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.t24 isoform g9524.t24 3888292 3889611
chr_1 g9524 g9524.t24 TTS g9524.t24 3888292 3888292
chr_1 g9524 g9524.t24 exon g9524.t24.exon1 3888292 3888673
chr_1 g9524 g9524.t24 cds g9524.t24.CDS1 3888353 3888673
chr_1 g9524 g9524.t24 exon g9524.t24.exon2 3888871 3888920
chr_1 g9524 g9524.t24 cds g9524.t24.CDS2 3888871 3888920
chr_1 g9524 g9524.t24 exon g9524.t24.exon3 3888966 3889289
chr_1 g9524 g9524.t24 cds g9524.t24.CDS3 3888966 3889289
chr_1 g9524 g9524.t24 exon g9524.t24.exon4 3889490 3889611
chr_1 g9524 g9524.t24 cds g9524.t24.CDS4 3889490 3889610
chr_1 g9524 g9524.t24 TSS g9524.t24 3890000 3890000

Sequences

>g9524.t24 Gene=g9524 Length=878
AATGGCGGACACAGCTCCAGCCCGTGGTGGGTTTAAACAAGGTTTCGGAGGTGCAGCTGG
TGGTGGTACCGGCGGTGGTGGATCACGAGGAAGAGGTCGACGCGGAGGTCGCGGTGGAAG
AGGTCGTGGCGGACGTGGACGAGGTGACAAAGAAGGAAATCAAAAAGAATGGGTACCAGT
CACTAAATTGGGTCGTTTAGTTCGTGATGGAAAGATTCGTTCATTGGAAGAAATTTACTT
GTACTCATTGCCAATCAAAGAATTCGAAATCATTGATTTCTTCTTGGGACGTTCATTGCG
TGATGAGGTTTTGAAGATCATGCCTGTTCAGAAACAAACACGTGCCGGTCAACGTACGCG
CTTCAAGGCTTTCGTTGCTATCGGTGATTCAAACGGTCACATTGGTCTTGGTGTAAAATG
CAGCAAAGAAGTCGCCACTGCTATTCGTGGTTATTGGGGTAACAAAATCGGTAAACCTCA
TACAGTACCTTGCAAGGTTACTGGCAAATGTGGTTCAGTTCAAGTCAAATTGATTCCAGC
ACCAAGAGGAACAGGCATTGTTAGTGCTCCAGTTCCAAAGAAATTACTTCAAATGGCTGG
TATTGAAGATTGCTACACTCAATGTCGCGGTTCAACTACAACTTTGGGTAACTTCGCAAA
AGCCACTTACTCAGCTATCATGAAGACTTATGCTTTCTTGACACCTGATTTGTGGAAAGA
AATTCCTTTAAGCAAATCACCATACGAAGTTTATGCTGACTTCCTTGCGAAACCAGCTGG
TAAAACTGGAGGCATTCGCAACATTGATTTGTCTTAAAATGTTAAAAATGCCCTTTGAAA
AACATTCACAAATAAAATGACATCCATTTTTAAAGTGA

>g9524.t24 Gene=g9524 Length=271
MADTAPARGGFKQGFGGAAGGGTGGGGSRGRGRRGGRGGRGRGGRGRGDKEGNQKEWVPV
TKLGRLVRDGKIRSLEEIYLYSLPIKEFEIIDFFLGRSLRDEVLKIMPVQKQTRAGQRTR
FKAFVAIGDSNGHIGLGVKCSKEVATAIRGYWGNKIGKPHTVPCKVTGKCGSVQVKLIPA
PRGTGIVSAPVPKKLLQMAGIEDCYTQCRGSTTTLGNFAKATYSAIMKTYAFLTPDLWKE
IPLSKSPYEVYADFLAKPAGKTGGIRNIDLS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g9524.t24 Gene3D G3DSA:3.30.160.770 - 56 151 6.1E-49
7 g9524.t24 Gene3D G3DSA:3.30.230.10 - 152 240 3.0E-53
10 g9524.t24 MobiDBLite mobidb-lite consensus disorder prediction 1 55 -
3 g9524.t24 PANTHER PTHR13718:SF93 40S RIBOSOMAL PROTEIN S2 3 258 3.3E-111
4 g9524.t24 PANTHER PTHR13718 RIBOSOMAL S SUBUNIT 3 258 3.3E-111
1 g9524.t24 Pfam PF00333 Ribosomal protein S5, N-terminal domain 99 150 8.3E-23
2 g9524.t24 Pfam PF03719 Ribosomal protein S5, C-terminal domain 167 238 1.2E-24
9 g9524.t24 ProSitePatterns PS00585 Ribosomal protein S5 signature. 116 148 -
11 g9524.t24 ProSiteProfiles PS50881 S5 double stranded RNA-binding domain profile. 99 149 18.041
6 g9524.t24 SUPERFAMILY SSF54768 dsRNA-binding domain-like 93 150 1.36E-16
5 g9524.t24 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like 160 240 2.3E-25
12 g9524.t24 TIGRFAM TIGR01020 uS5_euk_arch: ribosomal protein uS5 53 243 5.1E-81

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

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