General information for g3754.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g3754 is located on chr_3: 27831360..27831861 (- 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 | g3754 | g3754.t1 | TTS | g3754.t1 | 27831104 | 27831104 |
| chr_3 | g3754 | g3754.t1 | isoform | g3754.t1 | 27831164 | 27831861 |
| chr_3 | g3754 | g3754.t1 | exon | g3754.t1.exon1 | 27831164 | 27831286 |
| chr_3 | g3754 | g3754.t1 | cds | g3754.t1.CDS1 | 27831164 | 27831286 |
| chr_3 | g3754 | g3754.t1 | exon | g3754.t1.exon2 | 27831343 | 27831861 |
| chr_3 | g3754 | g3754.t1 | cds | g3754.t1.CDS2 | 27831343 | 27831861 |
| chr_3 | g3754 | g3754.t1 | TSS | g3754.t1 | 27831935 | 27831935 |
Sequences
>g3754.t1 Gene=g3754 Length=642
ATGTATCAATATCGTAATTCAAGCTTCACAAAGGAGCAGTTAACTAATCTAGGCATCACA
AAAGAGATGAACACATCTCAGCAATTCAATAGACCGCTTTTTCCACTACTGCAAAATAAA
CCAATCGAGATTGAGAAAAATAATAAGGCTATGGATTATAAGGTATTATTCAAAGAAGAT
TTTAGAAGTCGATTATTTGAAATTCACAATACAGCAAGTTCAGCGAAGAAAGGCACAGAA
ATGGACAATTATAGTTTACAAATTGCAGCAGCATTAGAAAAGGAACATAAGAAAAATTTA
AAATTTACGATAGCAAGGAAAATGATGCCTGCAGAGTTAAACTATCAATCGAATCCTAAG
AAACGAAAAGATATTGCTCCTGCATTGAAATCTTCTAAAAAACGAATTATAGATGTAGAA
AAACGACTTGAAGTTTTAGAAAAGAAAGAAGCCAATGAAAAAGAAGAAGATGAAGAAAGT
GAAAAACCAAACAATGATAGTGATGCAGAAGCTGAGAATCAAGAAGACATTGAAGATCCG
GAACTTGATGATGAGACAGATTATCATAACAATTATTTTGATAATGGAGATAATTTTTAT
GCAGACGAAGATGATGCACTAGATGATGGTCCAATTTATTAG
>g3754.t1 Gene=g3754 Length=213
MYQYRNSSFTKEQLTNLGITKEMNTSQQFNRPLFPLLQNKPIEIEKNNKAMDYKVLFKED
FRSRLFEIHNTASSAKKGTEMDNYSLQIAAALEKEHKKNLKFTIARKMMPAELNYQSNPK
KRKDIAPALKSSKKRIIDVEKRLEVLEKKEANEKEEDEESEKPNNDSDAEAENQEDIEDP
ELDDETDYHNNYFDNGDNFYADEDDALDDGPIY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g3754.t1 | Coils | Coil | Coil | 129 | 156 | - |
| 6 | g3754.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 148 | 213 | - |
| 5 | g3754.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 159 | 185 | - |
| 4 | g3754.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 198 | 213 | - |
| 2 | g3754.t1 | PANTHER | PTHR15367:SF4 | DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC7-LIKE | 22 | 209 | 6.7E-13 |
| 3 | g3754.t1 | PANTHER | PTHR15367 | DNA-DIRECTED RNA POLYMERASE III | 22 | 209 | 6.7E-13 |
| 1 | g3754.t1 | Pfam | PF11705 | DNA-directed RNA polymerase III subunit Rpc31 | 10 | 198 | 2.3E-13 |
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:0006383 | transcription by RNA polymerase III | BP |
KEGG
Orthology
- This transcript has been annotated with K03024 (DNA-directed RNA polymerase III subunit RPC7)
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.
