General information for g1608.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative DNA-directed RNA polymerase I subunit RPA12.
Parent gene
- The parent gene g1608 is located on chr_3: 12101736..12102151 (+ 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 | g1608 | g1608.t6 | TSS | g1608.t6 | 12101003 | 12101003 |
| chr_3 | g1608 | g1608.t6 | isoform | g1608.t6 | 12101136 | 12102151 |
| chr_3 | g1608 | g1608.t6 | exon | g1608.t6.exon1 | 12101136 | 12101228 |
| chr_3 | g1608 | g1608.t6 | exon | g1608.t6.exon2 | 12101647 | 12101862 |
| chr_3 | g1608 | g1608.t6 | cds | g1608.t6.CDS1 | 12101736 | 12101862 |
| chr_3 | g1608 | g1608.t6 | exon | g1608.t6.exon3 | 12101919 | 12102151 |
| chr_3 | g1608 | g1608.t6 | cds | g1608.t6.CDS2 | 12101919 | 12102151 |
| chr_3 | g1608 | g1608.t6 | TTS | g1608.t6 | 12102190 | 12102190 |
Sequences
>g1608.t6 Gene=g1608 Length=542
ACTTTAGAGGGTAATATGTTTGTCATTTGATAGCTAAATATTGTGTAGAATCAAAGAGAA
AAAGAATCTTATCAGATATGAAGAAAAAATGGCAGAGGTTTTCAATTTTTAAAGATTCAA
CGATTTTTATAAACAACAACTCGTGTTTAACATCAACTTTATAAATTATTTCATCAAAAA
CAATGGAATCACAGTTAAAAGTTATTGATACACCAGGTTTTTGTCCGAATTGCGGATCAG
TTTTACCACCAATGAAATCTCATGGAGGATTATTGTGCTTTATTTGTGATAAAGAACACG
ATGCTCAAGTATTTGGTGAAATGAGAACAGAATATAACATTCATTTCAATAAAATACCAG
ATAAAGAAGAATTTGATGAAGAAAGCGATACTGAGGAAGGTGCACTTGTAGATAGAAAAT
GTGTCAAATGCGGAAATGATAAATTTCGATATGCAACATTACAATTAAGATCAGCAGATG
AAGGACAAACTGTTTTCTATACATGCACTAAATGTAATTACAAAGAAACAGAGAATTCAT
AA
>g1608.t6 Gene=g1608 Length=119
MESQLKVIDTPGFCPNCGSVLPPMKSHGGLLCFICDKEHDAQVFGEMRTEYNIHFNKIPD
KEEFDEESDTEEGALVDRKCVKCGNDKFRYATLQLRSADEGQTVFYTCTKCNYKETENS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g1608.t6 | CDD | cd10507 | Zn-ribbon_RPA12 | 72 | 118 | 2.23306E-25 |
| 5 | g1608.t6 | Gene3D | G3DSA:2.20.25.10 | - | 64 | 117 | 1.6E-16 |
| 2 | g1608.t6 | PANTHER | PTHR11239 | DNA-DIRECTED RNA POLYMERASE | 12 | 118 | 8.9E-25 |
| 3 | g1608.t6 | PANTHER | PTHR11239:SF14 | DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA12 | 12 | 118 | 8.9E-25 |
| 6 | g1608.t6 | PIRSF | PIRSF005586 | RNApol_RpoM | 12 | 119 | 1.0E-23 |
| 1 | g1608.t6 | Pfam | PF01096 | Transcription factor S-II (TFIIS) | 79 | 114 | 4.6E-15 |
| 8 | g1608.t6 | ProSitePatterns | PS00466 | Zinc finger TFIIS-type signature. | 80 | 115 | - |
| 10 | g1608.t6 | ProSiteProfiles | PS51133 | Zinc finger TFIIS-type profile. | 76 | 116 | 12.566 |
| 9 | g1608.t6 | SMART | SM00440 | Cys4_2 | 78 | 117 | 7.8E-13 |
| 4 | g1608.t6 | SUPERFAMILY | SSF57783 | Zinc beta-ribbon | 69 | 118 | 1.42E-15 |
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:0008270 | zinc ion binding | MF |
| GO:0006379 | mRNA cleavage | BP |
| GO:0006351 | transcription, DNA-templated | BP |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K03000 (DNA-directed RNA polymerase I subunit RPA12)
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.
