Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 60S acidic ribosomal protein P1.

Parent gene

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.t5 TSS g4868.t5 5572287 5572287
chr_2 g4868 g4868.t5 isoform g4868.t5 5572420 5573006
chr_2 g4868 g4868.t5 exon g4868.t5.exon1 5572420 5572488
chr_2 g4868 g4868.t5 cds g4868.t5.CDS1 5572420 5572488
chr_2 g4868 g4868.t5 exon g4868.t5.exon2 5572677 5572845
chr_2 g4868 g4868.t5 cds g4868.t5.CDS2 5572677 5572845
chr_2 g4868 g4868.t5 exon g4868.t5.exon3 5572909 5573006
chr_2 g4868 g4868.t5 cds g4868.t5.CDS3 5572909 5573006
chr_2 g4868 g4868.t5 TTS g4868.t5 5573076 5573076

Sequences

>g4868.t5 Gene=g4868 Length=336
ATGGACAAGAGTGAATTGGCCTGTGTTTATGCTGCTTTAATCCTCGTTGATGATGAAATC
GCCATTACTAAAATCTCAACAATCTTGAAGGCTGCCAATGTTGAAGTTGAGCCATACTGG
CCAGGACTTTTTGCAAAGGCCCTTGAAGGAATCGATGTTAAGTCATTGATCACATCAATT
GGATCTGGAGCTGGATCAGGGCCAGCAACAGGCGGAGCAGCACCAGCAGCTGCAGCAGGC
GGTGCACCAGCAGGTGATGCCAAGAAAGAGGAAAAGAAGAAGGAAGAATCTGAACCAGAA
TCAGACGACGACATGGGCTTCGGTCTCTTTGACTAA

>g4868.t5 Gene=g4868 Length=111
MDKSELACVYAALILVDDEIAITKISTILKAANVEVEPYWPGLFAKALEGIDVKSLITSI
GSGAGSGPATGGAAPAAAAGGAPAGDAKKEEKKKEESEPESDDDMGFGLFD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g4868.t5 CDD cd05831 Ribosomal_P1 5 110 2.26962E-29
6 g4868.t5 Gene3D G3DSA:1.10.10.1410 - 2 61 1.8E-28
3 g4868.t5 Hamap MF_01478 50S ribosomal protein L12 [rpl12]. 6 111 15.308081
5 g4868.t5 MobiDBLite mobidb-lite consensus disorder prediction 68 111 -
4 g4868.t5 MobiDBLite mobidb-lite consensus disorder prediction 85 100 -
2 g4868.t5 PANTHER PTHR45696 60S ACIDIC RIBOSOMAL PROTEIN P1 1 111 9.0E-40
1 g4868.t5 Pfam PF00428 60s Acidic ribosomal protein 20 110 1.6E-26

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 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