General information for g9153.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA-directed RNA polymerases I, II, and III subunit RPABC3.
Parent gene
- The parent gene g9153 is located on chr_1: 522650..524086 (+ 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_1 | g9153 | g9153.t1 | TSS | g9153.t1 | 521996 | 521996 |
| chr_1 | g9153 | g9153.t1 | isoform | g9153.t1 | 522084 | 522650 |
| chr_1 | g9153 | g9153.t1 | exon | g9153.t1.exon1 | 522084 | 522210 |
| chr_1 | g9153 | g9153.t1 | cds | g9153.t1.CDS1 | 522084 | 522210 |
| chr_1 | g9153 | g9153.t1 | exon | g9153.t1.exon2 | 522268 | 522351 |
| chr_1 | g9153 | g9153.t1 | cds | g9153.t1.CDS2 | 522268 | 522351 |
| chr_1 | g9153 | g9153.t1 | exon | g9153.t1.exon3 | 522415 | 522650 |
| chr_1 | g9153 | g9153.t1 | cds | g9153.t1.CDS3 | 522415 | 522650 |
| chr_1 | g9153 | g9153.t1 | TTS | g9153.t1 | NA | NA |
Sequences
>g9153.t1 Gene=g9153 Length=447
ATGTCTGGAATTTTATTTGAAGATATCTTTAATGTAAAAGACATGGATCCAGAAGGAAAG
AAATTTGATCGAGTTTCTCGATTACATTGTGAGTCAGAATCTTTCAAAATGGACCTCATT
CTTGATGTGAATTCTTGGATTTATCCGATGGATCTTGGTGATAAATTTCGACTTGTATTA
GCTACAACACTTCAAGAAGACGGTCGTCCAGCAAGTCAAGAGTACATAGCGAGTGAAATT
GAAGGATCAAGAGCTGACAGTTTTGAATATGTAATGTTTGGTCAAGTTTACAGAATAGAA
GGAGATGATTCAGAAGCATCAAGTCGACTCTCAGCTTTTGTGTCATTTGGAGGTTTGTTG
ATGAGACTGCAAGGTGATGCTAATAACTTGCATGGATTTGAAATAGATCAGAAAATTTAT
CTACTCATGAAGAAATTGGCTTTCTAA
>g9153.t1 Gene=g9153 Length=148
MSGILFEDIFNVKDMDPEGKKFDRVSRLHCESESFKMDLILDVNSWIYPMDLGDKFRLVL
ATTLQEDGRPASQEYIASEIEGSRADSFEYVMFGQVYRIEGDDSEASSRLSAFVSFGGLL
MRLQGDANNLHGFEIDQKIYLLMKKLAF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g9153.t1 | Gene3D | G3DSA:2.40.50.140 | - | 6 | 148 | 0 |
| 2 | g9153.t1 | PANTHER | PTHR10917 | DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3 | 1 | 146 | 0 |
| 6 | g9153.t1 | PIRSF | PIRSF000779 | RPB8 | 1 | 147 | 0 |
| 1 | g9153.t1 | Pfam | PF03870 | RNA polymerase Rpb8 | 7 | 145 | 0 |
| 4 | g9153.t1 | SMART | SM00658 | rpol8neu | 2 | 145 | 0 |
| 3 | g9153.t1 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 3 | 145 | 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:0006351 | transcription, DNA-templated | BP |
KEGG
Orthology
- This transcript has been annotated with K03016 (DNA-directed RNA polymerases I, II, and III subunit RPABC3)
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.
