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.t28 TTS g11240.t28 14863763 14863763
chr_1 g11240 g11240.t28 isoform g11240.t28 14864037 14864612
chr_1 g11240 g11240.t28 exon g11240.t28.exon1 14864037 14864612
chr_1 g11240 g11240.t28 cds g11240.t28.CDS1 14864037 14864459
chr_1 g11240 g11240.t28 TSS g11240.t28 14864714 14864714

Sequences

>g11240.t28 Gene=g11240 Length=576
TAATTTATACATTTTAAAGTAATAATAATATGGAGTTCAGTCAAAATATATATTATTTAT
TAAAAATCTTTGATTTTGAAGTTTCTACTTCACATCAACAAAATTTCGAGGTTAAAATCT
CAACATTAATATTTCTTATCGTTTAAATTACAGATGCGTTACGTTAGCGCTTACCTCTTG
GCAGTTTTGGGTGGAAATGCTTCGCCATCAAGTGCAGATCTCCAAAAGATCTTGTCATCA
GTCGGTATTGAAGTTGATAGCGAACGCCTCAACAAAGTCATTGATGAACTTAAAGGAAAG
AGCGTCGAGGAATTAATTGCTCAAGGACGCGAGAAACTCAGCTCAATGCCAAGTGGTGGT
GGTGCTGCTGCTGCACCAGCTGCCGGTAAATTCTCACTCATTAATTTATTTTTCTCATCA
TTAATTATGATTTTTTCTAAAAAGGTGGTGCCGCTCCAGCCGCAGCTGCAGAAGCCAAGA
AAGAAGAAAAGAAGCCAGAACCAGAGTCAGAAGAAGAGGATGATGACATGGGCTTCGGTC
TCTTTGAATAAAATGGTAAGCAATCAATTAATATAA

>g11240.t28 Gene=g11240 Length=140
MRYVSAYLLAVLGGNASPSSADLQKILSSVGIEVDSERLNKVIDELKGKSVEELIAQGRE
KLSSMPSGGGAAAAPAAGKFSLINLFFSSLIMIFSKKVVPLQPQLQKPRKKKRSQNQSQK
KRMMTWASVSLNKMVSNQLI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g11240.t28 CDD cd05833 Ribosomal_P2 1 67 8.99787E-41
5 g11240.t28 Gene3D G3DSA:1.10.10.1410 - 1 59 3.2E-29
3 g11240.t28 Hamap MF_01478 50S ribosomal protein L12 [rpl12]. 2 84 12.459991
4 g11240.t28 MobiDBLite mobidb-lite consensus disorder prediction 104 123 -
2 g11240.t28 PANTHER PTHR21141 60S ACIDIC RIBOSOMAL PROTEIN FAMILY MEMBER 1 78 1.3E-30
1 g11240.t28 Pfam PF00428 60s Acidic ribosomal protein 17 77 7.1E-13
7 g11240.t28 Phobius SIGNAL_PEPTIDE Signal peptide region 1 21 -
8 g11240.t28 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
9 g11240.t28 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 12 -
10 g11240.t28 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 13 21 -
6 g11240.t28 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 22 140 -

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

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.

Raw TPM values