General information for g6750.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative DNA-directed RNA polymerases I, II, and III subunit RPABC2.
Parent gene
- The parent gene g6750 is located on chr_2: 18472316..18474198 (+ strand)
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.t1 | TSS | g6750.t1 | 18471742 | 18471742 |
| chr_2 | g6750 | g6750.t1 | isoform | g6750.t1 | 18471826 | 18472316 |
| chr_2 | g6750 | g6750.t1 | exon | g6750.t1.exon1 | 18471826 | 18471854 |
| chr_2 | g6750 | g6750.t1 | cds | g6750.t1.CDS1 | 18471826 | 18471854 |
| chr_2 | g6750 | g6750.t1 | exon | g6750.t1.exon2 | 18471953 | 18472316 |
| chr_2 | g6750 | g6750.t1 | cds | g6750.t1.CDS2 | 18471953 | 18472316 |
| chr_2 | g6750 | g6750.t1 | TTS | g6750.t1 | 18472427 | 18472427 |
Sequences
>g6750.t1 Gene=g6750 Length=393
ATGGATGATGGAGATTATGATGGTGATGACGTCGGAGCTGATGATTATAATGATGATGAT
GTCGAAGAAGATATGGATGATATTCAGGAAGATGAAGGAGATAATATTGAGCTTGTAATG
TCAGGTCAGCAATCGGGAGGATCTGTTCCAAAAAATAAACGCATTACAACCAAATATATG
ACTAAATATGAACGTGCAAGAGTGTTGGGGACAAGAGCACTCCAAATTGCGATGTGTGCA
CCAATAATGGTGGAATTAGAAGGCGAAACAGATCCATTACAAATTGCAATGAAAGAATTA
AAGCAGAGAAAAATTCCTATAATTATAAGACGATATTTGCCCGATAATAGTTTTGAGGAT
TGGTCAATTGATGAACTCATTATTTCTGATTAA
>g6750.t1 Gene=g6750 Length=130
MDDGDYDGDDVGADDYNDDDVEEDMDDIQEDEGDNIELVMSGQQSGGSVPKNKRITTKYM
TKYERARVLGTRALQIAMCAPIMVELEGETDPLQIAMKELKQRKIPIIIRRYLPDNSFED
WSIDELIISD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g6750.t1 | Gene3D | G3DSA:3.90.940.10 | - | 1 | 130 | 1.4E-52 |
| 9 | g6750.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 26 | - |
| 2 | g6750.t1 | PANTHER | PTHR47227 | DNA-DIRECTED RNA POLYMERASE SUBUNIT K | 14 | 127 | 7.1E-43 |
| 5 | g6750.t1 | PIRSF | PIRSF000778 | RpoK/RPB6 | 1 | 130 | 6.8E-51 |
| 6 | g6750.t1 | PIRSF | PIRSF500154 | RPB6 | 1 | 130 | 8.0E-56 |
| 1 | g6750.t1 | Pfam | PF01192 | RNA polymerase Rpb6 | 54 | 107 | 2.1E-16 |
| 7 | g6750.t1 | ProSitePatterns | PS01111 | RNA polymerases K / 14 to 18 Kd subunits signature. | 61 | 75 | - |
| 8 | g6750.t1 | SMART | SM01409 | RNA_pol_Rpb6_2 | 54 | 107 | 2.9E-6 |
| 3 | g6750.t1 | SUPERFAMILY | SSF63562 | RPB6/omega subunit-like | 1 | 129 | 1.31E-48 |
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
- This transcript has been annotated with K03014 (DNA-directed RNA polymerases I, II, and III subunit RPABC2)
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.
