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.t9 isoform g11240.t9 14863745 14864903
chr_1 g11240 g11240.t9 exon g11240.t9.exon1 14863745 14863878
chr_1 g11240 g11240.t9 TTS g11240.t9 14863763 14863763
chr_1 g11240 g11240.t9 cds g11240.t9.CDS1 14863777 14863878
chr_1 g11240 g11240.t9 exon g11240.t9.exon2 14864058 14864153
chr_1 g11240 g11240.t9 cds g11240.t9.CDS2 14864058 14864153
chr_1 g11240 g11240.t9 exon g11240.t9.exon3 14864217 14864459
chr_1 g11240 g11240.t9 cds g11240.t9.CDS3 14864217 14864459
chr_1 g11240 g11240.t9 exon g11240.t9.exon4 14864625 14864903
chr_1 g11240 g11240.t9 TSS g11240.t9 NA NA

Sequences

>g11240.t9 Gene=g11240 Length=752
ATGGACTCATCATGGTTCAGTTATTTTTTTACACACTAAATTTCATTTCTACTATTTTAA
TTCCTTCGAATTCAACAAAATATTTTAAAATTTTAAAAATGAAAGAAATATTTCGAAATT
TAATCATTTTTAGGGGGGTCAACAGCAAAAAATTATTTTACAAAAGAAAGCTACGCGCTT
GCATCTTTCTTTCTTTTCTGCGACATAAAGTAGAATACACACGATTTTCTAAAATTTTGG
TAATTGACAACGTTTCGTGTCAAATAAACAGACTTAAAAATGCGTTACGTTAGCGCTTAC
CTCTTGGCAGTTTTGGGTGGAAATGCTTCGCCATCAAGTGCAGATCTCCAAAAGATCTTG
TCATCAGTCGGTATTGAAGTTGATAGCGAACGCCTCAACAAAGTCATTGATGAACTTAAA
GGAAAGAGCGTCGAGGAATTAATTGCTCAAGGACGCGAGAAACTCAGCTCAATGCCAAGT
GGTGGTGGTGCTGCTGCTGCACCAGCTGCCGGTAAATTCTCACCGCAGCTGCAGAAGCCA
AGAAAGAAGAAAAGAAGCCAGAACCAGAGTCAGAAGAAGAGGATGATGACATGGGCTTCG
GTCTCTTTGAATAAAATGGTTGAAGCAAAAACGGTGTGTATTAGATATAAACTCCATCTT
ATAAGTACAATCAAACTTTGTAAACAAAAGTTTGTAATAAAAATAATCTATACACAATAA
GAATTCCAAAATCTAAATCTTTTATTATCAAT

>g11240.t9 Gene=g11240 Length=146
MRYVSAYLLAVLGGNASPSSADLQKILSSVGIEVDSERLNKVIDELKGKSVEELIAQGRE
KLSSMPSGGGAAAAPAAGKFSPQLQKPRKKKRSQNQSQKKRMMTWASVSLNKMVEAKTVC
IRYKLHLISTIKLCKQKFVIKIIYTQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g11240.t9 CDD cd05833 Ribosomal_P2 1 67 9.11538E-41
6 g11240.t9 Gene3D G3DSA:1.10.10.1410 - 1 59 3.5E-29
4 g11240.t9 Hamap MF_01478 50S ribosomal protein L12 [rpl12]. 2 81 12.436646
5 g11240.t9 MobiDBLite mobidb-lite consensus disorder prediction 62 102 -
2 g11240.t9 PANTHER PTHR21141:SF5 60S ACIDIC RIBOSOMAL PROTEIN P2 1 103 9.7E-33
3 g11240.t9 PANTHER PTHR21141 60S ACIDIC RIBOSOMAL PROTEIN FAMILY MEMBER 1 103 9.7E-33
1 g11240.t9 Pfam PF00428 60s Acidic ribosomal protein 17 91 6.2E-14
8 g11240.t9 Phobius SIGNAL_PEPTIDE Signal peptide region 1 21 -
9 g11240.t9 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
10 g11240.t9 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 12 -
11 g11240.t9 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 13 21 -
7 g11240.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 22 146 -

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. There were no conditions that were differentially expressed