General information for g3384.t56
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.t56 | TTS | g3384.t56 | 25009832 | 25009832 |
| chr_3 | g3384 | g3384.t56 | isoform | g3384.t56 | 25010043 | 25011604 |
| chr_3 | g3384 | g3384.t56 | exon | g3384.t56.exon1 | 25010043 | 25010140 |
| chr_3 | g3384 | g3384.t56 | cds | g3384.t56.CDS1 | 25010043 | 25010140 |
| chr_3 | g3384 | g3384.t56 | exon | g3384.t56.exon2 | 25010203 | 25010694 |
| chr_3 | g3384 | g3384.t56 | cds | g3384.t56.CDS2 | 25010203 | 25010694 |
| chr_3 | g3384 | g3384.t56 | exon | g3384.t56.exon3 | 25010872 | 25011001 |
| chr_3 | g3384 | g3384.t56 | cds | g3384.t56.CDS3 | 25010872 | 25011001 |
| chr_3 | g3384 | g3384.t56 | exon | g3384.t56.exon4 | 25011277 | 25011370 |
| chr_3 | g3384 | g3384.t56 | cds | g3384.t56.CDS4 | 25011277 | 25011330 |
| chr_3 | g3384 | g3384.t56 | exon | g3384.t56.exon5 | 25011567 | 25011604 |
| chr_3 | g3384 | g3384.t56 | TSS | g3384.t56 | 25011604 | 25011604 |
Sequences
>g3384.t56 Gene=g3384 Length=852
CTTTTTCGTTCAGAAATTTATTGAATACACACGTCTTGTTCTTTAAATCTGAAATCAGTA
CCTTACTAATAATTCAAAATGGTTAGGGAGAACAAGGCCACCTGGAAAGCTAACTACTTC
TTAAAAGTCGTGACATATCTCGACGAATATCCAAAATGTTTCATCGTCGGTGCCGATAAC
GTTGGTTCAAAGCAAATGCAGCAAATTCGTATCTCACTTCGTGGACTCGCTGTAGTCTTG
ATGGGCAAGAACACTATGATGCTAATTATTCCTGCTCAAAATACTGGTTTGGGTCCAGAA
AAAACAAGTTTCTTCCAAGCTCTTTCAATTCCAACAAAGATTTCAAAGGGTACTATTGAA
ATTATCAATGATGTGCCCATCTTAAAGCCTGGTGACAAAGTCGGTGCTTCTGAAGCTACT
TTGCTCAACATGTTGAACATCTCTCCATTCTCATATGGTTTGGTAATTGAGCAAGTTTAT
GATTCAGGAAGCATCTTCTCTCCAAATATCTTGGACATCAAACCAGAAGATTTGCGTGCT
AAATTCCAACAAGGAGTTGCAAACGTTGCCGCTCTTTCATTGGCTATGGGCTATCCAACA
ATTGCCTCTGCTCCACATTCAATTGCCAATGGTTTCAAGAACTTGCTCGCTATCGCAGCT
GTTACCGATGTCGAATTCAAGCAGGCTGAAACTGTTAAAGAATTCCTTAAGGATCCATCT
AAGTTTGCCGCTGCTGCTGCTGCATCAGCTCCAGCTGCTTCTGCCGCTGCACCAGCTGCT
AAAGCTGAAGCCAAGAAAGAAGAGTCAGAACCAGAGTCTGATGACGACATGGGATTCGGA
CTTTTTGATTAA
>g3384.t56 Gene=g3384 Length=257
MVRENKATWKANYFLKVVTYLDEYPKCFIVGADNVGSKQMQQIRISLRGLAVVLMGKNTM
MLIIPAQNTGLGPEKTSFFQALSIPTKISKGTIEIINDVPILKPGDKVGASEATLLNMLN
ISPFSYGLVIEQVYDSGSIFSPNILDIKPEDLRAKFQQGVANVAALSLAMGYPTIASAPH
SIANGFKNLLAIAAVTDVEFKQAETVKEFLKDPSKFAAAAAASAPAASAAAPAAKAEAKK
EESEPESDDDMGFGLFD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g3384.t56 | Gene3D | G3DSA:3.30.70.1730 | - | 4 | 60 | 1.5E-17 |
| 10 | g3384.t56 | Gene3D | G3DSA:3.90.105.20 | - | 61 | 125 | 1.5E-24 |
| 9 | g3384.t56 | MobiDBLite | mobidb-lite | consensus disorder prediction | 225 | 257 | - |
| 4 | g3384.t56 | PANTHER | PTHR45699 | 60S ACIDIC RIBOSOMAL PROTEIN P0 | 1 | 61 | 3.5E-108 |
| 6 | g3384.t56 | PANTHER | PTHR45699:SF3 | 60S ACIDIC RIBOSOMAL PROTEIN P0 | 1 | 61 | 3.5E-108 |
| 5 | g3384.t56 | PANTHER | PTHR45699 | 60S ACIDIC RIBOSOMAL PROTEIN P0 | 63 | 257 | 3.5E-108 |
| 7 | g3384.t56 | PANTHER | PTHR45699:SF3 | 60S ACIDIC RIBOSOMAL PROTEIN P0 | 63 | 257 | 3.5E-108 |
| 2 | g3384.t56 | Pfam | PF00466 | Ribosomal protein L10 | 7 | 63 | 7.5E-10 |
| 1 | g3384.t56 | Pfam | PF17777 | Insertion domain in 60S ribosomal protein L10P | 62 | 121 | 1.6E-15 |
| 3 | g3384.t56 | Pfam | PF00428 | 60s Acidic ribosomal protein | 172 | 256 | 1.1E-18 |
| 8 | g3384.t56 | SUPERFAMILY | SSF160369 | Ribosomal protein L10-like | 8 | 70 | 1.57E-6 |
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 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.
