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.t14 isoform g9524.t14 3888292 3889610
chr_1 g9524 g9524.t14 TTS g9524.t14 3888292 3888292
chr_1 g9524 g9524.t14 exon g9524.t14.exon1 3888292 3888673
chr_1 g9524 g9524.t14 cds g9524.t14.CDS1 3888353 3888673
chr_1 g9524 g9524.t14 exon g9524.t14.exon2 3888871 3888935
chr_1 g9524 g9524.t14 cds g9524.t14.CDS2 3888871 3888935
chr_1 g9524 g9524.t14 exon g9524.t14.exon3 3889017 3889289
chr_1 g9524 g9524.t14 cds g9524.t14.CDS3 3889017 3889289
chr_1 g9524 g9524.t14 exon g9524.t14.exon4 3889490 3889610
chr_1 g9524 g9524.t14 cds g9524.t14.CDS4 3889490 3889610
chr_1 g9524 g9524.t14 TSS g9524.t14 3890000 3890000

Sequences

>g9524.t14 Gene=g9524 Length=841
ATGGCGGACACAGCTCCAGCCCGTGGTGGGTTTAAACAAGGTTTCGGAGGTGCAGCTGGT
GGTGGTACCGGCGGTGGTGGATCACGAGGAAGAGGTCGACGCGGAGGTCGCGGTGGAAGA
GGTCGTGGCGGACGTGGACGAGGTGACAAAGAAGGAAATCAAAAAGAATGGGTACCAGTC
ACTAAATTGGGTCGTTTAGTTCGTGATGGAAAGATTCGTTCATTGGAAGAAATTTACTTG
TACTCATTGCCAATCAAAGAATTCGAAATCATTGATTTCTTCTTGGGACGTTCATTGCGT
GATGAGGTTTTGAAGATCATGCCTGTTCAGAAACAAACACGTGCCGGTCAACGTACGCGC
TTCAAGGCTTTCGTTGCTATCGGTGATTCAAACGTAGTTCCGGTTCGTCGTGGTTATTGG
GGTAACAAAATCGGTAAACCTCATACAGTACCTTGCAAGGTTACTGGCAAATGTGGTTCA
GTTCAAGTCAAATTGATTCCAGCACCAAGAGGAACAGGCATTGTTAGTGCTCCAGTTCCA
AAGAAATTACTTCAAATGGCTGGTATTGAAGATTGCTACACTCAATGTCGCGGTTCAACT
ACAACTTTGGGTAACTTCGCAAAAGCCACTTACTCAGCTATCATGAAGACTTATGCTTTC
TTGACACCTGATTTGTGGAAAGAAATTCCTTTAAGCAAATCACCATACGAAGTTTATGCT
GACTTCCTTGCGAAACCAGCTGGTAAAACTGGAGGCATTCGCAACATTGATTTGTCTTAA
AATGTTAAAAATGCCCTTTGAAAAACATTCACAAATAAAATGACATCCATTTTTAAAGTG
A

>g9524.t14 Gene=g9524 Length=259
MADTAPARGGFKQGFGGAAGGGTGGGGSRGRGRRGGRGGRGRGGRGRGDKEGNQKEWVPV
TKLGRLVRDGKIRSLEEIYLYSLPIKEFEIIDFFLGRSLRDEVLKIMPVQKQTRAGQRTR
FKAFVAIGDSNVVPVRRGYWGNKIGKPHTVPCKVTGKCGSVQVKLIPAPRGTGIVSAPVP
KKLLQMAGIEDCYTQCRGSTTTLGNFAKATYSAIMKTYAFLTPDLWKEIPLSKSPYEVYA
DFLAKPAGKTGGIRNIDLS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g9524.t14 Gene3D G3DSA:3.30.160.770 - 54 147 9.4E-33
10 g9524.t14 Gene3D G3DSA:3.30.230.10 - 148 218 2.0E-22
9 g9524.t14 MobiDBLite mobidb-lite consensus disorder prediction 1 55 -
3 g9524.t14 PANTHER PTHR13718:SF93 40S RIBOSOMAL PROTEIN S2 3 131 3.6E-100
5 g9524.t14 PANTHER PTHR13718 RIBOSOMAL S SUBUNIT 3 131 3.6E-100
4 g9524.t14 PANTHER PTHR13718:SF93 40S RIBOSOMAL PROTEIN S2 132 246 3.6E-100
6 g9524.t14 PANTHER PTHR13718 RIBOSOMAL S SUBUNIT 132 246 3.6E-100
1 g9524.t14 Pfam PF00333 Ribosomal protein S5, N-terminal domain 99 131 2.9E-11
2 g9524.t14 Pfam PF03719 Ribosomal protein S5, C-terminal domain 155 226 1.1E-24
12 g9524.t14 ProSiteProfiles PS50881 S5 double stranded RNA-binding domain profile. 99 131 11.218
8 g9524.t14 SUPERFAMILY SSF54768 dsRNA-binding domain-like 93 151 2.62E-8
7 g9524.t14 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like 148 228 2.1E-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:0003723 RNA binding MF
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