General information for g4868.t21
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.t21 | TSS | g4868.t21 | 5572287 | 5572287 |
| chr_2 | g4868 | g4868.t21 | isoform | g4868.t21 | 5572420 | 5580814 |
| chr_2 | g4868 | g4868.t21 | exon | g4868.t21.exon1 | 5572420 | 5572488 |
| chr_2 | g4868 | g4868.t21 | cds | g4868.t21.CDS1 | 5572420 | 5572488 |
| chr_2 | g4868 | g4868.t21 | exon | g4868.t21.exon2 | 5572671 | 5572845 |
| chr_2 | g4868 | g4868.t21 | cds | g4868.t21.CDS2 | 5572671 | 5572845 |
| chr_2 | g4868 | g4868.t21 | exon | g4868.t21.exon3 | 5572909 | 5573088 |
| chr_2 | g4868 | g4868.t21 | cds | g4868.t21.CDS3 | 5572909 | 5573006 |
| chr_2 | g4868 | g4868.t21 | exon | g4868.t21.exon4 | 5580767 | 5580814 |
| chr_2 | g4868 | g4868.t21 | TTS | g4868.t21 | NA | NA |
Sequences
>g4868.t21 Gene=g4868 Length=472
ATGGACAAGAGTGAATTGGCCTGTGTTTATGCTGCTTTAATCCTCGTTGATGATGAAATC
GCCATTACTGGTGAGAAAATCTCAACAATCTTGAAGGCTGCCAATGTTGAAGTTGAGCCA
TACTGGCCAGGACTTTTTGCAAAGGCCCTTGAAGGAATCGATGTTAAGTCATTGATCACA
TCAATTGGATCTGGAGCTGGATCAGGGCCAGCAACAGGCGGAGCAGCACCAGCAGCTGCA
GCAGGCGGTGCACCAGCAGGTGATGCCAAGAAAGAGGAAAAGAAGAAGGAAGAATCTGAA
CCAGAATCAGACGACGACATGGGCTTCGGTCTCTTTGACTAAATTTCCTCAAGTACAAAT
ATTCATTAGTTTGTACACTTGAAATATGAAATAAAAACAAAATTCCACCAACAAAAAAAA
CCAACGAAATATTCTATTGCATTGTTCTGTTGATTGTACAATACAATAAAAA
>g4868.t21 Gene=g4868 Length=113
MDKSELACVYAALILVDDEIAITGEKISTILKAANVEVEPYWPGLFAKALEGIDVKSLIT
SIGSGAGSGPATGGAAPAAAAGGAPAGDAKKEEKKKEESEPESDDDMGFGLFD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g4868.t21 | CDD | cd05831 | Ribosomal_P1 | 5 | 112 | 6.25837E-32 |
| 6 | g4868.t21 | Gene3D | G3DSA:1.10.10.1410 | - | 2 | 63 | 1.1E-31 |
| 3 | g4868.t21 | Hamap | MF_01478 | 50S ribosomal protein L12 [rpl12]. | 6 | 113 | 15.817001 |
| 4 | g4868.t21 | MobiDBLite | mobidb-lite | consensus disorder prediction | 70 | 113 | - |
| 5 | g4868.t21 | MobiDBLite | mobidb-lite | consensus disorder prediction | 87 | 102 | - |
| 2 | g4868.t21 | PANTHER | PTHR45696 | 60S ACIDIC RIBOSOMAL PROTEIN P1 | 1 | 113 | 1.9E-41 |
| 1 | g4868.t21 | Pfam | PF00428 | 60s Acidic ribosomal protein | 22 | 112 | 2.8E-27 |
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:0006414 | translational elongation | BP |
| GO:0003735 | structural constituent of ribosome | MF |
KEGG
Orthology
- This transcript has been annotated with K02942 (large subunit ribosomal protein LP1)
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.
