ID B3DL15_XENTR Unreviewed; 142 AA.
AC B3DL15; F7DHV3;
DT 22-JUL-2008, integrated into UniProtKB/TrEMBL.
DT 22-JUL-2008, sequence version 1.
DT 27-MAR-2024, entry version 101.
DE SubName: Full=DNA-directed RNA polymerase II subunit RPB4 {ECO:0000313|RefSeq:NP_001016248.1};
DE EC=2.7.7.6 {ECO:0000313|RefSeq:NP_001016248.1};
DE SubName: Full=Polymerase (RNA) II (DNA directed) polypeptide D {ECO:0000313|EMBL:AAI67273.1, ECO:0000313|Ensembl:ENSXETP00000006449};
GN Name=polr2d {ECO:0000313|EMBL:AAI67273.1,
GN ECO:0000313|Ensembl:ENSXETP00000006449,
GN ECO:0000313|RefSeq:NP_001016248.1,
GN ECO:0000313|Xenbase:XB-GENE-1004238};
OS Xenopus tropicalis (Western clawed frog) (Silurana tropicalis).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia;
OC Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Silurana.
OX NCBI_TaxID=8364 {ECO:0000313|EMBL:AAI67273.1};
RN [1] {ECO:0000313|RefSeq:NP_001016248.1}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=12454917; DOI=10.1002/dvdy.10174;
RA Klein S.L., Strausberg R.L., Wagner L., Pontius J., Clifton S.W.,
RA Richardson P.;
RT "Genetic and genomic tools for Xenopus research: The NIH Xenopus
RT initiative.";
RL Dev. Dyn. 225:384-391(2002).
RN [2] {ECO:0000313|EMBL:AAI67273.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Whole embryo {ECO:0000313|EMBL:AAI67273.1};
RG NIH - Xenopus Gene Collection (XGC) project;
RL Submitted (JUN-2008) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0000313|Ensembl:ENSXETP00000006449}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Nigerian {ECO:0000313|Ensembl:ENSXETP00000006449};
RX PubMed=20431018; DOI=10.1126/science.1183670;
RA Hellsten U., Harland R.M., Gilchrist M.J., Hendrix D., Jurka J.,
RA Kapitonov V., Ovcharenko I., Putnam N.H., Shu S., Taher L., Blitz I.L.,
RA Blumberg B., Dichmann D.S., Dubchak I., Amaya E., Detter J.C., Fletcher R.,
RA Gerhard D.S., Goodstein D., Graves T., Grigoriev I.V., Grimwood J.,
RA Kawashima T., Lindquist E., Lucas S.M., Mead P.E., Mitros T., Ogino H.,
RA Ohta Y., Poliakov A.V., Pollet N., Robert J., Salamov A., Sater A.K.,
RA Schmutz J., Terry A., Vize P.D., Warren W.C., Wells D., Wills A.,
RA Wilson R.K., Zimmerman L.B., Zorn A.M., Grainger R., Grammer T.,
RA Khokha M.K., Richardson P.M., Rokhsar D.S.;
RT "The genome of the Western clawed frog Xenopus tropicalis.";
RL Science 328:633-636(2010).
RN [4] {ECO:0000313|Ensembl:ENSXETP00000006449}
RP IDENTIFICATION.
RG Ensembl;
RL Submitted (JUN-2011) to UniProtKB.
RN [5] {ECO:0000313|RefSeq:NP_001016248.1}
RP IDENTIFICATION.
RG RefSeq;
RL Submitted (NOV-2023) to UniProtKB.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000256|ARBA:ARBA00004123}.
CC -!- SIMILARITY: Belongs to the eukaryotic RPB4 RNA polymerase subunit
CC family. {ECO:0000256|ARBA:ARBA00025724}.
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DR EMBL; BC167273; AAI67273.1; -; mRNA.
DR EMBL; BC167274; AAI67274.1; -; mRNA.
DR RefSeq; NP_001016248.1; NM_001016248.2.
DR STRING; 8364.ENSXETP00000014247; -.
DR PaxDb; 8364-ENSXETP00000006449; -.
DR Ensembl; ENSXETT00000006449; ENSXETP00000006449; ENSXETG00000002955.
DR GeneID; 549002; -.
DR KEGG; xtr:549002; -.
DR AGR; Xenbase:XB-GENE-1004238; -.
DR CTD; 5433; -.
DR Xenbase; XB-GENE-1004238; polr2d.
DR eggNOG; KOG2351; Eukaryota.
DR HOGENOM; CLU_110332_2_1_1; -.
DR OMA; TMRKFQS; -.
DR OrthoDB; 5477031at2759; -.
DR TreeFam; TF103039; -.
DR Reactome; R-XTR-113418; Formation of the Early Elongation Complex.
DR Reactome; R-XTR-5578749; Transcriptional regulation by small RNAs.
DR Reactome; R-XTR-674695; RNA Polymerase II Pre-transcription Events.
DR Reactome; R-XTR-6781823; Formation of TC-NER Pre-Incision Complex.
DR Reactome; R-XTR-6782135; Dual incision in TC-NER.
DR Reactome; R-XTR-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
DR Reactome; R-XTR-6796648; TP53 Regulates Transcription of DNA Repair Genes.
DR Reactome; R-XTR-6803529; FGFR2 alternative splicing.
DR Reactome; R-XTR-6807505; RNA polymerase II transcribes snRNA genes.
DR Reactome; R-XTR-72086; mRNA Capping.
DR Reactome; R-XTR-72165; mRNA Splicing - Minor Pathway.
DR Reactome; R-XTR-72203; Processing of Capped Intron-Containing Pre-mRNA.
DR Reactome; R-XTR-73776; RNA Polymerase II Promoter Escape.
DR Reactome; R-XTR-73779; RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
DR Reactome; R-XTR-75953; RNA Polymerase II Transcription Initiation.
DR Reactome; R-XTR-75955; RNA Polymerase II Transcription Elongation.
DR Reactome; R-XTR-76042; RNA Polymerase II Transcription Initiation And Promoter Clearance.
DR Reactome; R-XTR-77075; RNA Pol II CTD phosphorylation and interaction with CE.
DR Reactome; R-XTR-9018519; Estrogen-dependent gene expression.
DR Proteomes; UP000008143; Chromosome 5.
DR Bgee; ENSXETG00000002955; Expressed in 2-cell stage embryo and 12 other cell types or tissues.
DR GO; GO:0000428; C:DNA-directed RNA polymerase complex; IEA:UniProtKB-KW.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0000166; F:nucleotide binding; IEA:InterPro.
DR GO; GO:0006352; P:DNA-templated transcription initiation; IEA:InterPro.
DR GO; GO:0006366; P:transcription by RNA polymerase II; IEA:UniProt.
DR Gene3D; 1.20.1250.40; -; 1.
DR InterPro; IPR010997; HRDC-like_sf.
DR InterPro; IPR006590; RNA_pol_Rpb4/RPC9_core.
DR InterPro; IPR045222; Rpb4-like.
DR InterPro; IPR005574; Rpb4/RPC9.
DR InterPro; IPR038324; Rpb4/RPC9_sf.
DR PANTHER; PTHR21297; DNA-DIRECTED RNA POLYMERASE II; 1.
DR PANTHER; PTHR21297:SF0; DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4; 1.
DR Pfam; PF03874; RNA_pol_Rpb4; 1.
DR SMART; SM00657; RPOL4c; 1.
DR SUPFAM; SSF47819; HRDC-like; 1.
PE 2: Evidence at transcript level;
KW DNA-directed RNA polymerase {ECO:0000313|RefSeq:NP_001016248.1};
KW Nucleus {ECO:0000256|ARBA:ARBA00023242};
KW Reference proteome {ECO:0000313|Proteomes:UP000008143};
KW Transcription {ECO:0000313|RefSeq:NP_001016248.1}.
FT DOMAIN 24..141
FT /note="RNA polymerase Rpb4/RPC9 core"
FT /evidence="ECO:0000259|SMART:SM00657"
FT REGION 1..20
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 142 AA; 16290 MW; 46DB87C7FD85E99B CRC64;
MAAGGAEAHS GDPEEDASQL LFPKEFESAE TLLNSEVHML LEHRKQQNES AEEEQELSEV
FMKTLNYTAR FSRFKNRETI ASVRSLLLQK KLHRFELACL ANLCPETADE AKALIPSLEG
RFEEEELQQI LDDIQTKRSF QY
//
