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.t4 TSS g4868.t4 5572287 5572287
chr_2 g4868 g4868.t4 isoform g4868.t4 5572420 5573006
chr_2 g4868 g4868.t4 exon g4868.t4.exon1 5572420 5572488
chr_2 g4868 g4868.t4 cds g4868.t4.CDS1 5572420 5572488
chr_2 g4868 g4868.t4 exon g4868.t4.exon2 5572671 5572845
chr_2 g4868 g4868.t4 cds g4868.t4.CDS2 5572671 5572845
chr_2 g4868 g4868.t4 exon g4868.t4.exon3 5572921 5573006
chr_2 g4868 g4868.t4 cds g4868.t4.CDS3 5572921 5573006
chr_2 g4868 g4868.t4 TTS g4868.t4 5573076 5573076

Sequences

>g4868.t4 Gene=g4868 Length=330
ATGGACAAGAGTGAATTGGCCTGTGTTTATGCTGCTTTAATCCTCGTTGATGATGAAATC
GCCATTACTGGTGAGAAAATCTCAACAATCTTGAAGGCTGCCAATGTTGAAGTTGAGCCA
TACTGGCCAGGACTTTTTGCAAAGGCCCTTGAAGGAATCGATGTTAAGTCATTGATCACA
TCAATTGGATCTGGAGCTGGATCAGGGCCAGCAACAGGCGGAGCAGCACCAGCAGCTGCA
GCAGCAGGTGATGCCAAGAAAGAGGAAAAGAAGAAGGAAGAATCTGAACCAGAATCAGAC
GACGACATGGGCTTCGGTCTCTTTGACTAA

>g4868.t4 Gene=g4868 Length=109
MDKSELACVYAALILVDDEIAITGEKISTILKAANVEVEPYWPGLFAKALEGIDVKSLIT
SIGSGAGSGPATGGAAPAAAAAGDAKKEEKKKEESEPESDDDMGFGLFD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g4868.t4 CDD cd05831 Ribosomal_P1 5 108 1.32659E-32
6 g4868.t4 Gene3D G3DSA:1.10.10.1410 - 2 63 1.0E-31
3 g4868.t4 Hamap MF_01478 50S ribosomal protein L12 [rpl12]. 6 109 15.466826
4 g4868.t4 MobiDBLite mobidb-lite consensus disorder prediction 67 109 -
5 g4868.t4 MobiDBLite mobidb-lite consensus disorder prediction 83 98 -
2 g4868.t4 PANTHER PTHR45696 60S ACIDIC RIBOSOMAL PROTEIN P1 1 109 3.0E-41
1 g4868.t4 Pfam PF00428 60s Acidic ribosomal protein 22 108 6.5E-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

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.

Raw TPM values