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.t35 TTS g9524.t35 3888292 3888292
chr_1 g9524 g9524.t35 isoform g9524.t35 3888296 3889610
chr_1 g9524 g9524.t35 exon g9524.t35.exon1 3888296 3888597
chr_1 g9524 g9524.t35 cds g9524.t35.CDS1 3888353 3888597
chr_1 g9524 g9524.t35 exon g9524.t35.exon2 3888909 3889289
chr_1 g9524 g9524.t35 cds g9524.t35.CDS2 3888909 3889289
chr_1 g9524 g9524.t35 exon g9524.t35.exon3 3889490 3889610
chr_1 g9524 g9524.t35 cds g9524.t35.CDS3 3889490 3889610
chr_1 g9524 g9524.t35 TSS g9524.t35 3890000 3890000

Sequences

>g9524.t35 Gene=g9524 Length=804
ATGGCGGACACAGCTCCAGCCCGTGGTGGGTTTAAACAAGGTTTCGGAGGTGCAGCTGGT
GGTGGTACCGGCGGTGGTGGATCACGAGGAAGAGGTCGACGCGGAGGTCGCGGTGGAAGA
GGTCGTGGCGGACGTGGACGAGGTGACAAAGAAGGAAATCAAAAAGAATGGGTACCAGTC
ACTAAATTGGGTCGTTTAGTTCGTGATGGAAAGATTCGTTCATTGGAAGAAATTTACTTG
TACTCATTGCCAATCAAAGAATTCGAAATCATTGATTTCTTCTTGGGACGTTCATTGCGT
GATGAGGTTTTGAAGATCATGCCTGTTCAGAAACAAACACGTGCCGGTCAACGTACGCGC
TTCAAGGCTTTCGTTGCTATCGGTGATTCAAACGGTCACATTGGTCTTGGTGTAAAATGC
AGCAAAGAAGTCGCCACTGCTATTCGTGGAGCTATCATTTTGGCTAAACTTTCAGTAGTT
CCGGTTCGTCGTGGTTATTGGGTTCCAAAGAAATTACTTCAAATGGCTGGTATTGAAGAT
TGCTACACTCAATGTCGCGGTTCAACTACAACTTTGGGTAACTTCGCAAAAGCCACTTAC
TCAGCTATCATGAAGACTTATGCTTTCTTGACACCTGATTTGTGGAAAGAAATTCCTTTA
AGCAAATCACCATACGAAGTTTATGCTGACTTCCTTGCGAAACCAGCTGGTAAAACTGGA
GGCATTCGCAACATTGATTTGTCTTAAAATGTTAAAAATGCCCTTTGAAAAACATTCACA
AATAAAATGACATCCATTTTTAAA

>g9524.t35 Gene=g9524 Length=248
MADTAPARGGFKQGFGGAAGGGTGGGGSRGRGRRGGRGGRGRGGRGRGDKEGNQKEWVPV
TKLGRLVRDGKIRSLEEIYLYSLPIKEFEIIDFFLGRSLRDEVLKIMPVQKQTRAGQRTR
FKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILAKLSVVPVRRGYWVPKKLLQMAGIED
CYTQCRGSTTTLGNFAKATYSAIMKTYAFLTPDLWKEIPLSKSPYEVYADFLAKPAGKTG
GIRNIDLS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g9524.t35 Gene3D G3DSA:3.30.160.770 - 56 158 1.3E-55
11 g9524.t35 Gene3D G3DSA:3.30.230.10 - 159 206 1.5E-6
10 g9524.t35 MobiDBLite mobidb-lite consensus disorder prediction 1 55 -
3 g9524.t35 PANTHER PTHR13718:SF99 GENE 8225-RELATED 17 166 1.3E-98
5 g9524.t35 PANTHER PTHR13718 RIBOSOMAL S SUBUNIT 17 166 1.3E-98
4 g9524.t35 PANTHER PTHR13718:SF99 GENE 8225-RELATED 168 235 1.3E-98
6 g9524.t35 PANTHER PTHR13718 RIBOSOMAL S SUBUNIT 168 235 1.3E-98
1 g9524.t35 Pfam PF00333 Ribosomal protein S5, N-terminal domain 99 163 4.7E-29
2 g9524.t35 Pfam PF03719 Ribosomal protein S5, C-terminal domain 168 215 1.1E-11
9 g9524.t35 ProSitePatterns PS00585 Ribosomal protein S5 signature. 116 148 -
13 g9524.t35 ProSiteProfiles PS50881 S5 double stranded RNA-binding domain profile. 99 162 22.324
8 g9524.t35 SUPERFAMILY SSF54768 dsRNA-binding domain-like 93 164 2.3E-21
7 g9524.t35 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like 156 217 7.08E-12

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. There were no conditions that were differentially expressed