - Sequence 383970 from Patent EP1572962. JD534975 - Sequence 515999 from Patent EP1572962. JD096838 - Sequence 77862 from Patent EP1572962. JD043921 - Sequence 24945 from Patent EP1572962. JD294433 - Sequence 275457 from Patent EP1572962. JD491123 - Sequence 472147 from Patent EP1572962. JD544467 - Sequence 525491 from Patent EP1572962. DQ592603 - Homo sapiens piRNA piR-59715, complete sequence. JD456170 - Sequence 437194 from Patent EP1572962. JD410535 - Sequence 391559 from Patent EP1572962. JD130065 - Sequence 111089 from Patent EP1572962. JD275403 - Sequence 256427 from Patent EP1572962. JD024365 - Sequence 5389 from Patent EP1572962. JD031136 - Sequence 12160 from Patent EP1572962. JD106814 - Sequence 87838 from Patent EP1572962. JD505229 - Sequence 486253 from Patent EP1572962. JD177610 - Sequence 158634 from Patent EP1572962. JD060851 - Sequence 41875 from Patent EP1572962. JD120421 - Sequence 101445 from Patent EP1572962. JD379389 - Sequence 360413 from Patent EP1572962. JD255815 - Sequence 236839 from Patent EP1572962. JD480540 - Sequence 461564 from Patent EP1572962. JD174737 - Sequence 155761 from Patent EP1572962. JD493305 - Sequence 474329 from Patent EP1572962. JD427120 - Sequence 408144 from Patent EP1572962. JD466783 - Sequence 447807 from Patent EP1572962. JD490404 - Sequence 471428 from Patent EP1572962. JD066315 - Sequence 47339 from Patent EP1572962. JD552739 - Sequence 533763 from Patent EP1572962. JD311360 - Sequence 292384 from Patent EP1572962. JD250107 - Sequence 231131 from Patent EP1572962. JD518520 - Sequence 499544 from Patent EP1572962. JD295869 - Sequence 276893 from Patent EP1572962. JD262375 - Sequence 243399 from Patent EP1572962. JD154244 - Sequence 135268 from Patent EP1572962. JD326158 - Sequence 307182 from Patent EP1572962. JD308465 - Sequence 289489 from Patent EP1572962. JD236515 - Sequence 217539 from Patent EP1572962. JD284491 - Sequence 265515 from Patent EP1572962. JD029663 - Sequence 10687 from Patent EP1572962. JD486015 - Sequence 467039 from Patent EP1572962. JD455771 - Sequence 436795 from Patent EP1572962. JD334926 - Sequence 315950 from Patent EP1572962. JD122162 - Sequence 103186 from Patent EP1572962. JD420689 - Sequence 401713 from Patent EP1572962. JD115227 - Sequence 96251 from Patent EP1572962. JD040775 - Sequence 21799 from Patent EP1572962. BC093795 - Homo sapiens polymerase (RNA) II (DNA directed) polypeptide D, mRNA (cDNA clone MGC:120830 IMAGE:7939640), complete cds. BC093797 - Homo sapiens polymerase (RNA) II (DNA directed) polypeptide D, mRNA (cDNA clone MGC:120832 IMAGE:7939642), complete cds. KJ891844 - Synthetic construct Homo sapiens clone ccsbBroadEn_01238 POLR2D gene, encodes complete protein. AB464041 - Synthetic construct DNA, clone: pF1KB7519, Homo sapiens POLR2D gene for polymerase (RNA) II (DNA directed) polypeptide D, without stop codon, in Flexi system.
Biochemical and Signaling Pathways
Reactome (by CSHL, EBI, and GO)
Protein O15514 (Reactome details) participates in the following event(s):
R-HSA-113429 Elongating transcript encounters a lesion in the template R-HSA-5578742 AGO1,2:small RNA complexes interact with chromatin R-HSA-6810238 RNA polymerase II binds initiation factors at promoter of snRNA gene (U1, U2, U4, U4atac, U5, U11, U12) R-HSA-112395 Abortive termination of elongation after arrest R-HSA-167459 Abortive termination of HIV-1 elongation after arrest (Tat-containing elongation complex) R-HSA-167481 Abortive termination of HIV-1 elongation after arrest R-HSA-6781840 ERCC6 binds stalled RNA Pol II R-HSA-109638 Recruitment of RNA Polymerase II Holoenzyme by TFIIF to the pol II promoter:TFIID:TFIIA:TFIIB complex R-HSA-73946 Abortive initiation R-HSA-75856 Abortive Initiation Before Second Transition R-HSA-75891 Abortive Initiation After Second Transition R-HSA-167468 Abortive HIV-1 Initiation After Second Transition R-HSA-167474 Abortive HIV-1 Initiation Before Second Transition R-HSA-167477 Abortive HIV-1 initiation after formation of the first phosphodiester bond R-HSA-113407 DSIF complex binds to RNA Pol II (hypophosphorylated) R-HSA-112383 Hypophosphorylation of RNA Pol II CTD by FCP1P protein R-HSA-167083 DSIF complex binds to RNA Pol II (hypophosphorylated) R-HSA-167072 Hypophosphorylation of RNA Pol II CTD by FCP1P protein R-HSA-9012315 ESR1:ESTG:P-TEFb recruited to paused RNA polymerase II on MYB gene R-HSA-9012319 p-TEFb phosphorylates serine 2 in RNA polymerase II CTD R-HSA-6782211 DNA polymerases delta, epsilon or kappa bind the TC-NER site R-HSA-6782204 5' incision of damaged DNA strand by ERCC1:ERCC4 in TC-NER R-HSA-6782224 3' incision by ERCC5 (XPG) in TC-NER R-HSA-6782227 Ligation of newly synthesized repair patch to incised DNA in TC-NER R-HSA-6782208 Repair DNA synthesis of ~27-30 bases long patch by POLD, POLE or POLK in TC-NER R-HSA-6810235 RPAP2 binds RNA polymerase II phosphorylated at serine-7 residues of heptad repeats in the C-terminal domain R-HSA-6810233 CDK7 phosphorylates serine-5 and serine-7 of heptad repeats in C-terminal domain of RNA polymerase II at snRNA promoter R-HSA-112379 Recruitment of elongation factors to form elongation complex R-HSA-112381 Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex R-HSA-113411 2-4 nt.backtracking of Pol II complex on the template leading to elongation pausing R-HSA-113412 Pol II elongation complex moves on the template as transcript elongates R-HSA-113414 7-14 nt. Backtracking of Pol II complex on the template leading to elongation arrest R-HSA-112385 Addition of nucleotides leads to transcript elongation R-HSA-112392 Resumption of elongation after recovery from pausing R-HSA-113413 TFIIS-mediated recovery of elongation from arrest R-HSA-112396 Separation of elongating transcript from template R-HSA-167150 Resumption of elongation of HIV-1 transcript after recovery from pausing R-HSA-167076 2-4 nt.backtracking of Pol II complex on the HIV-1 template leading to elongation pausing R-HSA-167077 Recruitment of elongation factors to form HIV-1 elongation complex R-HSA-167084 Hyperphosphorylation (Ser2) of RNA Pol II CTD by P-TEFb complex R-HSA-167282 2-4 nt.backtracking of Pol II complex on the HIV-1 template leading to elongation pausing R-HSA-167284 7-14 nt. Backtracking of Pol II complex on the HIV-1 template leading to elongation arrest R-HSA-167288 TFIIS-mediated recovery of HIV-1 elongation from arrest R-HSA-167292 Resumption of elongation of HIV-1 transcript after recovery from pausing R-HSA-167148 TFIIS-mediated recovery of elongation from arrest R-HSA-167090 7-14 nt. Backtracking of Pol II complex on the HIV-1 template leading to elongation arrest R-HSA-170706 Phosphorylation of NEFL by the P-TEFb(Cyclin T1:Cdk9) complex R-HSA-167191 Hyperphosphorylation (Ser2) of RNA Pol II CTD by the P-TEFb(Cyclin T1:Cdk9) complex R-HSA-167192 Pol II elongation complex moves on the HIV-1 template as transcript elongates R-HSA-167181 Addition of nucleotides leads to HIV-1 transcript elongation R-HSA-167197 Separation of elongating HIV-1 transcript from template R-HSA-170704 Phosphorylation of DSIF by the P-TEFb(Cyclin T1:Cdk9) complex R-HSA-167196 Recruitment of elongation factors to form HIV-1 elongation complex R-HSA-6781833 ERCC8 (CSA) binds stalled RNA Pol II R-HSA-72103 Formation of pre-mRNPs R-HSA-75080 Formation of AT-AC A complex R-HSA-72095 Internal Methylation of mRNA R-HSA-75873 Addition of Nucleotides 5 through 9 on the growing Transcript R-HSA-76576 Addition of nucleotides 10 and 11 on the growing transcript: Third Transition R-HSA-111264 Addition of nucleotides between position +11 and +30 R-HSA-75864 Newly Formed Phosphodiester Bond Stabilized and PPi Released R-HSA-75866 Nucleophillic Attack by 3'-hydroxyl Oxygen of nascent transcript on the Alpha Phosphate of NTP R-HSA-75095 Binding of TFIIE to the growing preinitiation complex R-HSA-75861 NTP Binds Active Site of RNA Polymerase II R-HSA-75862 Fall Back to Closed Pre-initiation Complex R-HSA-75949 RNA Polymerase II Promoter Opening: First Transition R-HSA-113430 Extrusion of 5'-end of 30 nt long transcript through the pore in Pol II complex R-HSA-77071 Phosphorylation (Ser5) of RNA pol II CTD R-HSA-167117 Addition of nucleotides 10 and 11 on the growing HIV-1 transcript: Third Transition R-HSA-167136 Addition of nucleotides 5 through 9 on the growing HIV-1 transcript R-HSA-167134 Newly formed phosphodiester bond stabilized and PPi released R-HSA-167098 Phosphorylation (Ser5) of RNA pol II CTD R-HSA-167111 Extrusion of 5'-end of 30 nt long HIV-1 transcript through the pore in Pol II complex R-HSA-167130 Nucleophillic attack by 3'-hydroxyl oxygen of nascent HIV-1 transcript on the Alpha phosphate of NTP R-HSA-167115 Addition of nucleotides between position +11 and +30 on HIV-1 transcript R-HSA-167118 NTP binds active site of RNA Polymerase II in HIV-1 open pre-initiation complex R-HSA-167484 Fall Back to Closed Pre-initiation Complex R-HSA-167097 HIV Promoter Opening: First Transition R-HSA-6803523 PTB and hnRNPA1 bind FGFR2 pre-mRNA to repress IIIb splicing and promote formation of FGFR2c mRNA R-HSA-6803527 ESRP1 and 2 bind FGFR2 pre-mRNA to promote FGFR2b maturation and expression R-HSA-113402 Formation of DSIF:NELF:early elongation complex R-HSA-167085 Formation of DSIF:NELF:HIV-1 early elongation complex R-HSA-77068 Activation of GT R-HSA-77069 RNA Polymerase II CTD (phosphorylated) binds to CE R-HSA-77073 SPT5 subunit of Pol II binds the RNA triphosphatase (RTP) R-HSA-77077 Capping complex formation R-HSA-156661 Formation of Exon Junction Complex R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage R-HSA-77095 Recognition and binding of the mRNA cap by the cap-binding complex R-HSA-77090 Methylation of GMP-cap by RNA Methyltransferase R-HSA-167089 Recognition and binding of the HIV-1 mRNA cap by the cap-binding complex R-HSA-167133 Activation of GT R-HSA-167128 RNA Polymerase II CTD (phosphorylated) binds to CE R-HSA-167153 SPT5 subunit of Pol II binds the RNA triphosphatase (RTP) R-HSA-6814885 CBCAP complex binds 7-methylguanosine cap of snRNA R-HSA-6797616 CCNK:CDK12 binds RNA Pol II at DNA repair genes R-HSA-6781867 ERCC8:DDB1:CUL4:RBX1 ubiquitinates ERCC6 and RNA Pol II R-HSA-72107 Formation of the Spliceosomal E complex R-HSA-72139 Formation of the active Spliceosomal C (B*) complex R-HSA-72124 Formation of the Spliceosomal A Complex R-HSA-72127 Formation of the Spliceosomal B Complex R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex R-HSA-75081 Formation of AT-AC B Complex R-HSA-75082 ATAC spliceosome mediated Lariat formation,5' splice site cleavage R-HSA-75079 Formation of AT-AC C complex R-HSA-75083 ATAC spliceosome mediated 3' splice site cleavage, exon ligation R-HSA-109639 Formation of the closed pre-initiation complex R-HSA-113409 Abortive termination of early transcription elongation by DSIF:NELF R-HSA-167087 Limited elongation of the HIV-1 transcript R-HSA-167478 Abortive termination of HIV-1 early transcription elongation by DSIF:NELF R-HSA-167147 Separation of abortive HIV-1 transcript from template R-HSA-77078 Hydrolysis of the 5'-end of the nascent transcript by the capping enzyme R-HSA-77081 Formation of the CE:GMP intermediate complex R-HSA-77085 Dissociation of transcript with 5'-GMP from GT R-HSA-77083 Transfer of GMP from the capping enzyme GT site to 5'-end of mRNA R-HSA-6782004 Assembly of the pre-incision complex in TC-NER R-HSA-6797606 CDK12 phosphorylates RNA Pol II CTD at DNA repair genes R-HSA-6782069 UVSSA:USP7 deubiquitinates ERCC6 R-HSA-6782131 RNA Pol II backtracking in TC-NER R-HSA-6782138 ERCC5 and RPA bind TC-NER site R-HSA-6782141 Binding of ERCC1:ERCC4 (ERCC1:XPF) to pre-incision complex in TC-NER R-HSA-674695 RNA Polymerase II Pre-transcription Events R-HSA-6781827 Transcription-Coupled Nucleotide Excision Repair (TC-NER) R-HSA-5578749 Transcriptional regulation by small RNAs R-HSA-6781823 Formation of TC-NER Pre-Incision Complex R-HSA-6807505 RNA polymerase II transcribes snRNA genes R-HSA-5617472 Activation of anterior HOX genes in hindbrain development during early embryogenesis R-HSA-167243 Tat-mediated HIV elongation arrest and recovery R-HSA-167287 HIV elongation arrest and recovery R-HSA-73857 RNA Polymerase II Transcription R-HSA-5696398 Nucleotide Excision Repair R-HSA-73779 RNA Polymerase II Transcription Pre-Initiation And Promoter Opening R-HSA-167162 RNA Polymerase II HIV Promoter Escape R-HSA-167161 HIV Transcription Initiation R-HSA-211000 Gene Silencing by RNA R-HSA-113418 Formation of the Early Elongation Complex R-HSA-167158 Formation of the HIV-1 Early Elongation Complex R-HSA-9018519 Estrogen-dependent gene expression R-HSA-72163 mRNA Splicing - Major Pathway R-HSA-5619507 Activation of HOX genes during differentiation R-HSA-203927 MicroRNA (miRNA) biogenesis R-HSA-452723 Transcriptional regulation of pluripotent stem cells R-HSA-5601884 PIWI-interacting RNA (piRNA) biogenesis R-HSA-6782135 Dual incision in TC-NER R-HSA-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER R-HSA-112382 Formation of RNA Pol II elongation complex R-HSA-75955 RNA Polymerase II Transcription Elongation R-HSA-167238 Pausing and recovery of Tat-mediated HIV elongation R-HSA-167152 Formation of HIV elongation complex in the absence of HIV Tat R-HSA-167290 Pausing and recovery of HIV elongation R-HSA-167200 Formation of HIV-1 elongation complex containing HIV-1 Tat R-HSA-167246 Tat-mediated elongation of the HIV-1 transcript R-HSA-167172 Transcription of the HIV genome R-HSA-74160 Gene expression (Transcription) R-HSA-73894 DNA Repair R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA R-HSA-72165 mRNA Splicing - Minor Pathway R-HSA-73776 RNA Polymerase II Promoter Escape R-HSA-75953 RNA Polymerase II Transcription Initiation R-HSA-76042 RNA Polymerase II Transcription Initiation And Promoter Clearance R-HSA-77075 RNA Pol II CTD phosphorylation and interaction with CE R-HSA-167160 RNA Pol II CTD phosphorylation and interaction with CE during HIV infection R-HSA-6803529 FGFR2 alternative splicing R-HSA-8851708 Signaling by FGFR2 IIIa TM R-HSA-167169 HIV Transcription Elongation R-HSA-8939211 ESR-mediated signaling R-HSA-72086 mRNA Capping R-HSA-72172 mRNA Splicing R-HSA-1266738 Developmental Biology R-HSA-6796648 TP53 Regulates Transcription of DNA Repair Genes R-HSA-162599 Late Phase of HIV Life Cycle R-HSA-8953854 Metabolism of RNA R-HSA-5654738 Signaling by FGFR2 R-HSA-1839126 FGFR2 mutant receptor activation R-HSA-167242 Abortive elongation of HIV-1 transcript in the absence of Tat R-HSA-9006931 Signaling by Nuclear Receptors R-HSA-3700989 Transcriptional Regulation by TP53 R-HSA-162587 HIV Life Cycle R-HSA-190236 Signaling by FGFR R-HSA-5655253 Signaling by FGFR2 in disease R-HSA-162582 Signal Transduction R-HSA-212436 Generic Transcription Pathway R-HSA-162906 HIV Infection R-HSA-9006934 Signaling by Receptor Tyrosine Kinases R-HSA-1226099 Signaling by FGFR in disease R-HSA-5663205 Infectious disease R-HSA-5663202 Diseases of signal transduction R-HSA-1643685 Disease
US Server
Sequence and Links to Tools and Databases 
Common Gene Haplotype Alleles 
