General information for g5425.t2
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.t2 | TSS | g5425.t2 | 9521770 | 9521770 |
| chr_2 | g5425 | g5425.t2 | isoform | g5425.t2 | 9521785 | 9522918 |
| chr_2 | g5425 | g5425.t2 | exon | g5425.t2.exon1 | 9521785 | 9521795 |
| chr_2 | g5425 | g5425.t2 | exon | g5425.t2.exon2 | 9521864 | 9522441 |
| chr_2 | g5425 | g5425.t2 | cds | g5425.t2.CDS1 | 9522064 | 9522441 |
| chr_2 | g5425 | g5425.t2 | exon | g5425.t2.exon3 | 9522502 | 9522918 |
| chr_2 | g5425 | g5425.t2 | cds | g5425.t2.CDS2 | 9522502 | 9522918 |
| chr_2 | g5425 | g5425.t2 | TTS | g5425.t2 | 9522933 | 9522933 |
Sequences
>g5425.t2 Gene=g5425 Length=1006
TGTGAGCTCAGGTGACAAAAAGCCTAAAGTGATCTTGGAAGAGTTTAAAATTAAAGAAAA
TTCAGAGGATTACGGTTTTGCAGATGAACAATTCAACCGAGAAGATTTTAAGCGAAATTT
TAAGCTTAAAGTTATTAAGAAATCAAATTTAGATATTGAATTTGATTTAATAGGAATAAC
ACCTGCTATTGCAAATGCATTTCGTAGAATAATGTTAAGTGAAGTTCCTTCAATGGCAAT
TGAAAAAGTTTACATTTACAACAATACTTCAATTATTCCTGATGAAGTTCTTGCTCATAG
ATTTGGATTAATACCTCTTAAAGCCGATCCACGTCTATTTGAATATAAACTAGATGAAAA
AGACGAAGAGGGAAATGAATTAGATACACTAGAATTCAAACTTGAGATTAAATGCACATG
GAAGAATAAAGATGTAAAAGATTCTCGAAACTTTGATGCTATGTACAAAAATCATAACAT
TTATAGTGAACACATTAAATGGGTACCAAGAGGAAAACAAGGTACACTCTATAATGAAGC
AAATATTGGACCATGTGATGACAAGATTTTAATCTCTAAAATGAGACCGGGACACGAGTT
CAATATTAAATTACTTGCAGTGAAAGGGATTGGAAAAGATCATGCAAAATTTAGTCCGGT
TTCGCTTGCCACTTACAGATTATTGCCGGAAATCACATTGTTAAAAGAAATTCGTGGAAA
GGATGCACAACTTCTTCAGAAATGTTTCTCACCAGGAGTAATTGAAATCGATAAAAGTGG
CATTGCTTATGTCAAAAATGCAAGATATGATAATTGCAGCCGAAACGTATATCGATATCC
TGAATTATCAAAAAACGTTGAAATATCACGAGTTCGCAATCATTTCATTTTTAATATTGA
GTCTCTGGGTGCTTATAAACCAGAAGAAATTTTCATACTCGCAGTAAAGACCCTCAAAAA
TAAATGCGATGTATTATTGGAAGAATTGAATTTTGAAAATAAATGA
>g5425.t2 Gene=g5425 Length=264
MLSEVPSMAIEKVYIYNNTSIIPDEVLAHRFGLIPLKADPRLFEYKLDEKDEEGNELDTL
EFKLEIKCTWKNKDVKDSRNFDAMYKNHNIYSEHIKWVPRGKQGTLYNEANIGPCDDKIL
ISKMRPGHEFNIKLLAVKGIGKDHAKFSPVSLATYRLLPEITLLKEIRGKDAQLLQKCFS
PGVIEIDKSGIAYVKNARYDNCSRNVYRYPELSKNVEISRVRNHFIFNIESLGAYKPEEI
FILAVKTLKNKCDVLLEELNFENK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g5425.t2 | CDD | cd07032 | RNAP_I_II_AC40 | 1 | 258 | 0 |
| 9 | g5425.t2 | Gene3D | G3DSA:3.30.1360.270 | - | 1 | 251 | 0 |
| 8 | g5425.t2 | Gene3D | G3DSA:2.170.120.12 | RNA Polymerase Alpha Subunit; Chain A | 7 | 145 | 0 |
| 3 | g5425.t2 | PANTHER | PTHR11800 | DNA-DIRECTED RNA POLYMERASE | 1 | 260 | 0 |
| 4 | g5425.t2 | PANTHER | PTHR11800:SF13 | DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC1 | 1 | 260 | 0 |
| 2 | g5425.t2 | Pfam | PF01193 | RNA polymerase Rpb3/Rpb11 dimerisation domain | 1 | 252 | 0 |
| 1 | g5425.t2 | Pfam | PF01000 | RNA polymerase Rpb3/RpoA insert domain | 13 | 148 | 0 |
| 7 | g5425.t2 | SMART | SM00662 | rpoldneu2 | 1 | 258 | 0 |
| 6 | g5425.t2 | SUPERFAMILY | SSF55257 | RBP11-like subunits of RNA polymerase | 1 | 260 | 0 |
| 5 | g5425.t2 | SUPERFAMILY | SSF56553 | Insert subdomain of RNA polymerase alpha subunit | 6 | 149 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5425/g5425.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5425.t2.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.
