General information for g8398.t1
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.t1 | TTS | g8398.t1 | 30152534 | 30152534 |
| chr_2 | g8398 | g8398.t1 | isoform | g8398.t1 | 30152579 | 30153338 |
| chr_2 | g8398 | g8398.t1 | exon | g8398.t1.exon1 | 30152579 | 30152799 |
| chr_2 | g8398 | g8398.t1 | cds | g8398.t1.CDS1 | 30152579 | 30152799 |
| chr_2 | g8398 | g8398.t1 | exon | g8398.t1.exon2 | 30152860 | 30153073 |
| chr_2 | g8398 | g8398.t1 | cds | g8398.t1.CDS2 | 30152860 | 30153073 |
| chr_2 | g8398 | g8398.t1 | exon | g8398.t1.exon3 | 30153132 | 30153338 |
| chr_2 | g8398 | g8398.t1 | cds | g8398.t1.CDS3 | 30153132 | 30153338 |
| chr_2 | g8398 | g8398.t1 | TSS | g8398.t1 | 30153376 | 30153376 |
Sequences
>g8398.t1 Gene=g8398 Length=642
ATGCTAAATTTACTAAAAACTTCAAGTTTATTGATAAGAAATGAAGTGAATTTGATAAAT
TCTCAAATTGGCGCATTATTCCATACATCAACAGTTGTTGATGCAAAGAATAGCAATGCA
GGACACAGTAATAAACCAAAAAGATTTTTAAGACAAAATAAGAAAATTTTTGAGCCACAA
TTACCAGATGAAACACCGAGACCAGCATTCGTTTGTCATCAAAAAGAGAACATTCGATAT
AGTCCTAAGAAAATGTGGTACATTGCGGCATTTGTGCGAGGAATGACTGTAGATGAAGCT
GTGAAGCAATTAAGCTTTCAACTTAAAAAAGGTGCTGCAGCTGTTAAAGAAACGCTTTTA
GAAGCTCAAGAGATTGCTGTCAAACAGCACAATGTTGAATTCAAAAGTAATTTGTGGATC
TCCGAATCATTTGTTGGTAAAGGAGTAGTCTTTAAAGGAATTAGACGACATGCAAAAGGT
AGAATGGGAAGAGTAGAATATAAACATTGTCACTATTTCGTAAAGCTCGAAGAAGGAACA
CCTCCGGAACATTATTATTTGCCTTATCCTAAAACACCAGAGCAACAACTTGATGATTGG
ATGAGTCAAATGAGAAAGAGAAAAATAACGAATTCATTGTAG
>g8398.t1 Gene=g8398 Length=213
MLNLLKTSSLLIRNEVNLINSQIGALFHTSTVVDAKNSNAGHSNKPKRFLRQNKKIFEPQ
LPDETPRPAFVCHQKENIRYSPKKMWYIAAFVRGMTVDEAVKQLSFQLKKGAAAVKETLL
EAQEIAVKQHNVEFKSNLWISESFVGKGVVFKGIRRHAKGRMGRVEYKHCHYFVKLEEGT
PPEHYYLPYPKTPEQQLDDWMSQMRKRKITNSL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g8398.t1 | CDD | cd00336 | Ribosomal_L22 | 71 | 176 | 0 |
| 5 | g8398.t1 | Gene3D | G3DSA:3.90.470.10 | Ribosomal Protein L22; Chain A | 46 | 213 | 0 |
| 2 | g8398.t1 | PANTHER | PTHR13501:SF8 | 39S RIBOSOMAL PROTEIN L22, MITOCHONDRIAL | 42 | 207 | 0 |
| 3 | g8398.t1 | PANTHER | PTHR13501 | CHLOROPLAST 50S RIBOSOMAL PROTEIN L22-RELATED | 42 | 207 | 0 |
| 1 | g8398.t1 | Pfam | PF00237 | Ribosomal protein L22p/L17e | 74 | 176 | 0 |
| 4 | g8398.t1 | SUPERFAMILY | SSF54843 | Ribosomal protein L22 | 62 | 180 | 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 transcript has been annotated with K02890 (large subunit ribosomal protein L22)
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.
