Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 60S acidic ribosomal protein P2.

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_1 g11240 g11240.t29 TTS g11240.t29 14863763 14863763
chr_1 g11240 g11240.t29 isoform g11240.t29 14864050 14864903
chr_1 g11240 g11240.t29 exon g11240.t29.exon1 14864050 14864168
chr_1 g11240 g11240.t29 cds g11240.t29.CDS1 14864062 14864168
chr_1 g11240 g11240.t29 exon g11240.t29.exon2 14864228 14864459
chr_1 g11240 g11240.t29 cds g11240.t29.CDS2 14864228 14864459
chr_1 g11240 g11240.t29 exon g11240.t29.exon3 14864625 14864903
chr_1 g11240 g11240.t29 TSS g11240.t29 NA NA

Sequences

>g11240.t29 Gene=g11240 Length=630
ATGGACTCATCATGGTTCAGTTATTTTTTTACACACTAAATTTCATTTCTACTATTTTAA
TTCCTTCGAATTCAACAAAATATTTTAAAATTTTAAAAATGAAAGAAATATTTCGAAATT
TAATCATTTTTAGGGGGGTCAACAGCAAAAAATTATTTTACAAAAGAAAGCTACGCGCTT
GCATCTTTCTTTCTTTTCTGCGACATAAAGTAGAATACACACGATTTTCTAAAATTTTGG
TAATTGACAACGTTTCGTGTCAAATAAACAGACTTAAAAATGCGTTACGTTAGCGCTTAC
CTCTTGGCAGTTTTGGGTGGAAATGCTTCGCCATCAAGTGCAGATCTCCAAAAGATCTTG
TCATCAGTCGGTATTGAAGTTGATAGCGAACGCCTCAACAAAGTCATTGATGAACTTAAA
GGAAAGAGCGTCGAGGAATTAATTGCTCAAGGACGCGAGAAACTCAGCTCAATGCCAAGT
GGTGGTGGTGCTGCTGCTGCACCAGCTGCCGGTGGTGCCGCTCCAGCCGCAGCTGCAGAA
GCCAAGAAAGAAGAAAAGAAGCCAGAACCAGAGTCAGAAGAAGAGGATGATGACATGGGC
TTCGGTCTCTTTGAATAAAATGGTAAGCAA

>g11240.t29 Gene=g11240 Length=112
MRYVSAYLLAVLGGNASPSSADLQKILSSVGIEVDSERLNKVIDELKGKSVEELIAQGRE
KLSSMPSGGGAAAAPAAGGAAPAAAAEAKKEEKKPEPESEEEDDDMGFGLFE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g11240.t29 CDD cd05833 Ribosomal_P2 1 112 1.53901E-35
7 g11240.t29 Gene3D G3DSA:1.10.10.1410 - 1 59 1.8E-29
4 g11240.t29 Hamap MF_01478 50S ribosomal protein L12 [rpl12]. 2 112 17.59589
5 g11240.t29 MobiDBLite mobidb-lite consensus disorder prediction 58 112 -
6 g11240.t29 MobiDBLite mobidb-lite consensus disorder prediction 97 112 -
2 g11240.t29 PANTHER PTHR21141:SF5 60S ACIDIC RIBOSOMAL PROTEIN P2 1 112 1.5E-42
3 g11240.t29 PANTHER PTHR21141 60S ACIDIC RIBOSOMAL PROTEIN FAMILY MEMBER 1 112 1.5E-42
1 g11240.t29 Pfam PF00428 60s Acidic ribosomal protein 17 111 1.5E-27
9 g11240.t29 Phobius SIGNAL_PEPTIDE Signal peptide region 1 21 -
10 g11240.t29 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
11 g11240.t29 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 12 -
12 g11240.t29 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 13 21 -
8 g11240.t29 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 22 112 -

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:0002182 cytoplasmic translational elongation BP
GO:0022625 cytosolic large ribosomal subunit 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