Gene loci information

Transcript annotation

  • This transcript has been annotated as DNA-directed RNA polymerase II subunit RPB1.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_3 g303 g303.t1 TTS g303.t1 2626661 2626661
chr_3 g303 g303.t1 isoform g303.t1 2626913 2633157
chr_3 g303 g303.t1 exon g303.t1.exon1 2626913 2627090
chr_3 g303 g303.t1 cds g303.t1.CDS1 2626913 2627090
chr_3 g303 g303.t1 exon g303.t1.exon2 2627156 2627317
chr_3 g303 g303.t1 cds g303.t1.CDS2 2627156 2627317
chr_3 g303 g303.t1 exon g303.t1.exon3 2627376 2627500
chr_3 g303 g303.t1 cds g303.t1.CDS3 2627376 2627500
chr_3 g303 g303.t1 exon g303.t1.exon4 2627561 2627585
chr_3 g303 g303.t1 cds g303.t1.CDS4 2627561 2627585
chr_3 g303 g303.t1 exon g303.t1.exon5 2627658 2627678
chr_3 g303 g303.t1 cds g303.t1.CDS5 2627658 2627678
chr_3 g303 g303.t1 exon g303.t1.exon6 2627759 2627779
chr_3 g303 g303.t1 cds g303.t1.CDS6 2627759 2627779
chr_3 g303 g303.t1 exon g303.t1.exon7 2627846 2628027
chr_3 g303 g303.t1 cds g303.t1.CDS7 2627846 2628027
chr_3 g303 g303.t1 exon g303.t1.exon8 2628100 2628993
chr_3 g303 g303.t1 cds g303.t1.CDS8 2628100 2628993
chr_3 g303 g303.t1 exon g303.t1.exon9 2629059 2631488
chr_3 g303 g303.t1 cds g303.t1.CDS9 2629059 2631488
chr_3 g303 g303.t1 exon g303.t1.exon10 2631547 2631578
chr_3 g303 g303.t1 cds g303.t1.CDS10 2631547 2631578
chr_3 g303 g303.t1 exon g303.t1.exon11 2631638 2633015
chr_3 g303 g303.t1 cds g303.t1.CDS11 2631638 2633015
chr_3 g303 g303.t1 exon g303.t1.exon12 2633083 2633157
chr_3 g303 g303.t1 cds g303.t1.CDS12 2633083 2633157
chr_3 g303 g303.t1 TSS g303.t1 2633431 2633431

Sequences

>g303.t1 Gene=g303 Length=5523
ATGTCAAGTGACTCAAAGGCGCCTGTGCGCCATGTTAAACGTGTCCAGTTTGGAATTTTA
TCACCTGATGAAATTCGACGAATGTCAGTTACTGAAGGCGGAATTCAATTTCCAGAAACA
ATGGAAGGTGGAAGACCAAAATTAGGAGGTTTAATGGATCCTAGACAAGGAGTAATTGAC
AGAACATCGCGTTGTCAAACTTGTGCTGGAAATTTAACAGAATGTCCTGGTCATTTTGGA
CATATTGACTTATCAAAACCTGTATTTCATGTCGGCTTCTTGACTAAGACTATTAAAATT
CTTCGCTGTGTCTGCTTCTACTGTTCGAAACTTTTAGTGAGTCCACACAATCCGAAAATT
AAAGAAATTGTTATGAAATCAAAGGGACAACCACGAAAAAGATTGGCTTACGTTTATGAC
TTGTGTAAGGGTAAAAATATTTGCGAAGGTGGCGAAGATATGGATTTGACGAAAGATGGA
CAACAATTGCAACCTGATCCTAATAAAAAGAATGGCATGGGACATGGTGGTTGTGGAAAT
CATCAGCCTTCAATTCGTCGTGCTGGTTTAGAATTGACAGCAGAATGGAAGCATTTGAAT
GAGGAAACACAAGAGAAGAAAATTGCTGTAACTGCAGAACGTGTTTTAGAAATCTTTCGA
CACATTACTGACGAAGAATGTTACATTCTTGGAATGGATCCAAAATTTGCACGACCTGAT
TGGATGATTGTCAGTGTTCTGCCAGTTCCACCTTTGCCTGTTAGACCTGCTGTCGTTATG
TTTGGTGCAACGAAGAATCAAGATGATTTAACTCACAAACTTGCTGATATTATTAAAGCA
AATAATGAATTGAAAAAGAATGAGACTTCTGGAGCTGCTGCTCATGTTATTGCTGAAAAT
ATAAAAATGCTTCAATTTCATGTTGCTACATTTGTTGATAATGACATGCCTGGTATGCCT
CGTGCTATGCAAAAGTCTGGCAAACCATTAAAAGCAATTAAAGCTCGTTTAAAGGGAAAA
GAAGGACGTATTCGTGGAAATTTGATGGGAAAACGTGTTGATTTTTCAGCCCGTACTGTC
ATTACACCAGATCCAAATTTGCGTATTGATCAAGTCGGTGTACCTCGTTCTATTGCTCAA
AATTTAACTTTCCCTGAGCTTGTTACACCATTTAATATTGATAGAATGCAAGAACTCGTT
CGTCGTGGAAATTCACAATATCCCGGTGCAAAATATATCATACGTGATAATGGTGAGCGT
ATTGATTTACGTTTTCATCCTAAGCCAAGTGATTTACATCTTCAATGTGGTTACAAAGTT
GAACGACATTTACGTGACGATGATTTAGTTATTTTCAATCGTCAACCAACATTGCATAAG
ATGAGTATGATGGGACATCGTGTAAAAGTTTTACCTTGGTCAACTTTTCGTATGAATTTG
AGTTGTACATCTCCTTACAATGCTGATTTTGATGGAGATGAAATGAATTTACACGTTCCA
CAATCAATGGAAACTCGTGCTGAAGTTGAAAATATTCACATAACTCCTCGTCAGATTATT
ACACCGCAAGCCAATAAACCAGTTATGGGTATTGTGCAAGATACATTGACTGCTGTTCGT
AAAATGACTAAGCGTGATGTATTTATCGATAAAGAACAAATGATGAATCTTTTAATGTTT
TTACCAACATGGGATGGAAAAATGCCACAACCATGCATTCTCAAACCAAAACCATTGTGG
ACAGGAAAACAATTATTTTCACTTATTATTCCTGGAAATGTTAATATGATAAGAACTCAT
TCAACACATCCTGATGATGAAGATGATGGACCTTATAAATGGATTTCGCCAGGTGATACA
AAAGTAATGGTAGAGCATGGCGAGTTATTGATGGGAATTTTGTGTAAAAAAACACTTGGT
ACTTCTGCGGGATCATTGCTTCATATTGTTTTTCTCGAACTTGGTCATGAGATTGCTGGT
CGATTTTACGGAAATATTCAGACTGTCATTAACAATTGGTTGCTATTGGAAGGCCACAGT
ATTGGTATCGGGGACACAATTGCTGATCCTCAAACGTATCAAGAAATTCAAAAGACTATT
CGTAAAGCCAAAGAAGATGTCATTGGCGTTATTCAAAAAGCTCACAATATGGAATTAGAA
CCCACTCCTGGTAATACACTTCGTCAAACTTTCGAGAATCAAGTCAATCGTATTCTTAAC
GATGCTCGTGACAAAACTGGTGGTTCAGCGAAAAAATCTCTTACTGAATACAACAATTTA
AAAGCTATGGTCGTTTCTGGTTCTAAAGGTTCAAACATTAACATTTCACAAGTTATTGCT
TGTGTCGGTCAACAAAATGTTGAAGGAAAACGTATTCCATTTGGTTTTCGTAAGCGAACA
CTTCCACATTTCATTAAAGATGATTATGGTCCAGAATCTCGTGGTTTTGTTGAAAATTCA
TATCTTGCCGGCTTAACACCTTCAGAATTCTATTTTCACGCTATGGGAGGACGTGAAGGT
CTTATTGATACTGCTGTCAAAACTGCAGAAACTGGTTATATTCAACGTCGTCTTATCAAA
GCTATGGAGAGTGTTATGGTACATTATGATGGTACAGTCAGAAATTCAGTTGGGCAACTT
ATTCAATTGCGTTACGGTGAAGACGGTTTGGCTGGTGAAACTGTAGAATTTCAGAATTTG
CCAACAGTTAAATTATCAAACAAAGTTTTTGAGAAAAGATTCAAATTTGATATTTCCAAC
GAGCGACATACTAAAAAGTTATTCACTGAAGATGTTGTGAAAACACTCACAGAATCTGGC
TATGTCATTCAAGAACTTGAAAATGAATATGAACAGTTGATGAAAGATCGAAATACATTA
AGAGAAATCTTCCCGAATGGTGAAAGCAAAGTTGTATTACCATGCAATTTACAACGTATG
ATTTGGAACGTTCAAAAAATTTTCCACATTAATAAACGTGCACCAACAGATTTGAGTCCA
ATTCAAGTGATTAAAGGTGTTCGTGAGTTATTGAGCAAGTGTGTTATTGTCGCTGGCAAT
GATCGTTTGTCAAAGCAAGCAAATGAAAATGCAACATTATTGTTCCAATGTCTTGTGAGA
TCTACTTTATGCACAAAAATAGTAGCTGAAGATCATCGTTTAAATACAGAAGCATTTGAA
TGGTTGATTGGTGAAATTGAAACACGTTTCCAACAAGCACAAGCCAATCCTGGCGAGATG
GTTGGAGCTCTTGCTGCTCAATCACTTGGTGAACCTGCTACACAGATGACACTTAATACT
TTCCATTTTGCTGGTGTGTCTTCGAAAAATGTAACATTGGGTGTGCCACGTTTGAAGGAA
ATTATCAATATTTCAAAGAAACCAAAGGCTCCATCACTTACTGTTTTCTTAACTGGAGGT
GCTGCACGTGATGCTGAAAAAGCAAAGAATGTCTTGTGTCGTTTAGAACATACAACTTTG
CGTAAAGTTACTGCAAATACTGCAATTTATTATGATCCTGATCCACAAAGGACTGTCATT
CAAGAAGATCAAGAATTTGTCAACATTTATTATGAAATGCCTGATTTTGATCCAACAAAA
ATTTCACCTTGGCTCTTGCGTATTGAACTCGATCGCAAACGTATGACTGATAAAAAATTG
ACTATGGAACAGATTGCTGAAAAGATTAATGCTGGATTTGGTGATGATTTGAATTGCATT
TTCAATGACGACAATTCTGATAAATTGGTTCTTCGAATTCGTATAATGAATAAGGGTGAC
AATAAATTTGGAATGGATGGTGAAGAAGATATGGAAAAAATGGATGAAGATATGTTCTTG
AGATGCATCGAGTCAAATATGCTTTCAGAATTGACTCTACAGGGAATTGAAGCTATTGGG
AAAGTATACATGCATCTTCCACAAACTGATGCAAAGAAACGAATTGTTATTACTGAAAAT
GGTGAATTTAAAGCTATTGGAGAATGGCTTCTTGAAACTGATGGTACTTCATTAATGAAA
GTTTTGAGCGAACGAGATGTTGATCCAGTACGAACATTCAGTAACGATATTTGTGAAATC
TTTAGTGTACTTGGTATCGAAGCTGTTCGTAAATCAGTTGAAAAAGAAATGAATGCTGTC
TTGCAATTTTATGGTTTGTACGTCAACTATCGTCATTTGGCTTTGTTGTGTGACGTTATG
ACAGCTAAAGGACATTTGATGGCTATCACTCGTCACGGTATCAATCGTCAAGATACTGGT
GCTCTTATGAGATGTTCATTCGAAGAAACTGTGGATGTTTTGATGGATGCTGCAAGTCAT
GCTGAAGTTGATCCAATGCGTGGTGTTTCTGAAAATATTATTATGGGTCAATTGCCTCGT
ATGGGAACAGGATGTTTTGATCTCTTACTCGATGCTGATAAATGTAAAGATGGAATGGAA
ATTCCTCATACAAGCATTATGGGAACAACAGGAATGTTTTTCGGTCCTGGTCAAAGTCCT
TCAGCAATGAGTCCACAAATGACACCATGGCAAAGCGGTACACCCGCTTATGGAGCTGAA
TGGTCTCCAGCAAGCGGCATGACACCCGGTGGTCCTAGTTTTTCACCAAGTGCACAATCT
GATGCATCTGGGATGTCACCAAGTTGGTCTCCCAATCCTGGCTCACCTTCTTCACCTGGT
GGAATGTCTCCTTATTTCCAACATTCTCCTTCAGCTTCACCTTCTTATTCACCTTCAAGT
CCCAATTATCAAGCATCTGCATCACCATCATATTCTCCTACGAGTCCTTCGTATTCACCT
ACATCAACTATTTACAGTCCTTCATCTCCACACTATTCGCCTACGAGTCCAAATTATAAT
CCAGCATCGCCGGCATATTCGCCAAACTCATCATATAGTCCAACTTCACCATCTTATTCA
CCAACGAGTCCTAATTATCAAGCCACAAGTCCAGGATATACAGCATCTTACAGTCCAACA
AGCCCTTATAGTCCTTCAAGTCCATCATACAGTCCAACGAGTCCTTCATACAGTCCAACG
AGTCCATCTTATAGTCCGTCATCACCAAGCTATAGATCACCGATTGCAACTCCAAGTTAT
TCACCAAGTTCACCAAATTATACTCCTACGACTCCTAGTTACAGTCCAAGCTCTCCTCAA
TATTCGACTCATTATAGTCCTAGTTCTCCATCATATTCACCATCATCGACAAAATATTCG
CCAAGCTCTCCATCGTATTCACCAACGAGCCCATCGCATTGTGCAAGTCCTCAATATACA
CCAACGAGCCCGCCAAGTTATTATTCACCGGTTTCACCAACTTATCCGAGCTCACCAGGC
CCTGGATACAGTCCAACTTATAGTCCGAGCTCTAAATATTCACCATCATCACCGGTTTAT
AGTCCCACTTCACCAATTTATTCTGAAGATCCTCATACCGATCCAAGTCCTTCATATACA
AGTCCACCCGCTGGAAGCCCTGAAGAAGATCCACAAGATAAATATCATGGAAAACGTTGG
TAA

>g303.t1 Gene=g303 Length=1840
MSSDSKAPVRHVKRVQFGILSPDEIRRMSVTEGGIQFPETMEGGRPKLGGLMDPRQGVID
RTSRCQTCAGNLTECPGHFGHIDLSKPVFHVGFLTKTIKILRCVCFYCSKLLVSPHNPKI
KEIVMKSKGQPRKRLAYVYDLCKGKNICEGGEDMDLTKDGQQLQPDPNKKNGMGHGGCGN
HQPSIRRAGLELTAEWKHLNEETQEKKIAVTAERVLEIFRHITDEECYILGMDPKFARPD
WMIVSVLPVPPLPVRPAVVMFGATKNQDDLTHKLADIIKANNELKKNETSGAAAHVIAEN
IKMLQFHVATFVDNDMPGMPRAMQKSGKPLKAIKARLKGKEGRIRGNLMGKRVDFSARTV
ITPDPNLRIDQVGVPRSIAQNLTFPELVTPFNIDRMQELVRRGNSQYPGAKYIIRDNGER
IDLRFHPKPSDLHLQCGYKVERHLRDDDLVIFNRQPTLHKMSMMGHRVKVLPWSTFRMNL
SCTSPYNADFDGDEMNLHVPQSMETRAEVENIHITPRQIITPQANKPVMGIVQDTLTAVR
KMTKRDVFIDKEQMMNLLMFLPTWDGKMPQPCILKPKPLWTGKQLFSLIIPGNVNMIRTH
STHPDDEDDGPYKWISPGDTKVMVEHGELLMGILCKKTLGTSAGSLLHIVFLELGHEIAG
RFYGNIQTVINNWLLLEGHSIGIGDTIADPQTYQEIQKTIRKAKEDVIGVIQKAHNMELE
PTPGNTLRQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVSGSKGSNINISQVIA
CVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFYFHAMGGREG
LIDTAVKTAETGYIQRRLIKAMESVMVHYDGTVRNSVGQLIQLRYGEDGLAGETVEFQNL
PTVKLSNKVFEKRFKFDISNERHTKKLFTEDVVKTLTESGYVIQELENEYEQLMKDRNTL
REIFPNGESKVVLPCNLQRMIWNVQKIFHINKRAPTDLSPIQVIKGVRELLSKCVIVAGN
DRLSKQANENATLLFQCLVRSTLCTKIVAEDHRLNTEAFEWLIGEIETRFQQAQANPGEM
VGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGG
AARDAEKAKNVLCRLEHTTLRKVTANTAIYYDPDPQRTVIQEDQEFVNIYYEMPDFDPTK
ISPWLLRIELDRKRMTDKKLTMEQIAEKINAGFGDDLNCIFNDDNSDKLVLRIRIMNKGD
NKFGMDGEEDMEKMDEDMFLRCIESNMLSELTLQGIEAIGKVYMHLPQTDAKKRIVITEN
GEFKAIGEWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFSVLGIEAVRKSVEKEMNAV
LQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAASH
AEVDPMRGVSENIIMGQLPRMGTGCFDLLLDADKCKDGMEIPHTSIMGTTGMFFGPGQSP
SAMSPQMTPWQSGTPAYGAEWSPASGMTPGGPSFSPSAQSDASGMSPSWSPNPGSPSSPG
GMSPYFQHSPSASPSYSPSSPNYQASASPSYSPTSPSYSPTSTIYSPSSPHYSPTSPNYN
PASPAYSPNSSYSPTSPSYSPTSPNYQATSPGYTASYSPTSPYSPSSPSYSPTSPSYSPT
SPSYSPSSPSYRSPIATPSYSPSSPNYTPTTPSYSPSSPQYSTHYSPSSPSYSPSSTKYS
PSSPSYSPTSPSHCASPQYTPTSPPSYYSPVSPTYPSSPGPGYSPTYSPSSKYSPSSPVY
SPTSPIYSEDPHTDPSPSYTSPPAGSPEEDPQDKYHGKRW

Protein features from InterProScan

Transcript Database ID Name Start End E.value
22 g303.t1 CDD cd02733 RNAP_II_RPB1_N 13 870 0.0
23 g303.t1 CDD cd02584 RNAP_II_Rpb1_C 1052 1471 0.0
21 g303.t1 Coils Coil Coil 267 287 -
20 g303.t1 Coils Coil Coil 943 963 -
11 g303.t1 Gene3D G3DSA:1.20.120.1280 - 2 114 1.7E-34
12 g303.t1 Gene3D G3DSA:1.20.120.1280 - 260 313 7.3E-12
18 g303.t1 Gene3D G3DSA:2.40.40.20 - 340 510 1.3E-76
19 g303.t1 Gene3D G3DSA:3.30.1490.180 RNA polymerase ii 383 446 1.3E-76
14 g303.t1 Gene3D G3DSA:1.10.274.100 - 519 680 1.5E-53
13 g303.t1 Gene3D G3DSA:1.10.132.30 - 681 826 2.6E-56
17 g303.t1 Gene3D G3DSA:2.20.25.410 - 864 899 2.2E-9
16 g303.t1 Gene3D G3DSA:3.30.1360.140 - 1158 1295 1.5E-58
15 g303.t1 Gene3D G3DSA:1.10.150.390 - 1421 1466 8.4E-18
35 g303.t1 MobiDBLite mobidb-lite consensus disorder prediction 1530 1559 -
36 g303.t1 MobiDBLite mobidb-lite consensus disorder prediction 1530 1551 -
38 g303.t1 MobiDBLite mobidb-lite consensus disorder prediction 1587 1664 -
39 g303.t1 MobiDBLite mobidb-lite consensus disorder prediction 1587 1840 -
33 g303.t1 MobiDBLite mobidb-lite consensus disorder prediction 1670 1762 -
34 g303.t1 MobiDBLite mobidb-lite consensus disorder prediction 1763 1783 -
37 g303.t1 MobiDBLite mobidb-lite consensus disorder prediction 1784 1815 -
8 g303.t1 PANTHER PTHR19376 DNA-DIRECTED RNA POLYMERASE 5 1540 0.0
9 g303.t1 PANTHER PTHR19376:SF56 DNA-DIRECTED RNA POLYMERASE SUBUNIT 5 1540 0.0
4 g303.t1 Pfam PF04997 RNA polymerase Rpb1, domain 1 10 348 6.0E-107
3 g303.t1 Pfam PF00623 RNA polymerase Rpb1, domain 2 350 513 6.0E-74
2 g303.t1 Pfam PF04983 RNA polymerase Rpb1, domain 3 518 686 1.3E-49
7 g303.t1 Pfam PF05000 RNA polymerase Rpb1, domain 4 715 817 1.7E-37
1 g303.t1 Pfam PF04998 RNA polymerase Rpb1, domain 5 824 1421 2.6E-100
5 g303.t1 Pfam PF04992 RNA polymerase Rpb1, domain 6 890 1073 4.2E-67
6 g303.t1 Pfam PF04990 RNA polymerase Rpb1, domain 7 1158 1294 1.9E-55
31 g303.t1 ProSitePatterns PS00115 Eukaryotic RNA polymerase II heptapeptide repeat. 1612 1618 -
27 g303.t1 ProSitePatterns PS00115 Eukaryotic RNA polymerase II heptapeptide repeat. 1663 1669 -
30 g303.t1 ProSitePatterns PS00115 Eukaryotic RNA polymerase II heptapeptide repeat. 1670 1676 -
26 g303.t1 ProSitePatterns PS00115 Eukaryotic RNA polymerase II heptapeptide repeat. 1677 1683 -
25 g303.t1 ProSitePatterns PS00115 Eukaryotic RNA polymerase II heptapeptide repeat. 1684 1690 -
28 g303.t1 ProSitePatterns PS00115 Eukaryotic RNA polymerase II heptapeptide repeat. 1725 1731 -
29 g303.t1 ProSitePatterns PS00115 Eukaryotic RNA polymerase II heptapeptide repeat. 1739 1745 -
24 g303.t1 ProSitePatterns PS00115 Eukaryotic RNA polymerase II heptapeptide repeat. 1746 1752 -
32 g303.t1 SMART SM00663 rpolaneu7 240 543 2.3E-197
10 g303.t1 SUPERFAMILY SSF64484 beta and beta-prime subunits of DNA dependent RNA-polymerase 6 1473 0.0

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0003899 DNA-directed 5’-3’ RNA polymerase activity MF
GO:0003677 DNA binding MF
GO:0006351 transcription, DNA-templated BP
GO:0006366 transcription by RNA polymerase II BP

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values