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.t7 isoform g14133.t7 34847935 34849283
chr_1 g14133 g14133.t7 exon g14133.t7.exon1 34847935 34848464
chr_1 g14133 g14133.t7 TTS g14133.t7 34847948 34847948
chr_1 g14133 g14133.t7 cds g14133.t7.CDS1 34848031 34848464
chr_1 g14133 g14133.t7 exon g14133.t7.exon2 34848537 34848633
chr_1 g14133 g14133.t7 cds g14133.t7.CDS2 34848537 34848633
chr_1 g14133 g14133.t7 exon g14133.t7.exon3 34848823 34849072
chr_1 g14133 g14133.t7 cds g14133.t7.CDS3 34848823 34849041
chr_1 g14133 g14133.t7 exon g14133.t7.exon4 34849279 34849283
chr_1 g14133 g14133.t7 TSS g14133.t7 34849310 34849310

Sequences

>g14133.t7 Gene=g14133 Length=882
TAAACGTTTAATCGTTGCTCTATAAAATAACGTACAATGTCGGGAGGACTTGATGTACTC
GCTTTGCGCGATTCAGATGTAACAAAAATGCTTGCAGCAACTGCTCATCTCGGTTCAGAG
CATGTTAATTTCCAAATGGAACAATATGTTTTTAAGAGACGCTCTGATGGTGCCCATATT
ATTAACTTGGGACGAACATGGGAGAAGCTTTTGTTGGCTGCTCGTGCGATTGCTGCTATT
GAACATCCACAAGAGATCTATGCTATCTCATCACGAGCTTATGGACAGCGTGCTGTCTTG
AAATTTGCTCATTATACTGGAGCTACACCAATTGCTGGCCGTTTCACTCCTGATCATCAG
CCAGTCACTGAAGCTTCATATGTCAATATTCCTGTCATTGCTTTTTGCAATACTGACAGT
CCATTGAAATATGTCGATATTGCAATTCCATGTAATACAAAATCGACTCACTCAATTGGT
TTAATGTGGTGGCTATTGGCACGTGAAGTTTTACGTCTCCGTGGTCAAATTCCACGTGAA
CAACCATGGGAAGTTATGGTTGATTTGTTCTTCTATCGTGACCCAGAGGAAGCTGAAAAG
GAAGAGCAAGCCGCCAAGGAAGTTTTGCCAGTTAAAGATTACGCTGAAGATATTGCTGAA
GATCCAACTTATCCAGATGATCCATCAGGCGCAATTATTCCTACACCAGCAGTTGCAACA
GAAGATTGGAATGAAGACGAAACTGTTGTGCAATCAGAATGGGGTGGTGCCAACTCTGGC
TTCTAAATTCATGTGAAGAAATAATTTACATCATTTTCAAGTAAAAGGAAGAATGTTTCC
TTTTTTTAATAAATCATAATCTTGAAAAGAAAAGAAAATTTT

>g14133.t7 Gene=g14133 Length=249
MSGGLDVLALRDSDVTKMLAATAHLGSEHVNFQMEQYVFKRRSDGAHIINLGRTWEKLLL
AARAIAAIEHPQEIYAISSRAYGQRAVLKFAHYTGATPIAGRFTPDHQPVTEASYVNIPV
IAFCNTDSPLKYVDIAIPCNTKSTHSIGLMWWLLAREVLRLRGQIPREQPWEVMVDLFFY
RDPEEAEKEEQAAKEVLPVKDYAEDIAEDPTYPDDPSGAIIPTPAVATEDWNEDETVVQS
EWGGANSGF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g14133.t7 CDD cd01425 RPS2 18 160 8.78566E-45
10 g14133.t7 Gene3D G3DSA:3.40.50.10490 - 14 196 1.3E-82
8 g14133.t7 Hamap MF_03015 40S ribosomal protein SA [rps-0]. 2 245 43.85841
13 g14133.t7 MobiDBLite mobidb-lite consensus disorder prediction 226 249 -
5 g14133.t7 PANTHER PTHR11489 40S RIBOSOMAL PROTEIN SA 8 105 9.3E-96
7 g14133.t7 PANTHER PTHR11489:SF9 40S RIBOSOMAL PROTEIN SA 8 105 9.3E-96
4 g14133.t7 PANTHER PTHR11489 40S RIBOSOMAL PROTEIN SA 106 242 9.3E-96
6 g14133.t7 PANTHER PTHR11489:SF9 40S RIBOSOMAL PROTEIN SA 106 242 9.3E-96
1 g14133.t7 Pfam PF00318 Ribosomal protein S2 18 103 1.0E-6
2 g14133.t7 Pfam PF00318 Ribosomal protein S2 107 158 1.6E-8
3 g14133.t7 Pfam PF16122 40S ribosomal protein SA C-terminus 178 238 8.4E-10
12 g14133.t7 ProSitePatterns PS00962 Ribosomal protein S2 signature 1. 15 26 -
9 g14133.t7 SUPERFAMILY SSF52313 Ribosomal protein S2 12 176 1.44E-57

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