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.t22 TTS g14133.t22 34847948 34847948
chr_1 g14133 g14133.t22 isoform g14133.t22 34848031 34849291
chr_1 g14133 g14133.t22 exon g14133.t22.exon1 34848031 34848546
chr_1 g14133 g14133.t22 cds g14133.t22.CDS1 34848031 34848546
chr_1 g14133 g14133.t22 exon g14133.t22.exon2 34848909 34849072
chr_1 g14133 g14133.t22 cds g14133.t22.CDS2 34848909 34848932
chr_1 g14133 g14133.t22 exon g14133.t22.exon3 34849279 34849291
chr_1 g14133 g14133.t22 TSS g14133.t22 34849310 34849310

Sequences

>g14133.t22 Gene=g14133 Length=693
AGTGGCATTAAACGTTTAATCGTTGCTCTATAAAATAACGTACAATGTCGGGAGGACTTG
ATGTACTCGCTTTGCGCGATTCAGATGTAACAAAAATGCTTGCAGCAACTGCTCATCTCG
GTTCAGAGCATGTTAATTTCCAAATGGAACAATATGTTTTTAAGAGACGCTCTGATGTTC
ACTCCTGGTGCATTCACCAATCAGCAACAAACAACTTTCCGTGAACCACGTCTATTGATT
GTTACTGACCCATTGTCAGATCATCAGCCAGTCACTGAAGCTTCATATGTCAATATTCCT
GTCATTGCTTTTTGCAATACTGACAGTCCATTGAAATATGTCGATATTGCAATTCCATGT
AATACAAAATCGACTCACTCAATTGGTTTAATGTGGTGGCTATTGGCACGTGAAGTTTTA
CGTCTCCGTGGTCAAATTCCACGTGAACAACCATGGGAAGTTATGGTTGATTTGTTCTTC
TATCGTGACCCAGAGGAAGCTGAAAAGGAAGAGCAAGCCGCCAAGGAAGTTTTGCCAGTT
AAAGATTACGCTGAAGATATTGCTGAAGATCCAACTTATCCAGATGATCCATCAGGCGCA
ATTATTCCTACACCAGCAGTTGCAACAGAAGATTGGAATGAAGACGAAACTGTTGTGCAA
TCAGAATGGGGTGGTGCCAACTCTGGCTTCTAA

>g14133.t22 Gene=g14133 Length=179
MFLRDALMFTPGAFTNQQQTTFREPRLLIVTDPLSDHQPVTEASYVNIPVIAFCNTDSPL
KYVDIAIPCNTKSTHSIGLMWWLLAREVLRLRGQIPREQPWEVMVDLFFYRDPEEAEKEE
QAAKEVLPVKDYAEDIAEDPTYPDDPSGAIIPTPAVATEDWNEDETVVQSEWGGANSGF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g14133.t22 CDD cd01425 RPS2 9 90 1.20179E-36
9 g14133.t22 Gene3D G3DSA:3.40.50.10490 - 6 126 2.4E-60
12 g14133.t22 MobiDBLite mobidb-lite consensus disorder prediction 156 179 -
3 g14133.t22 PANTHER PTHR11489 40S RIBOSOMAL PROTEIN SA 8 172 4.4E-66
4 g14133.t22 PANTHER PTHR11489:SF9 40S RIBOSOMAL PROTEIN SA 8 172 4.4E-66
7 g14133.t22 PRINTS PR00395 Ribosomal protein S2 signature 25 42 1.3E-14
6 g14133.t22 PRINTS PR00395 Ribosomal protein S2 signature 42 53 1.3E-14
5 g14133.t22 PRINTS PR00395 Ribosomal protein S2 signature 63 77 1.3E-14
1 g14133.t22 Pfam PF00318 Ribosomal protein S2 19 88 3.1E-13
2 g14133.t22 Pfam PF16122 40S ribosomal protein SA C-terminus 108 168 4.4E-10
11 g14133.t22 ProSitePatterns PS00963 Ribosomal protein S2 signature 2. 25 49 -
8 g14133.t22 SUPERFAMILY SSF52313 Ribosomal protein S2 9 106 7.06E-39

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