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.t14 TTS g14133.t14 34847948 34847948
chr_1 g14133 g14133.t14 isoform g14133.t14 34848031 34849283
chr_1 g14133 g14133.t14 exon g14133.t14.exon1 34848031 34848600
chr_1 g14133 g14133.t14 cds g14133.t14.CDS1 34848031 34848600
chr_1 g14133 g14133.t14 exon g14133.t14.exon2 34848855 34849072
chr_1 g14133 g14133.t14 cds g14133.t14.CDS2 34848855 34848932
chr_1 g14133 g14133.t14 exon g14133.t14.exon3 34849279 34849283
chr_1 g14133 g14133.t14 TSS g14133.t14 34849310 34849310

Sequences

>g14133.t14 Gene=g14133 Length=793
TAAACGTTTAATCGTTGCTCTATAAAATAACGTACAATGTCGGGAGGACTTGATGTACTC
GCTTTGCGCGATTCAGATGTAACAAAAATGCTTGCAGCAACTGCTCATCTCGGTTCAGAG
CATGTTAATTTCCAAATGGAACAATATGTTTTTAAGAGACGCTCTGATGGTGCCCATATT
ATTAACTTGGGACGAACATGGGAGAAGCTTTTGTTGGCTGCTCCGTGCTGTCTTGAAATT
TGCTCATTATACTGGAGCTACACCAATTGCTGGCCGTTTCACTCCTGGTGCATTCACCAA
TCAGCAACAAACAACTTTCCGTGAACCACGTCTATTGATTGTTACTGACCCATTGTCAGA
TCATCAGCCAGTCACTGAAGCTTCATATGTCAATATTCCTGTCATTGCTTTTTGCAATAC
TGACAGTCCATTGAAATATGTCGATATTGCAATTCCATGTAATACAAAATCGACTCACTC
AATTGGTTTAATGTGGTGGCTATTGGCACGTGAAGTTTTACGTCTCCGTGGTCAAATTCC
ACGTGAACAACCATGGGAAGTTATGGTTGATTTGTTCTTCTATCGTGACCCAGAGGAAGC
TGAAAAGGAAGAGCAAGCCGCCAAGGAAGTTTTGCCAGTTAAAGATTACGCTGAAGATAT
TGCTGAAGATCCAACTTATCCAGATGATCCATCAGGCGCAATTATTCCTACACCAGCAGT
TGCAACAGAAGATTGGAATGAAGACGAAACTGTTGTGCAATCAGAATGGGGTGGTGCCAA
CTCTGGCTTCTAA

>g14133.t14 Gene=g14133 Length=215
MFLRDALMVPILLTWDEHGRSFCWLLRAVLKFAHYTGATPIAGRFTPGAFTNQQQTTFRE
PRLLIVTDPLSDHQPVTEASYVNIPVIAFCNTDSPLKYVDIAIPCNTKSTHSIGLMWWLL
AREVLRLRGQIPREQPWEVMVDLFFYRDPEEAEKEEQAAKEVLPVKDYAEDIAEDPTYPD
DPSGAIIPTPAVATEDWNEDETVVQSEWGGANSGF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g14133.t14 CDD cd01425 RPS2 27 126 1.01517E-44
11 g14133.t14 Gene3D G3DSA:3.40.50.10490 - 24 162 5.8E-70
3 g14133.t14 PANTHER PTHR11489 40S RIBOSOMAL PROTEIN SA 27 208 4.3E-77
4 g14133.t14 PANTHER PTHR11489:SF9 40S RIBOSOMAL PROTEIN SA 27 208 4.3E-77
6 g14133.t14 PRINTS PR00395 Ribosomal protein S2 signature 36 53 9.8E-22
5 g14133.t14 PRINTS PR00395 Ribosomal protein S2 signature 61 78 9.8E-22
7 g14133.t14 PRINTS PR00395 Ribosomal protein S2 signature 78 89 9.8E-22
8 g14133.t14 PRINTS PR00395 Ribosomal protein S2 signature 99 113 9.8E-22
1 g14133.t14 Pfam PF00318 Ribosomal protein S2 56 124 5.5E-13
2 g14133.t14 Pfam PF16122 40S ribosomal protein SA C-terminus 144 204 6.3E-10
10 g14133.t14 ProSitePatterns PS00963 Ribosomal protein S2 signature 2. 61 85 -
9 g14133.t14 SUPERFAMILY SSF52313 Ribosomal protein S2 26 142 8.89E-46

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