General information for g9646.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative DNA-directed RNA polymerase I subunit RPA1.
Parent gene
- The parent gene g9646 is located on chr_1: 4461541..4463062 (- 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 | g9646 | g9646.t3 | isoform | g9646.t3 | 4461541 | 4462260 |
| chr_1 | g9646 | g9646.t3 | exon | g9646.t3.exon1 | 4461541 | 4461704 |
| chr_1 | g9646 | g9646.t3 | cds | g9646.t3.CDS1 | 4461541 | 4461704 |
| chr_1 | g9646 | g9646.t3 | TTS | g9646.t3 | 4461555 | 4461555 |
| chr_1 | g9646 | g9646.t3 | exon | g9646.t3.exon2 | 4461760 | 4461954 |
| chr_1 | g9646 | g9646.t3 | cds | g9646.t3.CDS2 | 4461760 | 4461954 |
| chr_1 | g9646 | g9646.t3 | exon | g9646.t3.exon3 | 4462016 | 4462173 |
| chr_1 | g9646 | g9646.t3 | cds | g9646.t3.CDS3 | 4462016 | 4462169 |
| chr_1 | g9646 | g9646.t3 | exon | g9646.t3.exon4 | 4462246 | 4462260 |
| chr_1 | g9646 | g9646.t3 | TSS | g9646.t3 | 4462396 | 4462396 |
Sequences
>g9646.t3 Gene=g9646 Length=532
AATCAAAAAATTACCGAAAATGCCAGTGTCTTTGGCTAAAGAGCGTCCAGTTACGCTAAA
TATTGAAAATGTAGAGTTCAGTGTTTTCAATGCTGAAGAAATTCGTAAAATCAGTGTCTG
CAAAATTTTAAACCCTATTTCTTTTGATGGTCTTGGAAATTCTACTGCTGGAGGTCTATA
TGACAATCGTATGGGACCTTTATCACGTCGAGAACTTTGCGGAACTTGCAATAGTGGAGA
AAATGATTGTACCGGTCATTTTGGCCACATCGATTTAGTTATGACTGTCTATAATCCATT
TTTCATGAAAAACCTAGTTTCAATATTGAAATCAGTATGTACGAAATGCTTCAGACTTCA
AATAACTGATCGAATGAAGGAAATTGTTGAACTTCAGTTGCAATTAATTGATGCAGGATA
TGTTGCTGAAGCTTCGGATTTAGAAGATCAGAAACTTGTTTTCTGTAAGACAAAAACAAT
TTCAAAGAAGTTAACAAAAGAGAATATTGAAAATAATGAAAGAGATGAAAAA
>g9646.t3 Gene=g9646 Length=171
MPVSLAKERPVTLNIENVEFSVFNAEEIRKISVCKILNPISFDGLGNSTAGGLYDNRMGP
LSRRELCGTCNSGENDCTGHFGHIDLVMTVYNPFFMKNLVSILKSVCTKCFRLQITDRMK
EIVELQLQLIDAGYVAEASDLEDQKLVFCKTKTISKKLTKENIENNERDEK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g9646.t3 | Gene3D | G3DSA:1.20.120.1280 | - | 5 | 139 | 0 |
| 2 | g9646.t3 | PANTHER | PTHR19376:SF57 | DNA-DIRECTED RNA POLYMERASE SUBUNIT | 14 | 118 | 0 |
| 3 | g9646.t3 | PANTHER | PTHR19376 | DNA-DIRECTED RNA POLYMERASE | 14 | 118 | 0 |
| 1 | g9646.t3 | Pfam | PF04997 | RNA polymerase Rpb1, domain 1 | 14 | 128 | 0 |
| 4 | g9646.t3 | SUPERFAMILY | SSF64484 | beta and beta-prime subunits of DNA dependent RNA-polymerase | 15 | 148 | 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: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