General information for g3384.t23
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t23 | TTS | g3384.t23 | 25009832 | 25009832 |
| chr_3 | g3384 | g3384.t23 | isoform | g3384.t23 | 25010043 | 25011371 |
| chr_3 | g3384 | g3384.t23 | exon | g3384.t23.exon1 | 25010043 | 25010140 |
| chr_3 | g3384 | g3384.t23 | cds | g3384.t23.CDS1 | 25010043 | 25010140 |
| chr_3 | g3384 | g3384.t23 | exon | g3384.t23.exon2 | 25010203 | 25010796 |
| chr_3 | g3384 | g3384.t23 | cds | g3384.t23.CDS2 | 25010203 | 25010527 |
| chr_3 | g3384 | g3384.t23 | exon | g3384.t23.exon3 | 25010900 | 25011001 |
| chr_3 | g3384 | g3384.t23 | exon | g3384.t23.exon4 | 25011277 | 25011371 |
| chr_3 | g3384 | g3384.t23 | TSS | g3384.t23 | 25011604 | 25011604 |
Sequences
>g3384.t23 Gene=g3384 Length=889
GTTCTTTAAATCTGAAATCAGTACCTTACTAATAATTCAAAATGGTTAGGGAGAACAAGG
CCACCTGGAAAGCTAACTACTTCTTAAAAGTCGTGACATATCTCGACGAATATCCAAAAT
GTTTCATCGTCGGTGCCGATAACGTTGGTTCAAAGCAAATGCAGCAAATTCGTATCTCAC
TTCGTGGACTCGCTGTAGTTTCGTTTTCACAAAGGGAGATTTGAATGAAGTTCGCGAAAA
GTTGTTGCAAAACAAAGTTCGTGCTCCTGCTCGTGCTGGCGCAATTGCTCCTTGTGAAGT
AATTATTCCTGCTCAAAATACTGGTTTGGGTCCAGAAAAAACAAGTTTCTTCCAAGCTCT
TTCAATTCCAACAAAGATTTCAAAGGGTACTATTGAAATTATCAATGATGTGCCCATCTT
AAAGCCTGGTGACAAAGTCGGTGCTTCTGAAGCTACTTTGCTCAACATGTTGAACATCTC
TCCATTCTCATATGGTTTGGTAATTGAGCAAGTTTATGATTCAGGAAGCATCTTCTCTCC
AAATATCTTGGACATCAAACCAGAAGATTTGCGTGCTAAATTCCAACAAGGAGTTGCAAA
CGTTGCCGCTCTTTCATTGGCTATGGGCTATCCAACAATTGCCTCTGCTCCACATTCAAT
TGCCAATGGTTTCAAGAACTTGCTCGCTATCGCAGCTGTTACCGATGTCGAATTCAAGCA
GGCTGAAACTGTTAAAGAATTCCTTAAGGATCCATCTAAGTTTGCCGCTGCTGCTGCTGC
ATCAGCTCCAGCTGCTTCTGCCGCTGCACCAGCTGCTAAAGCTGAAGCCAAGAAAGAAGA
GTCAGAACCAGAGTCTGATGACGACATGGGATTCGGACTTTTTGATTAA
>g3384.t23 Gene=g3384 Length=140
MLNISPFSYGLVIEQVYDSGSIFSPNILDIKPEDLRAKFQQGVANVAALSLAMGYPTIAS
APHSIANGFKNLLAIAAVTDVEFKQAETVKEFLKDPSKFAAAAAASAPAASAAAPAAKAE
AKKEESEPESDDDMGFGLFD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g3384.t23 | Gene3D | G3DSA:3.30.70.1730 | - | 10 | 33 | 5.9E-7 |
| 4 | g3384.t23 | MobiDBLite | mobidb-lite | consensus disorder prediction | 108 | 140 | - |
| 2 | g3384.t23 | PANTHER | PTHR45699 | 60S ACIDIC RIBOSOMAL PROTEIN P0 | 2 | 140 | 2.7E-47 |
| 3 | g3384.t23 | PANTHER | PTHR45699:SF13 | 60S ACIDIC RIBOSOMAL PROTEIN P0-LIKE | 2 | 140 | 2.7E-47 |
| 1 | g3384.t23 | Pfam | PF00428 | 60s Acidic ribosomal protein | 55 | 139 | 2.6E-19 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
