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.t23 isoform g9524.t23 3888292 3889610
chr_1 g9524 g9524.t23 TTS g9524.t23 3888292 3888292
chr_1 g9524 g9524.t23 exon g9524.t23.exon1 3888292 3888673
chr_1 g9524 g9524.t23 cds g9524.t23.CDS1 3888353 3888673
chr_1 g9524 g9524.t23 exon g9524.t23.exon2 3888871 3889197
chr_1 g9524 g9524.t23 cds g9524.t23.CDS2 3888871 3889092
chr_1 g9524 g9524.t23 exon g9524.t23.exon3 3889499 3889610
chr_1 g9524 g9524.t23 TSS g9524.t23 3890000 3890000

Sequences

>g9524.t23 Gene=g9524 Length=821
ATGGCGGACACAGCTCCAGCCCGTGGTGGGTTTAAACAAGGTTTCGGAGGTGCAGCTGGT
GGTGGTACCGGCGGTGGTGGATCACGAGGAAGAGGTCGACGCGGAGGTCGCGATTCGTTC
ATTGGAAGAAATTTACTTGTACTCATTGCCAATCAAAGAATTCGAAATCATTGATTTCTT
CTTGGGACGTTCATTGCGTGATGAGGTTTTGAAGATCATGCCTGTTCAGAAACAAACACG
TGCCGGTCAACGTACGCGCTTCAAGGCTTTCGTTGCTATCGGTGATTCAAACGGTCACAT
TGGTCTTGGTGTAAAATGCAGCAAAGAAGTCGCCACTGCTATTCGTGGAGCTATCATTTT
GGCTAAACTTTCAGTAGTTCCGGTTCGTCGTGGTTATTGGGGTAACAAAATCGGTAAACC
TCATACAGTACCTTGCAAGGTTACTGGCAAATGTGGTTCAGTTCAAGTCAAATTGATTCC
AGCACCAAGAGGAACAGGCATTGTTAGTGCTCCAGTTCCAAAGAAATTACTTCAAATGGC
TGGTATTGAAGATTGCTACACTCAATGTCGCGGTTCAACTACAACTTTGGGTAACTTCGC
AAAAGCCACTTACTCAGCTATCATGAAGACTTATGCTTTCTTGACACCTGATTTGTGGAA
AGAAATTCCTTTAAGCAAATCACCATACGAAGTTTATGCTGACTTCCTTGCGAAACCAGC
TGGTAAAACTGGAGGCATTCGCAACATTGATTTGTCTTAAAATGTTAAAAATGCCCTTTG
AAAAACATTCACAAATAAAATGACATCCATTTTTAAAGTGA

>g9524.t23 Gene=g9524 Length=180
MPVQKQTRAGQRTRFKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILAKLSVVPVRRGY
WGNKIGKPHTVPCKVTGKCGSVQVKLIPAPRGTGIVSAPVPKKLLQMAGIEDCYTQCRGS
TTTLGNFAKATYSAIMKTYAFLTPDLWKEIPLSKSPYEVYADFLAKPAGKTGGIRNIDLS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g9524.t23 Gene3D G3DSA:3.30.160.770 - 1 55 1.5E-26
8 g9524.t23 Gene3D G3DSA:3.30.230.10 - 56 149 4.9E-55
3 g9524.t23 PANTHER PTHR13718:SF93 40S RIBOSOMAL PROTEIN S2 1 167 7.4E-89
4 g9524.t23 PANTHER PTHR13718 RIBOSOMAL S SUBUNIT 1 167 7.4E-89
1 g9524.t23 Pfam PF00333 Ribosomal protein S5, N-terminal domain 1 57 2.7E-25
2 g9524.t23 Pfam PF03719 Ribosomal protein S5, C-terminal domain 76 147 5.4E-25
7 g9524.t23 ProSitePatterns PS00585 Ribosomal protein S5 signature. 10 42 -
11 g9524.t23 ProSiteProfiles PS50881 S5 double stranded RNA-binding domain profile. 1 56 19.835
6 g9524.t23 SUPERFAMILY SSF54768 dsRNA-binding domain-like 2 58 1.57E-17
5 g9524.t23 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like 69 149 9.36E-26
10 g9524.t23 TIGRFAM TIGR01020 uS5_euk_arch: ribosomal protein uS5 2 152 1.6E-70

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
GO:0015935 small ribosomal subunit CC

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

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