Gene loci information

Transcript annotation

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

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 g14133 g14133.t21 TTS g14133.t21 34847948 34847948
chr_1 g14133 g14133.t21 isoform g14133.t21 34848031 34849291
chr_1 g14133 g14133.t21 exon g14133.t21.exon1 34848031 34848633
chr_1 g14133 g14133.t21 cds g14133.t21.CDS1 34848031 34848633
chr_1 g14133 g14133.t21 exon g14133.t21.exon2 34848909 34849072
chr_1 g14133 g14133.t21 cds g14133.t21.CDS2 34848909 34848932
chr_1 g14133 g14133.t21 exon g14133.t21.exon3 34849279 34849291
chr_1 g14133 g14133.t21 TSS g14133.t21 34849310 34849310

Sequences

>g14133.t21 Gene=g14133 Length=780
AGTGGCATTAAACGTTTAATCGTTGCTCTATAAAATAACGTACAATGTCGGGAGGACTTG
ATGTACTCGCTTTGCGCGATTCAGATGTAACAAAAATGCTTGCAGCAACTGCTCATCTCG
GTTCAGAGCATGTTAATTTCCAAATGGAACAATATGTTTTTAAGAGACGCTCTGATGATC
TATGCTATCTCATCACGAGCTTATGGACAGCGTGCTGTCTTGAAATTTGCTCATTATACT
GGAGCTACACCAATTGCTGGCCGTTTCACTCCTGGTGCATTCACCAATCAGCAACAAACA
ACTTTCCGTGAACCACGTCTATTGATTGTTACTGACCCATTGTCAGATCATCAGCCAGTC
ACTGAAGCTTCATATGTCAATATTCCTGTCATTGCTTTTTGCAATACTGACAGTCCATTG
AAATATGTCGATATTGCAATTCCATGTAATACAAAATCGACTCACTCAATTGGTTTAATG
TGGTGGCTATTGGCACGTGAAGTTTTACGTCTCCGTGGTCAAATTCCACGTGAACAACCA
TGGGAAGTTATGGTTGATTTGTTCTTCTATCGTGACCCAGAGGAAGCTGAAAAGGAAGAG
CAAGCCGCCAAGGAAGTTTTGCCAGTTAAAGATTACGCTGAAGATATTGCTGAAGATCCA
ACTTATCCAGATGATCCATCAGGCGCAATTATTCCTACACCAGCAGTTGCAACAGAAGAT
TGGAATGAAGACGAAACTGTTGTGCAATCAGAATGGGGTGGTGCCAACTCTGGCTTCTAA

>g14133.t21 Gene=g14133 Length=208
MFLRDALMIYAISSRAYGQRAVLKFAHYTGATPIAGRFTPGAFTNQQQTTFREPRLLIVT
DPLSDHQPVTEASYVNIPVIAFCNTDSPLKYVDIAIPCNTKSTHSIGLMWWLLAREVLRL
RGQIPREQPWEVMVDLFFYRDPEEAEKEEQAAKEVLPVKDYAEDIAEDPTYPDDPSGAII
PTPAVATEDWNEDETVVQSEWGGANSGF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g14133.t21 CDD cd01425 RPS2 9 119 4.61065E-48
11 g14133.t21 Gene3D G3DSA:3.40.50.10490 - 4 155 2.4E-74
3 g14133.t21 PANTHER PTHR11489 40S RIBOSOMAL PROTEIN SA 9 201 8.3E-83
4 g14133.t21 PANTHER PTHR11489:SF9 40S RIBOSOMAL PROTEIN SA 9 201 8.3E-83
7 g14133.t21 PRINTS PR00395 Ribosomal protein S2 signature 29 46 8.9E-22
6 g14133.t21 PRINTS PR00395 Ribosomal protein S2 signature 54 71 8.9E-22
8 g14133.t21 PRINTS PR00395 Ribosomal protein S2 signature 71 82 8.9E-22
5 g14133.t21 PRINTS PR00395 Ribosomal protein S2 signature 92 106 8.9E-22
1 g14133.t21 Pfam PF00318 Ribosomal protein S2 52 117 9.6E-13
2 g14133.t21 Pfam PF16122 40S ribosomal protein SA C-terminus 137 197 5.9E-10
10 g14133.t21 ProSitePatterns PS00963 Ribosomal protein S2 signature 2. 54 78 -
9 g14133.t21 SUPERFAMILY SSF52313 Ribosomal protein S2 8 135 5.1E-49

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
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