General information for g2571.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA-directed RNA polymerase III subunit RPC1.
Parent gene
- The parent gene g2571 is located on chr_3: 18809720..18811540 (+ 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_3 | g2571 | g2571.t3 | TSS | g2571.t3 | 18805220 | 18805220 |
| chr_3 | g2571 | g2571.t3 | isoform | g2571.t3 | 18805330 | 18806343 |
| chr_3 | g2571 | g2571.t3 | exon | g2571.t3.exon1 | 18805330 | 18805764 |
| chr_3 | g2571 | g2571.t3 | cds | g2571.t3.CDS1 | 18805330 | 18805764 |
| chr_3 | g2571 | g2571.t3 | exon | g2571.t3.exon2 | 18805826 | 18806343 |
| chr_3 | g2571 | g2571.t3 | cds | g2571.t3.CDS2 | 18805826 | 18806341 |
| chr_3 | g2571 | g2571.t3 | TTS | g2571.t3 | NA | NA |
Sequences
>g2571.t3 Gene=g2571 Length=953
ATGCCAAAGGAGCAGTACAGAGAGGCAGATGCCATTAAGGAAATATCACATGTTTCATTT
AGTCTCGATTCAGCTGAACAAATTCAACAATCGAGTCATTTACATGTCAAAGTAAAATCT
CTATATAATCAAGATCAGAAGCGAACTCCTATGACTTCTGGAGTTCTTGATTTACGGCTT
GGAGTCAGTCAAAAAGGCGCTACTTGTGAAACATGTAATCAAGGGTTGAACGAATGTGTA
GGTCATTTTGGATATCTCGATTTAGCTTTACCAGTATTTCATATTGGTCATTTTCGAGCG
ACTATAACTATATTACAAACAATTTGTAAAACATGTAGTCGTGTTATGCTTAAAGATGAA
GAAGCCAAAACGTTTAGTAAGAAACTTATGAATCCAAATCTCTCTTATCTCACAAAAAAA
GCTATTCATCAACAGGTTTTGAAAAAAGCAAAAAAAAACACAAAATGTCCACATTGTGAT
GCAATAAATGGTCCTGTCAAAAAAGGAGTTGGATTATTGAAAATTGTCCATGAACCATTT
AGAGGAAGAAAGAAAACTGATCCATTAGTAAATGATGCTCTTGAAGAACTTCTTTCAGCA
ACAGAAGAGAACAAGGAAGTATTTCAAAATGTTGGACAACAAACTTTAATTCATGAACTC
AATCCCGTAGAAGTACTGCATTTATTTAAAAATATACCAAAATGTGATATACCTCTTCTC
GGAATGACATCAGAAAATGCAGATCCAGCAAATTTAATTGTTACTCGGGTTTATGTTCCT
CCTGCTTGTATTCGCCCTTCTGTTGTCTCCGATATCAAATCTGGAACTACTGAAGACGAC
CTAACAATGAAACAAAGTGAAATTCTTCTCATTAATGATTTTATTGCAAAACATATGAAT
ACAAGTGGCAAAATTGAAATTATAGAGGAAGATTGGGATTATTTGCAGTTACA
>g2571.t3 Gene=g2571 Length=317
MPKEQYREADAIKEISHVSFSLDSAEQIQQSSHLHVKVKSLYNQDQKRTPMTSGVLDLRL
GVSQKGATCETCNQGLNECVGHFGYLDLALPVFHIGHFRATITILQTICKTCSRVMLKDE
EAKTFSKKLMNPNLSYLTKKAIHQQVLKKAKKNTKCPHCDAINGPVKKGVGLLKIVHEPF
RGRKKTDPLVNDALEELLSATEENKEVFQNVGQQTLIHELNPVEVLHLFKNIPKCDIPLL
GMTSENADPANLIVTRVYVPPACIRPSVVSDIKSGTTEDDLTMKQSEILLINDFIAKHMN
TSGKIEIIEEDWDYLQL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g2571.t3 | Coils | Coil | Coil | 190 | 211 | - |
| 5 | g2571.t3 | Gene3D | G3DSA:1.20.120.1280 | - | 1 | 125 | 2.8E-27 |
| 2 | g2571.t3 | PANTHER | PTHR19376:SF32 | DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC1 | 3 | 315 | 1.9E-65 |
| 3 | g2571.t3 | PANTHER | PTHR19376 | DNA-DIRECTED RNA POLYMERASE | 3 | 315 | 1.9E-65 |
| 1 | g2571.t3 | Pfam | PF04997 | RNA polymerase Rpb1, domain 1 | 13 | 317 | 5.0E-65 |
| 4 | g2571.t3 | SUPERFAMILY | SSF64484 | beta and beta-prime subunits of DNA dependent RNA-polymerase | 13 | 316 | 1.03E-61 |
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:0003899 | DNA-directed 5’-3’ RNA polymerase activity | MF |
| GO:0003677 | DNA binding | MF |
| GO:0006351 | transcription, DNA-templated | BP |
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