General information for g8398.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 39S ribosomal protein L22, mitochondrial.
Parent gene
- The parent gene g8398 is located on chr_2: 30152579..30154230 (- 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_2 | g8398 | g8398.t6 | TTS | g8398.t6 | 30152534 | 30152534 |
| chr_2 | g8398 | g8398.t6 | isoform | g8398.t6 | 30152579 | 30153338 |
| chr_2 | g8398 | g8398.t6 | exon | g8398.t6.exon1 | 30152579 | 30152799 |
| chr_2 | g8398 | g8398.t6 | cds | g8398.t6.CDS1 | 30152579 | 30152799 |
| chr_2 | g8398 | g8398.t6 | exon | g8398.t6.exon2 | 30152860 | 30153338 |
| chr_2 | g8398 | g8398.t6 | cds | g8398.t6.CDS2 | 30152860 | 30153028 |
| chr_2 | g8398 | g8398.t6 | TSS | g8398.t6 | 30153376 | 30153376 |
Sequences
>g8398.t6 Gene=g8398 Length=700
ATGCTAAATTTACTAAAAACTTCAAGTTTATTGATAAGAAATGAAGTGAATTTGATAAAT
TCTCAAATTGGCGCATTATTCCATACATCAACAGTTGTTGATGCAAAGAATAGCAATGCA
GGACACAGTAATAAACCAAAAAGATTTTTAAGACAAAATAAGAAAATTTTTGAGCCACAA
TTACCAGATGAAACACCGAGACCAGCAGTAAATTATACAATTAATCCATCAATAAACATA
ATGTAATTACTATTATCAATTATAGTTCGTTTGTCATCAAAAAGAGAACATTCGATATAG
TCCTAAGAAAATGTGGTACATTGCGGCATTTGTGCGAGGAATGACTGTAGATGAAGCTGT
GAAGCAATTAAGCTTTCAACTTAAAAAAGGTGCTGCAGCTGTTAAAGAAACGCTTTTAGA
AGCTCAAGAGATTGCTGTCAAACAGCACAATGTTGAATTCAAAAGTAATTTGTGGATCTC
CGAATCATTTGTTGGTAAAGGAGTAGTCTTTAAAGGAATTAGACGACATGCAAAAGGTAG
AATGGGAAGAGTAGAATATAAACATTGTCACTATTTCGTAAAGCTCGAAGAAGGAACACC
TCCGGAACATTATTATTTGCCTTATCCTAAAACACCAGAGCAACAACTTGATGATTGGAT
GAGTCAAATGAGAAAGAGAAAAATAACGAATTCATTGTAG
>g8398.t6 Gene=g8398 Length=129
MWYIAAFVRGMTVDEAVKQLSFQLKKGAAAVKETLLEAQEIAVKQHNVEFKSNLWISESF
VGKGVVFKGIRRHAKGRMGRVEYKHCHYFVKLEEGTPPEHYYLPYPKTPEQQLDDWMSQM
RKRKITNSL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g8398.t6 | CDD | cd00336 | Ribosomal_L22 | 1 | 92 | 0 |
| 5 | g8398.t6 | Gene3D | G3DSA:3.90.470.10 | Ribosomal Protein L22; Chain A | 1 | 129 | 0 |
| 2 | g8398.t6 | PANTHER | PTHR13501:SF8 | 39S RIBOSOMAL PROTEIN L22, MITOCHONDRIAL | 1 | 123 | 0 |
| 3 | g8398.t6 | PANTHER | PTHR13501 | CHLOROPLAST 50S RIBOSOMAL PROTEIN L22-RELATED | 1 | 123 | 0 |
| 1 | g8398.t6 | Pfam | PF00237 | Ribosomal protein L22p/L17e | 1 | 92 | 0 |
| 4 | g8398.t6 | SUPERFAMILY | SSF54843 | Ribosomal protein L22 | 1 | 96 | 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:0005840 | ribosome | CC |
| GO:0015934 | large ribosomal subunit | CC |
| GO:0006412 | translation | BP |
| GO:0003735 | structural constituent of ribosome | MF |
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.
