General information for g3384.t26
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 60S acidic ribosomal protein P0.
Parent gene
- The parent gene g3384 is located on chr_3: 25010458..25011604 (- 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 | g3384 | g3384.t26 | TTS | g3384.t26 | 25009832 | 25009832 |
| chr_3 | g3384 | g3384.t26 | isoform | g3384.t26 | 25010043 | 25011371 |
| chr_3 | g3384 | g3384.t26 | exon | g3384.t26.exon1 | 25010043 | 25010086 |
| chr_3 | g3384 | g3384.t26 | cds | g3384.t26.CDS1 | 25010074 | 25010086 |
| chr_3 | g3384 | g3384.t26 | exon | g3384.t26.exon2 | 25010235 | 25011001 |
| chr_3 | g3384 | g3384.t26 | cds | g3384.t26.CDS2 | 25010235 | 25011001 |
| chr_3 | g3384 | g3384.t26 | exon | g3384.t26.exon3 | 25011277 | 25011371 |
| chr_3 | g3384 | g3384.t26 | cds | g3384.t26.CDS3 | 25011277 | 25011330 |
| chr_3 | g3384 | g3384.t26 | TSS | g3384.t26 | 25011604 | 25011604 |
Sequences
>g3384.t26 Gene=g3384 Length=906
GTTCTTTAAATCTGAAATCAGTACCTTACTAATAATTCAAAATGGTTAGGGAGAACAAGG
CCACCTGGAAAGCTAACTACTTCTTAAAAGTCGTGACATATCTCGACGAATATCCAAAAT
GTTTCATCGTCGGTGCCGATAACGTTGGTTCAAAGCAAATGCAGCAAATTCGTATCTCAC
TTCGTGGACTCGCTGTAGTCTTGATGGGCAAGAACACTATGATGCGTAAAGCCATTAAGG
GCCATTTGGAAAACAATCAAGCCCTCGACAGAATTTTACCACACATTCGTGGTAATGTTG
GTTTCGTTTTCACAAAGGGAGATTTGAATGAAGTTCGCGAAAAGTTGTTGCAAAACAAAG
TTCGTGCTCCTGCTCGTGCTGGCGCAATTGCTCCTTGTGAAGTAATTATTCCTGCTCAAA
ATACTGGTTTGGGTCCAGAAAAAACAAGTTTCTTCCAAGCTCTTTCAATTCCAACAAAGA
TTTCAAAGGGTACTATTGAAATTATCAATGATGTGCCCATCTTAAAGCCTGGTGACAAAG
TCGGTGCTTCTGAAGCTACTTTGCTCAACATGTTGAACATCTCTCCATTCTCATATGGTT
TGGTAATTGAGCAAGTTTATGATTCAGGAAGCATCTTCTCTCCAAATATCTTGGACATCA
AACCAGAAGATTTGCGTGCTAAATTCCAACAAGGAGTTGCAAACGTTGCCGCTCTTTCAT
TGGCTATGGGCTATCCAACAATTGCCTCTGCTCCACATTCAATTGCCAATGGTTTCAAGA
ACTTGCTCGCTATCGCAGCTGTTACCGATGTCGAATTCAAGCAGGCTGAAACTGTTAAAG
AATTCCTTAAGGATCCATCTAAAACCAGAGTCTGATGACGACATGGGATTCGGACTTTTT
GATTAA
>g3384.t26 Gene=g3384 Length=277
MVRENKATWKANYFLKVVTYLDEYPKCFIVGADNVGSKQMQQIRISLRGLAVVLMGKNTM
MRKAIKGHLENNQALDRILPHIRGNVGFVFTKGDLNEVREKLLQNKVRAPARAGAIAPCE
VIIPAQNTGLGPEKTSFFQALSIPTKISKGTIEIINDVPILKPGDKVGASEATLLNMLNI
SPFSYGLVIEQVYDSGSIFSPNILDIKPEDLRAKFQQGVANVAALSLAMGYPTIASAPHS
IANGFKNLLAIAAVTDVEFKQAETVKEFLKDPSKTRV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g3384.t26 | CDD | cd05795 | Ribosomal_P0_L10e | 9 | 182 | 0 |
| 6 | g3384.t26 | Gene3D | G3DSA:3.90.105.20 | - | 110 | 182 | 0 |
| 3 | g3384.t26 | PANTHER | PTHR45699 | 60S ACIDIC RIBOSOMAL PROTEIN P0 | 1 | 275 | 0 |
| 4 | g3384.t26 | PANTHER | PTHR45699:SF3 | 60S ACIDIC RIBOSOMAL PROTEIN P0 | 1 | 275 | 0 |
| 7 | g3384.t26 | PIRSF | PIRSF039087 | L10E | 1 | 277 | 0 |
| 2 | g3384.t26 | Pfam | PF00466 | Ribosomal protein L10 | 7 | 104 | 0 |
| 1 | g3384.t26 | Pfam | PF17777 | Insertion domain in 60S ribosomal protein L10P | 111 | 180 | 0 |
| 5 | g3384.t26 | SUPERFAMILY | SSF160369 | Ribosomal protein L10-like | 8 | 131 | 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:0042254 | ribosome biogenesis | BP |
KEGG
Orthology
- This transcript has been annotated with K02941 (large subunit ribosomal protein LP0)
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.
