General information for g5425.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA-directed RNA polymerases I and III subunit RPAC1.
Parent gene
- The parent gene g5425 is located on chr_2: 9521851..9522918 (+ 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 | g5425 | g5425.t3 | TSS | g5425.t3 | 9521770 | 9521770 |
| chr_2 | g5425 | g5425.t3 | isoform | g5425.t3 | 9521851 | 9522438 |
| chr_2 | g5425 | g5425.t3 | exon | g5425.t3.exon1 | 9521851 | 9522438 |
| chr_2 | g5425 | g5425.t3 | cds | g5425.t3.CDS1 | 9521851 | 9522438 |
| chr_2 | g5425 | g5425.t3 | TTS | g5425.t3 | 9522933 | 9522933 |
Sequences
>g5425.t3 Gene=g5425 Length=588
ATGGCAAAAATAGGTGACAAAAAGCCTAAAGTGATCTTGGAAGAGTTTAAAATTAAAGAA
AATTCAGAGGATTACGGTTTTGCAGATGAACAATTCAACCGAGAAGATTTTAAGCGAAAT
TTTAAGCTTAAAGTTATTAAGAAATCAAATTTAGATATTGAATTTGATTTAATAGGAATA
ACACCTGCTATTGCAAATGCATTTCGTAGAATAATGTTAAGTGAAGTTCCTTCAATGGCA
ATTGAAAAAGTTTACATTTACAACAATACTTCAATTATTCCTGATGAAGTTCTTGCTCAT
AGATTTGGATTAATACCTCTTAAAGCCGATCCACGTCTATTTGAATATAAACTAGATGAA
AAAGACGAAGAGGGAAATGAATTAGATACACTAGAATTCAAACTTGAGATTAAATGCACA
TGGAAGAATAAAGATGTAAAAGATTCTCGAAACTTTGATGCTATGTACAAAAATCATAAC
ATTTATAGTGAACACATTAAATGGGTACCAAGAGGAAAACAAGGTACACTCTATAATGAA
GCAAATATTGGACCATGTGATGACAAGATTTTAATCTCTAAAATGAGA
>g5425.t3 Gene=g5425 Length=196
MAKIGDKKPKVILEEFKIKENSEDYGFADEQFNREDFKRNFKLKVIKKSNLDIEFDLIGI
TPAIANAFRRIMLSEVPSMAIEKVYIYNNTSIIPDEVLAHRFGLIPLKADPRLFEYKLDE
KDEEGNELDTLEFKLEIKCTWKNKDVKDSRNFDAMYKNHNIYSEHIKWVPRGKQGTLYNE
ANIGPCDDKILISKMR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g5425.t3 | Gene3D | G3DSA:2.170.120.12 | RNA Polymerase Alpha Subunit; Chain A | 78 | 196 | 0e+00 |
| 3 | g5425.t3 | PANTHER | PTHR11800 | DNA-DIRECTED RNA POLYMERASE | 21 | 196 | 0e+00 |
| 4 | g5425.t3 | PANTHER | PTHR11800:SF13 | DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC1 | 21 | 196 | 0e+00 |
| 2 | g5425.t3 | Pfam | PF01193 | RNA polymerase Rpb3/Rpb11 dimerisation domain | 54 | 83 | 0e+00 |
| 1 | g5425.t3 | Pfam | PF01000 | RNA polymerase Rpb3/RpoA insert domain | 84 | 196 | 0e+00 |
| 7 | g5425.t3 | SMART | SM00662 | rpoldneu2 | 52 | 196 | 2e-07 |
| 6 | g5425.t3 | SUPERFAMILY | SSF55257 | RBP11-like subunits of RNA polymerase | 39 | 82 | 0e+00 |
| 5 | g5425.t3 | SUPERFAMILY | SSF56553 | Insert subdomain of RNA polymerase alpha subunit | 77 | 196 | 0e+00 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5425/g5425.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5425.t3.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0003899 | DNA-directed 5’-3’ RNA polymerase activity | MF |
| GO:0001056 | RNA polymerase III activity | MF |
| GO:0006351 | transcription, DNA-templated | BP |
| GO:0001054 | RNA polymerase I activity | MF |
| GO:0046983 | protein dimerization activity | MF |
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. There were no conditions that were differentially expressed