General information for g4868.t11
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 60S acidic ribosomal protein P1.
Parent gene
- The parent gene g4868 is located on chr_2: 5572671..5580814 (+ 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 | g4868 | g4868.t11 | TSS | g4868.t11 | 5572287 | 5572287 |
| chr_2 | g4868 | g4868.t11 | isoform | g4868.t11 | 5572420 | 5573006 |
| chr_2 | g4868 | g4868.t11 | exon | g4868.t11.exon1 | 5572420 | 5572488 |
| chr_2 | g4868 | g4868.t11 | cds | g4868.t11.CDS1 | 5572420 | 5572488 |
| chr_2 | g4868 | g4868.t11 | exon | g4868.t11.exon2 | 5572671 | 5572835 |
| chr_2 | g4868 | g4868.t11 | cds | g4868.t11.CDS2 | 5572671 | 5572835 |
| chr_2 | g4868 | g4868.t11 | exon | g4868.t11.exon3 | 5572924 | 5573006 |
| chr_2 | g4868 | g4868.t11 | cds | g4868.t11.CDS3 | 5572924 | 5573004 |
| chr_2 | g4868 | g4868.t11 | TTS | g4868.t11 | 5573076 | 5573076 |
Sequences
>g4868.t11 Gene=g4868 Length=317
ATGGACAAGAGTGAATTGGCCTGTGTTTATGCTGCTTTAATCCTCGTTGATGATGAAATC
GCCATTACTGGTGAGAAAATCTCAACAATCTTGAAGGCTGCCAATGTTGAAGTTGAGCCA
TACTGGCCAGGACTTTTTGCAAAGGCCCTTGAAGGAATCGATGTTAAGTCATTGATCACA
TCAATTGGATCTGGAGCTGGATCAGGGCCAGCAACAGGCGGAGCAGCACCAGCAGTGATG
CCAAGAAAGAGGAAAAGAAGAAGGAAGAATCTGAACCAGAATCAGACGACGACATGGGCT
TCGGTCTCTTTGACTAA
>g4868.t11 Gene=g4868 Length=105
MDKSELACVYAALILVDDEIAITGEKISTILKAANVEVEPYWPGLFAKALEGIDVKSLIT
SIGSGAGSGPATGGAAPAVMPRKRKRRRKNLNQNQTTTWASVSLT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g4868.t11 | CDD | cd05831 | Ribosomal_P1 | 5 | 78 | 1.11095E-34 |
| 4 | g4868.t11 | Gene3D | G3DSA:1.10.10.1410 | - | 2 | 63 | 9.2E-32 |
| 3 | g4868.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 67 | 105 | - |
| 2 | g4868.t11 | PANTHER | PTHR45696 | 60S ACIDIC RIBOSOMAL PROTEIN P1 | 1 | 85 | 2.2E-29 |
| 1 | g4868.t11 | Pfam | PF00428 | 60s Acidic ribosomal protein | 22 | 78 | 1.9E-12 |
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. There were no conditions that were differentially expressed