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.t18 TTS g14133.t18 34847948 34847948
chr_1 g14133 g14133.t18 isoform g14133.t18 34848031 34849291
chr_1 g14133 g14133.t18 exon g14133.t18.exon1 34848031 34848633
chr_1 g14133 g14133.t18 cds g14133.t18.CDS1 34848031 34848633
chr_1 g14133 g14133.t18 exon g14133.t18.exon2 34848876 34849072
chr_1 g14133 g14133.t18 cds g14133.t18.CDS2 34848876 34848932
chr_1 g14133 g14133.t18 exon g14133.t18.exon3 34849279 34849291
chr_1 g14133 g14133.t18 TSS g14133.t18 34849310 34849310

Sequences

>g14133.t18 Gene=g14133 Length=813
AGTGGCATTAAACGTTTAATCGTTGCTCTATAAAATAACGTACAATGTCGGGAGGACTTG
ATGTACTCGCTTTGCGCGATTCAGATGTAACAAAAATGCTTGCAGCAACTGCTCATCTCG
GTTCAGAGCATGTTAATTTCCAAATGGAACAATATGTTTTTAAGAGACGCTCTGATGGTG
CCCATATTATTAACTTGGGACGAACATGGGATCTATGCTATCTCATCACGAGCTTATGGA
CAGCGTGCTGTCTTGAAATTTGCTCATTATACTGGAGCTACACCAATTGCTGGCCGTTTC
ACTCCTGGTGCATTCACCAATCAGCAACAAACAACTTTCCGTGAACCACGTCTATTGATT
GTTACTGACCCATTGTCAGATCATCAGCCAGTCACTGAAGCTTCATATGTCAATATTCCT
GTCATTGCTTTTTGCAATACTGACAGTCCATTGAAATATGTCGATATTGCAATTCCATGT
AATACAAAATCGACTCACTCAATTGGTTTAATGTGGTGGCTATTGGCACGTGAAGTTTTA
CGTCTCCGTGGTCAAATTCCACGTGAACAACCATGGGAAGTTATGGTTGATTTGTTCTTC
TATCGTGACCCAGAGGAAGCTGAAAAGGAAGAGCAAGCCGCCAAGGAAGTTTTGCCAGTT
AAAGATTACGCTGAAGATATTGCTGAAGATCCAACTTATCCAGATGATCCATCAGGCGCA
ATTATTCCTACACCAGCAGTTGCAACAGAAGATTGGAATGAAGACGAAACTGTTGTGCAA
TCAGAATGGGGTGGTGCCAACTCTGGCTTCTAA

>g14133.t18 Gene=g14133 Length=219
MFLRDALMVPILLTWDEHGIYAISSRAYGQRAVLKFAHYTGATPIAGRFTPGAFTNQQQT
TFREPRLLIVTDPLSDHQPVTEASYVNIPVIAFCNTDSPLKYVDIAIPCNTKSTHSIGLM
WWLLAREVLRLRGQIPREQPWEVMVDLFFYRDPEEAEKEEQAAKEVLPVKDYAEDIAEDP
TYPDDPSGAIIPTPAVATEDWNEDETVVQSEWGGANSGF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g14133.t18 CDD cd01425 RPS2 20 130 6.6848E-48
11 g14133.t18 Gene3D G3DSA:3.40.50.10490 - 6 166 1.0E-74
3 g14133.t18 PANTHER PTHR11489 40S RIBOSOMAL PROTEIN SA 19 212 6.5E-83
4 g14133.t18 PANTHER PTHR11489:SF9 40S RIBOSOMAL PROTEIN SA 19 212 6.5E-83
6 g14133.t18 PRINTS PR00395 Ribosomal protein S2 signature 40 57 1.0E-21
8 g14133.t18 PRINTS PR00395 Ribosomal protein S2 signature 65 82 1.0E-21
7 g14133.t18 PRINTS PR00395 Ribosomal protein S2 signature 82 93 1.0E-21
5 g14133.t18 PRINTS PR00395 Ribosomal protein S2 signature 103 117 1.0E-21
1 g14133.t18 Pfam PF00318 Ribosomal protein S2 63 128 9.5E-13
2 g14133.t18 Pfam PF16122 40S ribosomal protein SA C-terminus 148 208 6.6E-10
10 g14133.t18 ProSitePatterns PS00963 Ribosomal protein S2 signature 2. 65 89 -
9 g14133.t18 SUPERFAMILY SSF52313 Ribosomal protein S2 11 146 9.55E-50

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