General information for g17775.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g17775 is located on HiC_scaffold_345: 195..2377 (- 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 |
|---|---|---|---|---|---|---|
| HiC_scaffold_345 | g17775 | g17775.t3 | isoform | g17775.t3 | 320 | 1307 |
| HiC_scaffold_345 | g17775 | g17775.t3 | exon | g17775.t3.exon1 | 320 | 409 |
| HiC_scaffold_345 | g17775 | g17775.t3 | exon | g17775.t3.exon2 | 485 | 648 |
| HiC_scaffold_345 | g17775 | g17775.t3 | cds | g17775.t3.CDS1 | 512 | 648 |
| HiC_scaffold_345 | g17775 | g17775.t3 | exon | g17775.t3.exon3 | 702 | 847 |
| HiC_scaffold_345 | g17775 | g17775.t3 | cds | g17775.t3.CDS2 | 702 | 847 |
| HiC_scaffold_345 | g17775 | g17775.t3 | exon | g17775.t3.exon4 | 910 | 1307 |
| HiC_scaffold_345 | g17775 | g17775.t3 | cds | g17775.t3.CDS3 | 910 | 1307 |
| HiC_scaffold_345 | g17775 | g17775.t3 | TSS | g17775.t3 | NA | NA |
| HiC_scaffold_345 | g17775 | g17775.t3 | TTS | g17775.t3 | NA | NA |
Sequences
>g17775.t3 Gene=g17775 Length=798
ATGGAATCTAAAGTTGAAGGTAAATTAAAATTTATGTTAAATCATGCTAGTTTTTATAAA
CGTTTATTTACAGAAGTGCAGAATGTAATTGAACATCTCGTTCATCCACGAGAGAAGAAG
ACTTCAAATATTCAAGATTTAAATCAATTTCAAGAAATTGCAAATGTCAAAAGAAAAGAG
AAGAAGTTAAAGAAACTCAAGCCACAAAAGAAGAAGCTGTCAAGAAATGAAATGAAGAAT
CTTGGATTATATTCACTACCTAGAAAAACTATGAAATATGACGATTATAGAGAATTGAAT
GAACTATGGAATAGTTATATGGAACAAATTTTAGGCAGTGATATGGAAAATCTAAAGAAG
AAGTTTGATACAACAAGTAATCATTATGATAGTGTTAGTGCAACAATTCATAAAAGTGAC
TTTCATGGAGCTAAGTTGAAGATTGTGCAATCAAAGTGTGTTAGTTTAACTGGCCAAAAA
GGAATAGTTGTATTGGATACAAAAGGAACATTTAATATAATTTGTAAAGATAATGTTTTA
AGAATTGTACCTAAAAATGCATCAATATTCGAATTGAAATGGAGAAAAGCTAGATTTACA
GTTTATGGAAAGAATCTAGCAATAAGAACAGCAGAGAGATCTGTAAAGAAAATCAAAACA
GTTCGTCTGATAGAAATATAAAACAGTCAAATAAAATTCAAAATCGGGTTCAATTTTACC
ATCAAAATAGCTTCAAAAGCAAAATATCCACCGGATAACAAGTCACAGAGTAAAGATATT
TATATTCAGATCAAATCT
>g17775.t3 Gene=g17775 Length=226
MESKVEGKLKFMLNHASFYKRLFTEVQNVIEHLVHPREKKTSNIQDLNQFQEIANVKRKE
KKLKKLKPQKKKLSRNEMKNLGLYSLPRKTMKYDDYRELNELWNSYMEQILGSDMENLKK
KFDTTSNHYDSVSATIHKSDFHGAKLKIVQSKCVSLTGQKGIVVLDTKGTFNIICKDNVL
RIVPKNASIFELKWRKARFTVYGKNLAIRTAERSVKKIKTVRLIEI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g17775.t3 | Coils | Coil | Coil | 56 | 76 | - |
| 5 | g17775.t3 | Gene3D | G3DSA:2.30.30.210 | - | 112 | 220 | 5.9E-19 |
| 2 | g17775.t3 | PANTHER | PTHR13348 | RIBONUCLEASE P SUBUNIT P29 | 41 | 224 | 1.6E-43 |
| 7 | g17775.t3 | PIRSF | PIRSF027081 | RPP29 | 9 | 226 | 4.3E-47 |
| 1 | g17775.t3 | Pfam | PF01868 | Domain of unknown function UPF0086 | 135 | 215 | 2.6E-25 |
| 4 | g17775.t3 | SMART | SM00538 | pop4_2 | 130 | 221 | 5.9E-22 |
| 3 | g17775.t3 | SUPERFAMILY | SSF101744 | Rof/RNase P subunit-like | 134 | 224 | 4.01E-24 |
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:0006396 | RNA processing | BP |
| GO:0003723 | RNA binding | MF |
| GO:0030677 | ribonuclease P complex | CC |
| GO:0004540 | ribonuclease activity | MF |
| GO:0008033 | tRNA processing | BP |
KEGG
Orthology
- This transcript has been annotated with K03538 (ribonuclease P protein subunit POP4)
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.
