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.t2 TTS g303.t2 2626661 2626661
chr_3 g303 g303.t2 isoform g303.t2 2626662 2628993
chr_3 g303 g303.t2 exon g303.t2.exon1 2626662 2626846
chr_3 g303 g303.t2 exon g303.t2.exon2 2626905 2627090
chr_3 g303 g303.t2 exon g303.t2.exon3 2627156 2627317
chr_3 g303 g303.t2 exon g303.t2.exon4 2627376 2627585
chr_3 g303 g303.t2 cds g303.t2.CDS1 2627552 2627585
chr_3 g303 g303.t2 exon g303.t2.exon5 2627846 2628027
chr_3 g303 g303.t2 cds g303.t2.CDS2 2627846 2628027
chr_3 g303 g303.t2 exon g303.t2.exon6 2628100 2628993
chr_3 g303 g303.t2 cds g303.t2.CDS3 2628100 2628894
chr_3 g303 g303.t2 TSS g303.t2 NA NA

Sequences

>g303.t2 Gene=g303 Length=1819
CTTCCACAAACTGATGCAAAGAAACGAATTGTTATTACTGAAAATGGTGAATTTAAAGCT
ATTGGAGAATGGCTTCTTGAAACTGATGGTACTTCATTAATGAAAGTTTTGAGCGAACGA
GATGTTGATCCAGTACGAACATTCAGTAACGATATTTGTGAAATCTTTAGTGTACTTGGT
ATCGAAGCTGTTCGTAAATCAGTTGAAAAAGAAATGAATGCTGTCTTGCAATTTTATGGT
TTGTACGTCAACTATCGTCATTTGGCTTTGTTGTGTGACGTTATGACAGCTAAAGGACAT
TTGATGGCTATCACTCGTCACGGTATCAATCGTCAAGATACTGGTGCTCTTATGAGATGT
TCATTCGAAGAAACTGTGGATGTTTTGATGGATGCTGCAAGTCATGCTGAAGTTGATCCA
ATGCGTGGTGTTTCTGAAAATATTATTATGGGTCAATTGCCTCGTATGGGAACAGGATGT
TTTGATCTCTTACTCGATGCTGATAAATGTAAAGATGGAATGGAAATTCCTCATACAAGC
ATTATGGGAACAACAGGAATGTTTTTCGGTCCTGGTCAAAGTCCTTCAGCAATGAGTCCA
CAAATGACACCATGGCAAAGCGGTACACCCGCTTATGGAGCTGAATGGTCTCCAGCAAGC
GGCATGACACCCGGTGGTCCTAGTTTTTCACCAAGTGCACAATCTGATGCATCTGGGATG
TCACCAAGTTGGTCTCCCAATCCTGGCTCACCTTCTTCACCTGGTGGAATGTCTCCTTAT
TTCCAACATTCTCCTTCAGCTTCACCTTCTTATTCACCTTCAAGTCCCAATTATCAAGCA
TCTGCATCACCATCATATTCTCCTACGAGTCCTTCGTATTCACCTACATCAACTATTTAC
AGTCCTTCATCTCCACACTATTCGCCTACGAGTCCAAATTATAATCCAGCATCGCCGGCA
TATTCGCCAAACTCATCATATAGTCCAACTTCACCATCTTATTCACCAACGAGTCCTAAT
TATCAAGCCACAAGTCCAGGATATACAGCATCTTACAGTCCAACAAGCCCTTATAGTCCA
ACGAGTCCATCTTATAGTCCGGTAAGTTGATAAAAATTAAATTCAAAATTTATCAAAATA
GTTAATTAAATTTTGTTATAGTCATCACCAAGCTATAGATCACCGATTGCAACTCCAAGT
TATTCACCAAGTTCACCAAATTATACTCCTACGACTCCTAGTTACAGTCCAAGCTCTCCT
CAATATTCGACTCATTATAGTCCTAGTTCTCCATCATATTCACCATCATCGACAAAATAT
TCGCCAAGCTCTCCATCGTATTCACCAACGAGCCCATCGCATTGTGCAAGTCCTCAATAT
ACACCAACGAGCCCGCCAAGTTATTATTCACCGGTTTCACCAACTTATCCGAGCTCACCA
GGCCCTGGATACAGTCCAACTTATAGTCCGAGCTCTAAATATTCACCATCATCACCGGTT
TATAGTCCCACTTCACCAATTTATTCTGAAGATCCTCATACCGATCCAAGTCCTTCATAT
ACAAGTCCACCCGCTGGAAGCCCTGAAGAAGATCCACAAGATAAATATCATGGAAAACGT
TGGTAAAGGGTTAGACATACTATTTGATGAATTCAGCAGAAAAAGCAAAACTTTTTATAA
AACACTATTACAATTTGATTTTATAGCATTTGATAAAATATGATTAGAAAAACCTGATAA
AAATAAGAATTTGAACATTAAAGTATATGATGAACTTGAACTTTATTCTCAAAATAAACG
AAAACTATGAAAAACTAAA

>g303.t2 Gene=g303 Length=336
MKVLSERDVDPVRTFSNDICEIFSVLGIEAVRKSVEKEMNAVLQFYGLYVNYRHLALLCD
VMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAASHAEVDPMRGVSENIIMGQL
PRMGTGCFDLLLDADKCKDGMEIPHTSIMGTTGMFFGPGQSPSAMSPQMTPWQSGTPAYG
AEWSPASGMTPGGPSFSPSAQSDASGMSPSWSPNPGSPSSPGGMSPYFQHSPSASPSYSP
SSPNYQASASPSYSPTSPSYSPTSTIYSPSSPHYSPTSPNYNPASPAYSPNSSYSPTSPS
YSPTSPNYQATSPGYTASYSPTSPYSPTSPSYSPVS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g303.t2 Gene3D G3DSA:1.10.150.390 - 83 128 1.0E-18
16 g303.t2 MobiDBLite mobidb-lite consensus disorder prediction 192 221 -
17 g303.t2 MobiDBLite mobidb-lite consensus disorder prediction 192 213 -
15 g303.t2 MobiDBLite mobidb-lite consensus disorder prediction 249 336 -
2 g303.t2 PANTHER PTHR19376 DNA-DIRECTED RNA POLYMERASE 3 196 6.1E-50
3 g303.t2 PANTHER PTHR19376:SF56 DNA-DIRECTED RNA POLYMERASE SUBUNIT 3 196 6.1E-50
4 g303.t2 PRINTS PR01217 Proline rich extensin signature 165 177 5.1E-9
9 g303.t2 PRINTS PR01217 Proline rich extensin signature 206 218 5.1E-9
6 g303.t2 PRINTS PR01217 Proline rich extensin signature 231 252 5.1E-9
5 g303.t2 PRINTS PR01217 Proline rich extensin signature 258 274 5.1E-9
8 g303.t2 PRINTS PR01217 Proline rich extensin signature 282 299 5.1E-9
7 g303.t2 PRINTS PR01217 Proline rich extensin signature 309 334 5.1E-9
1 g303.t2 Pfam PF04998 RNA polymerase Rpb1, domain 5 2 83 2.4E-23
13 g303.t2 ProSitePatterns PS00115 Eukaryotic RNA polymerase II heptapeptide repeat. 274 280 -
12 g303.t2 ProSitePatterns PS00115 Eukaryotic RNA polymerase II heptapeptide repeat. 294 300 -
11 g303.t2 ProSitePatterns PS00115 Eukaryotic RNA polymerase II heptapeptide repeat. 301 307 -
14 g303.t2 ProSitePatterns PS00115 Eukaryotic RNA polymerase II heptapeptide repeat. 325 331 -
10 g303.t2 SUPERFAMILY SSF64484 beta and beta-prime subunits of DNA dependent RNA-polymerase 3 135 3.66E-50

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

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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