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.t30 TTS g14133.t30 34847948 34847948
chr_1 g14133 g14133.t30 isoform g14133.t30 34848031 34849386
chr_1 g14133 g14133.t30 exon g14133.t30.exon1 34848031 34848600
chr_1 g14133 g14133.t30 cds g14133.t30.CDS1 34848031 34848600
chr_1 g14133 g14133.t30 exon g14133.t30.exon2 34848823 34849072
chr_1 g14133 g14133.t30 cds g14133.t30.CDS2 34848823 34849041
chr_1 g14133 g14133.t30 exon g14133.t30.exon3 34849279 34849386
chr_1 g14133 g14133.t30 TSS g14133.t30 NA NA

Sequences

>g14133.t30 Gene=g14133 Length=928
TAATTTTAAAACTTTATTTTCAATCTCGTGTTTTTGTTTTTGAATTTATTTACAAATTCG
CTCTACTGAATTCGCCCTTTTTCAACTCGCTCTCAAGTGGCATTAAACGTTTAATCGTTG
CTCTATAAAATAACGTACAATGTCGGGAGGACTTGATGTACTCGCTTTGCGCGATTCAGA
TGTAACAAAAATGCTTGCAGCAACTGCTCATCTCGGTTCAGAGCATGTTAATTTCCAAAT
GGAACAATATGTTTTTAAGAGACGCTCTGATGGTGCCCATATTATTAACTTGGGACGAAC
ATGGGAGAAGCTTTTGTTGGCTGCTCGTGCGATTGCTGCTATTGAACATCCACAAGAGCG
TGCTGTCTTGAAATTTGCTCATTATACTGGAGCTACACCAATTGCTGGCCGTTTCACTCC
TGGTGCATTCACCAATCAGCAACAAACAACTTTCCGTGAACCACGTCTATTGATTGTTAC
TGACCCATTGTCAGATCATCAGCCAGTCACTGAAGCTTCATATGTCAATATTCCTGTCAT
TGCTTTTTGCAATACTGACAGTCCATTGAAATATGTCGATATTGCAATTCCATGTAATAC
AAAATCGACTCACTCAATTGGTTTAATGTGGTGGCTATTGGCACGTGAAGTTTTACGTCT
CCGTGGTCAAATTCCACGTGAACAACCATGGGAAGTTATGGTTGATTTGTTCTTCTATCG
TGACCCAGAGGAAGCTGAAAAGGAAGAGCAAGCCGCCAAGGAAGTTTTGCCAGTTAAAGA
TTACGCTGAAGATATTGCTGAAGATCCAACTTATCCAGATGATCCATCAGGCGCAATTAT
TCCTACACCAGCAGTTGCAACAGAAGATTGGAATGAAGACGAAACTGTTGTGCAATCAGA
ATGGGGTGGTGCCAACTCTGGCTTCTAA

>g14133.t30 Gene=g14133 Length=262
MSGGLDVLALRDSDVTKMLAATAHLGSEHVNFQMEQYVFKRRSDGAHIINLGRTWEKLLL
AARAIAAIEHPQERAVLKFAHYTGATPIAGRFTPGAFTNQQQTTFREPRLLIVTDPLSDH
QPVTEASYVNIPVIAFCNTDSPLKYVDIAIPCNTKSTHSIGLMWWLLAREVLRLRGQIPR
EQPWEVMVDLFFYRDPEEAEKEEQAAKEVLPVKDYAEDIAEDPTYPDDPSGAIIPTPAVA
TEDWNEDETVVQSEWGGANSGF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g14133.t30 CDD cd01425 RPS2 18 173 9.64279E-56
11 g14133.t30 Gene3D G3DSA:3.40.50.10490 - 14 209 1.6E-96
5 g14133.t30 Hamap MF_03015 40S ribosomal protein SA [rps-0]. 2 258 49.291515
3 g14133.t30 PANTHER PTHR11489 40S RIBOSOMAL PROTEIN SA 8 255 4.8E-106
4 g14133.t30 PANTHER PTHR11489:SF9 40S RIBOSOMAL PROTEIN SA 8 255 4.8E-106
7 g14133.t30 PRINTS PR00395 Ribosomal protein S2 signature 15 33 7.1E-19
8 g14133.t30 PRINTS PR00395 Ribosomal protein S2 signature 108 125 7.1E-19
9 g14133.t30 PRINTS PR00395 Ribosomal protein S2 signature 125 136 7.1E-19
6 g14133.t30 PRINTS PR00395 Ribosomal protein S2 signature 146 160 7.1E-19
1 g14133.t30 Pfam PF00318 Ribosomal protein S2 106 171 1.3E-12
2 g14133.t30 Pfam PF16122 40S ribosomal protein SA C-terminus 191 251 9.2E-10
13 g14133.t30 ProSitePatterns PS00962 Ribosomal protein S2 signature 1. 15 26 -
14 g14133.t30 ProSitePatterns PS00963 Ribosomal protein S2 signature 2. 108 132 -
10 g14133.t30 SUPERFAMILY SSF52313 Ribosomal protein S2 12 189 6.67E-66
15 g14133.t30 TIGRFAM TIGR01012 uS2_euk_arch: ribosomal protein uS2 13 194 2.0E-74

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