Gene loci information

Transcript annotation

  • This transcript has been annotated as 40S ribosomal protein S2.

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 g9524 g9524.t36 TTS g9524.t36 3888292 3888292
chr_1 g9524 g9524.t36 isoform g9524.t36 3888296 3889610
chr_1 g9524 g9524.t36 exon g9524.t36.exon1 3888296 3888673
chr_1 g9524 g9524.t36 cds g9524.t36.CDS1 3888353 3888673
chr_1 g9524 g9524.t36 exon g9524.t36.exon2 3888871 3888980
chr_1 g9524 g9524.t36 cds g9524.t36.CDS2 3888871 3888980
chr_1 g9524 g9524.t36 exon g9524.t36.exon3 3889071 3889289
chr_1 g9524 g9524.t36 cds g9524.t36.CDS3 3889071 3889289
chr_1 g9524 g9524.t36 exon g9524.t36.exon4 3889490 3889610
chr_1 g9524 g9524.t36 cds g9524.t36.CDS4 3889490 3889610
chr_1 g9524 g9524.t36 TSS g9524.t36 3890000 3890000

Sequences

>g9524.t36 Gene=g9524 Length=828
ATGGCGGACACAGCTCCAGCCCGTGGTGGGTTTAAACAAGGTTTCGGAGGTGCAGCTGGT
GGTGGTACCGGCGGTGGTGGATCACGAGGAAGAGGTCGACGCGGAGGTCGCGGTGGAAGA
GGTCGTGGCGGACGTGGACGAGGTGACAAAGAAGGAAATCAAAAAGAATGGGTACCAGTC
ACTAAATTGGGTCGTTTAGTTCGTGATGGAAAGATTCGTTCATTGGAAGAAATTTACTTG
TACTCATTGCCAATCAAAGAATTCGAAATCATTGATTTCTTCTTGGGACGTTCATTGCGT
GATGAGGTTTTGAAGATCATGCCTGTTCAGAAACAAACACTCGCCACTGCTATTCGTGGA
GCTATCATTTTGGCTAAACTTTCAGTAGTTCCGGTTCGTCGTGGTTATTGGGGTAACAAA
ATCGGTAAACCTCATACAGTACCTTGCAAGGTTACTGGCAAATGTGGTTCAGTTCAAGTC
AAATTGATTCCAGCACCAAGAGGAACAGGCATTGTTAGTGCTCCAGTTCCAAAGAAATTA
CTTCAAATGGCTGGTATTGAAGATTGCTACACTCAATGTCGCGGTTCAACTACAACTTTG
GGTAACTTCGCAAAAGCCACTTACTCAGCTATCATGAAGACTTATGCTTTCTTGACACCT
GATTTGTGGAAAGAAATTCCTTTAAGCAAATCACCATACGAAGTTTATGCTGACTTCCTT
GCGAAACCAGCTGGTAAAACTGGAGGCATTCGCAACATTGATTTGTCTTAAAATGTTAAA
AATGCCCTTTGAAAAACATTCACAAATAAAATGACATCCATTTTTAAA

>g9524.t36 Gene=g9524 Length=256
MADTAPARGGFKQGFGGAAGGGTGGGGSRGRGRRGGRGGRGRGGRGRGDKEGNQKEWVPV
TKLGRLVRDGKIRSLEEIYLYSLPIKEFEIIDFFLGRSLRDEVLKIMPVQKQTLATAIRG
AIILAKLSVVPVRRGYWGNKIGKPHTVPCKVTGKCGSVQVKLIPAPRGTGIVSAPVPKKL
LQMAGIEDCYTQCRGSTTTLGNFAKATYSAIMKTYAFLTPDLWKEIPLSKSPYEVYADFL
AKPAGKTGGIRNIDLS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g9524.t36 Gene3D G3DSA:3.30.160.770 - 56 115 1.6E-25
8 g9524.t36 Gene3D G3DSA:3.30.230.10 - 132 225 1.1E-54
7 g9524.t36 MobiDBLite mobidb-lite consensus disorder prediction 1 55 -
2 g9524.t36 PANTHER PTHR13718:SF93 40S RIBOSOMAL PROTEIN S2 3 115 1.8E-97
4 g9524.t36 PANTHER PTHR13718 RIBOSOMAL S SUBUNIT 3 115 1.8E-97
3 g9524.t36 PANTHER PTHR13718:SF93 40S RIBOSOMAL PROTEIN S2 115 243 1.8E-97
5 g9524.t36 PANTHER PTHR13718 RIBOSOMAL S SUBUNIT 115 243 1.8E-97
1 g9524.t36 Pfam PF03719 Ribosomal protein S5, C-terminal domain 152 223 1.1E-24
6 g9524.t36 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like 145 225 2.05E-25

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:0006412 translation 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