Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative DNA-directed RNA polymerases I, II, and III subunit RPABC2.

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_2 g6750 g6750.t2 TSS g6750.t2 18471742 18471742
chr_2 g6750 g6750.t2 isoform g6750.t2 18471957 18472416
chr_2 g6750 g6750.t2 exon g6750.t2.exon1 18471957 18472416
chr_2 g6750 g6750.t2 cds g6750.t2.CDS1 18471996 18472316
chr_2 g6750 g6750.t2 TTS g6750.t2 18472427 18472427

Sequences

>g6750.t2 Gene=g6750 Length=460
GGAGCTGATGATTATAATGATGATGATGTCGAAGAAGATATGGATGATATTCAGGAAGAT
GAAGGAGATAATATTGAGCTTGTAATGTCAGGTCAGCAATCGGGAGGATCTGTTCCAAAA
AATAAACGCATTACAACCAAATATATGACTAAATATGAACGTGCAAGAGTGTTGGGGACA
AGAGCACTCCAAATTGCGATGTGTGCACCAATAATGGTGGAATTAGAAGGCGAAACAGAT
CCATTACAAATTGCAATGAAAGAATTAAAGCAGAGAAAAATTCCTATAATTATAAGACGA
TATTTGCCCGATAATAGTTTTGAGGATTGGTCAATTGATGAACTCATTATTTCTGATTAA
AAAGTTTCCTAAATAAAATCCACATAAAGATTTCTAATTTTTCCAAAAAAAAACATTTTT
ATTAAGAAACAATTTTAAAATAAGTAATAAAGCTATAAAT

>g6750.t2 Gene=g6750 Length=106
MDDIQEDEGDNIELVMSGQQSGGSVPKNKRITTKYMTKYERARVLGTRALQIAMCAPIMV
ELEGETDPLQIAMKELKQRKIPIIIRRYLPDNSFEDWSIDELIISD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g6750.t2 Gene3D G3DSA:3.90.940.10 - 1 106 3.1E-49
10 g6750.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 29 -
9 g6750.t2 MobiDBLite mobidb-lite consensus disorder prediction 14 29 -
2 g6750.t2 PANTHER PTHR47227 DNA-DIRECTED RNA POLYMERASE SUBUNIT K 10 103 4.8E-41
5 g6750.t2 PIRSF PIRSF000778 RpoK/RPB6 1 106 2.9E-48
6 g6750.t2 PIRSF PIRSF500154 RPB6 1 106 3.9E-53
1 g6750.t2 Pfam PF01192 RNA polymerase Rpb6 30 83 1.3E-16
7 g6750.t2 ProSitePatterns PS01111 RNA polymerases K / 14 to 18 Kd subunits signature. 37 51 -
8 g6750.t2 SMART SM01409 RNA_pol_Rpb6_2 30 83 2.9E-6
3 g6750.t2 SUPERFAMILY SSF63562 RPB6/omega subunit-like 2 105 8.89E-46

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:0005665 RNA polymerase II, core complex CC
GO:0003899 DNA-directed 5’-3’ RNA polymerase activity MF
GO:0005634 nucleus CC
GO:0003677 DNA binding MF
GO:0006351 transcription, DNA-templated 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