General information for g17775.t2
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.t2 | isoform | g17775.t2 | 195 | 1307 |
| HiC_scaffold_345 | g17775 | g17775.t2 | exon | g17775.t2.exon1 | 195 | 409 |
| HiC_scaffold_345 | g17775 | g17775.t2 | exon | g17775.t2.exon2 | 485 | 648 |
| HiC_scaffold_345 | g17775 | g17775.t2 | cds | g17775.t2.CDS1 | 512 | 648 |
| HiC_scaffold_345 | g17775 | g17775.t2 | exon | g17775.t2.exon3 | 702 | 847 |
| HiC_scaffold_345 | g17775 | g17775.t2 | cds | g17775.t2.CDS2 | 702 | 847 |
| HiC_scaffold_345 | g17775 | g17775.t2 | exon | g17775.t2.exon4 | 910 | 1234 |
| HiC_scaffold_345 | g17775 | g17775.t2 | cds | g17775.t2.CDS3 | 910 | 1234 |
| HiC_scaffold_345 | g17775 | g17775.t2 | exon | g17775.t2.exon5 | 1289 | 1307 |
| HiC_scaffold_345 | g17775 | g17775.t2 | cds | g17775.t2.CDS4 | 1289 | 1307 |
| HiC_scaffold_345 | g17775 | g17775.t2 | TSS | g17775.t2 | NA | NA |
| HiC_scaffold_345 | g17775 | g17775.t2 | TTS | g17775.t2 | NA | NA |
Sequences
>g17775.t2 Gene=g17775 Length=869
ATGGAATCTAAAGTTGAAGAAGTGCAGAATGTAATTGAACATCTCGTTCATCCACGAGAG
AAGAAGACTTCAAATATTCAAGATTTAAATCAATTTCAAGAAATTGCAAATGTCAAAAGA
AAAGAGAAGAAGTTAAAGAAACTCAAGCCACAAAAGAAGAAGCTGTCAAGAAATGAAATG
AAGAATCTTGGATTATATTCACTACCTAGAAAAACTATGAAATATGACGATTATAGAGAA
TTGAATGAACTATGGAATAGTTATATGGAACAAATTTTAGGCAGTGATATGGAAAATCTA
AAGAAGAAGTTTGATACAACAAGTAATCATTATGATAGTGTTAGTGCAACAATTCATAAA
AGTGACTTTCATGGAGCTAAGTTGAAGATTGTGCAATCAAAGTGTGTTAGTTTAACTGGC
CAAAAAGGAATAGTTGTATTGGATACAAAAGGAACATTTAATATAATTTGTAAAGATAAT
GTTTTAAGAATTGTACCTAAAAATGCATCAATATTCGAATTGAAATGGAGAAAAGCTAGA
TTTACAGTTTATGGAAAGAATCTAGCAATAAGAACAGCAGAGAGATCTGTAAAGAAAATC
AAAACAGTTCGTCTGATAGAAATATAAAACAGTCAAATAAAATTCAAAATCGGGTTCAAT
TTTACCATCAAAATAGCTTCAAAAGCAAAATATCCACCGGATAACAAGTCACAGAGTAAA
GATATTTATATTCAGATCAAATCTGTGAGTAAAAATACATTTTTAATAAGTGGCCTTTGT
TTTCATACAAATAACTTGTTCCATTTTTTCTTCCTATTTTGATTTCGCAGTTATTTTTAG
TTCATAATAAAAACAATGTCGGAAATTGA
>g17775.t2 Gene=g17775 Length=208
MESKVEEVQNVIEHLVHPREKKTSNIQDLNQFQEIANVKRKEKKLKKLKPQKKKLSRNEM
KNLGLYSLPRKTMKYDDYRELNELWNSYMEQILGSDMENLKKKFDTTSNHYDSVSATIHK
SDFHGAKLKIVQSKCVSLTGQKGIVVLDTKGTFNIICKDNVLRIVPKNASIFELKWRKAR
FTVYGKNLAIRTAERSVKKIKTVRLIEI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g17775.t2 | Coils | Coil | Coil | 38 | 58 | - |
| 5 | g17775.t2 | Gene3D | G3DSA:2.30.30.210 | - | 94 | 202 | 4.9E-19 |
| 2 | g17775.t2 | PANTHER | PTHR13348 | RIBONUCLEASE P SUBUNIT P29 | 23 | 206 | 1.0E-43 |
| 7 | g17775.t2 | PIRSF | PIRSF027081 | RPP29 | 2 | 208 | 4.3E-47 |
| 1 | g17775.t2 | Pfam | PF01868 | Domain of unknown function UPF0086 | 117 | 197 | 2.2E-25 |
| 4 | g17775.t2 | SMART | SM00538 | pop4_2 | 112 | 203 | 5.9E-22 |
| 3 | g17775.t2 | SUPERFAMILY | SSF101744 | Rof/RNase P subunit-like | 116 | 206 | 3.31E-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.
