General information for g2267.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative DNA-directed RNA polymerase III subunit RPC8.
Parent gene
- The parent gene g2267 is located on chr_3: 16346454..16347131 (- 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 | g2267 | g2267.t4 | TTS | g2267.t4 | 16346396 | 16346396 |
| chr_3 | g2267 | g2267.t4 | isoform | g2267.t4 | 16346454 | 16347131 |
| chr_3 | g2267 | g2267.t4 | exon | g2267.t4.exon1 | 16346454 | 16346818 |
| chr_3 | g2267 | g2267.t4 | cds | g2267.t4.CDS1 | 16346454 | 16346818 |
| chr_3 | g2267 | g2267.t4 | exon | g2267.t4.exon2 | 16346942 | 16347131 |
| chr_3 | g2267 | g2267.t4 | cds | g2267.t4.CDS2 | 16346942 | 16347131 |
| chr_3 | g2267 | g2267.t4 | TSS | g2267.t4 | 16347147 | 16347147 |
Sequences
>g2267.t4 Gene=g2267 Length=555
ATGTTTGTAATTACAGAAATAAATTCTACAGTGGTTATTCAACCAAAAGACTTTAATAAG
AAGGTAGATGAAGTGTGTAAATATGAATTAAACAGAAAATTAGCTAATAAAATACTTCAT
AATGTGGGATTGTGCCTTTATATTCATGAAATCGTTTTTATTGGTGATGCACTTGTAAAG
CCAACAGATGGAACAGTAAGAAAATGCGAAAGAAATGGGATTTACGTGTCATTAGGATTC
TTCGATGATATTTTCATTCCTGAAAACAAATTACAATTTCCCTCACGATATGATGAAGTA
GAAAATGTTTGGGTTTGGCAATATTCTGTTGGAAATGATGAAACACATGATTTATTCATT
GATGAAGGAGAAAAGATAAAATTAAGAGTTGTTGATGAATATTTCTTTGAGCATGAACCA
GTAGGATCTTCTGAAGAAATCCAACAAGAGCAAGAACCGAGTTATATCATTATAGGTTCA
ATTAATGAGTGTGGACTTGGTCTTGATGCATGGTGGAATCAAGCGGCAAACAATGAAAAT
GATGAAGAATATTGA
>g2267.t4 Gene=g2267 Length=184
MFVITEINSTVVIQPKDFNKKVDEVCKYELNRKLANKILHNVGLCLYIHEIVFIGDALVK
PTDGTVRKCERNGIYVSLGFFDDIFIPENKLQFPSRYDEVENVWVWQYSVGNDETHDLFI
DEGEKIKLRVVDEYFFEHEPVGSSEEIQQEQEPSYIIIGSINECGLGLDAWWNQAANNEN
DEEY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g2267.t4 | Gene3D | G3DSA:2.40.50.140 | - | 53 | 173 | 0e+00 |
| 3 | g2267.t4 | PANTHER | PTHR12709:SF1 | DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC8 | 1 | 66 | 0e+00 |
| 5 | g2267.t4 | PANTHER | PTHR12709 | DNA-DIRECTED RNA POLYMERASE II, III | 1 | 66 | 0e+00 |
| 4 | g2267.t4 | PANTHER | PTHR12709:SF1 | DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC8 | 63 | 175 | 0e+00 |
| 6 | g2267.t4 | PANTHER | PTHR12709 | DNA-DIRECTED RNA POLYMERASE II, III | 63 | 175 | 0e+00 |
| 2 | g2267.t4 | Pfam | PF03876 | SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 | 11 | 64 | 5e-07 |
| 1 | g2267.t4 | Pfam | PF08292 | RNA polymerase III subunit Rpc25 | 64 | 172 | 0e+00 |
| 7 | g2267.t4 | SUPERFAMILY | SSF88798 | N-terminal, heterodimerisation domain of RBP7 (RpoE) | 1 | 67 | 0e+00 |
| 8 | g2267.t4 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 62 | 167 | 0e+00 |
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: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