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.t26 TTS g14133.t26 34847948 34847948
chr_1 g14133 g14133.t26 isoform g14133.t26 34848031 34849291
chr_1 g14133 g14133.t26 exon g14133.t26.exon1 34848031 34848437
chr_1 g14133 g14133.t26 cds g14133.t26.CDS1 34848031 34848437
chr_1 g14133 g14133.t26 exon g14133.t26.exon2 34848504 34848633
chr_1 g14133 g14133.t26 cds g14133.t26.CDS2 34848504 34848633
chr_1 g14133 g14133.t26 exon g14133.t26.exon3 34848823 34849072
chr_1 g14133 g14133.t26 cds g14133.t26.CDS3 34848823 34849041
chr_1 g14133 g14133.t26 exon g14133.t26.exon4 34849279 34849291
chr_1 g14133 g14133.t26 TSS g14133.t26 34849310 34849310

Sequences

>g14133.t26 Gene=g14133 Length=800
AGTGGCATTAAACGTTTAATCGTTGCTCTATAAAATAACGTACAATGTCGGGAGGACTTG
ATGTACTCGCTTTGCGCGATTCAGATGTAACAAAAATGCTTGCAGCAACTGCTCATCTCG
GTTCAGAGCATGTTAATTTCCAAATGGAACAATATGTTTTTAAGAGACGCTCTGATGGTG
CCCATATTATTAACTTGGGACGAACATGGGAGAAGCTTTTGTTGGCTGCTCGTGCGATTG
CTGCTATTGAACATCCACAAGAGATCTATGCTATCTCATCACGAGCTTATGGACAGCGTG
CTGTCTTGAAATTTGCTCATTATACTGGAGCTACACCAATTGCTGGCCGTTTCACTCCTG
GTGCATTCACCAATCAGCAACAAACAACTTTCCATGTCAATATTCCTGTCATTGCTTTTT
GCAATACTGACAGTCCATTGAAATATGTCGATATTGCAATTCCATGTAATACAAAATCGA
CTCACTCAATTGGTTTAATGTGGTGGCTATTGGCACGTGAAGTTTTACGTCTCCGTGGTC
AAATTCCACGTGAACAACCATGGGAAGTTATGGTTGATTTGTTCTTCTATCGTGACCCAG
AGGAAGCTGAAAAGGAAGAGCAAGCCGCCAAGGAAGTTTTGCCAGTTAAAGATTACGCTG
AAGATATTGCTGAAGATCCAACTTATCCAGATGATCCATCAGGCGCAATTATTCCTACAC
CAGCAGTTGCAACAGAAGATTGGAATGAAGACGAAACTGTTGTGCAATCAGAATGGGGTG
GTGCCAACTCTGGCTTCTAA

>g14133.t26 Gene=g14133 Length=251
MSGGLDVLALRDSDVTKMLAATAHLGSEHVNFQMEQYVFKRRSDGAHIINLGRTWEKLLL
AARAIAAIEHPQEIYAISSRAYGQRAVLKFAHYTGATPIAGRFTPGAFTNQQQTTFHVNI
PVIAFCNTDSPLKYVDIAIPCNTKSTHSIGLMWWLLAREVLRLRGQIPREQPWEVMVDLF
FYRDPEEAEKEEQAAKEVLPVKDYAEDIAEDPTYPDDPSGAIIPTPAVATEDWNEDETVV
QSEWGGANSGF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g14133.t26 CDD cd01425 RPS2 18 162 1.35935E-43
11 g14133.t26 Gene3D G3DSA:3.40.50.10490 - 14 198 5.7E-87
6 g14133.t26 Hamap MF_03015 40S ribosomal protein SA [rps-0]. 2 247 43.894875
4 g14133.t26 PANTHER PTHR11489 40S RIBOSOMAL PROTEIN SA 8 244 5.9E-96
5 g14133.t26 PANTHER PTHR11489:SF9 40S RIBOSOMAL PROTEIN SA 8 244 5.9E-96
9 g14133.t26 PRINTS PR00395 Ribosomal protein S2 signature 15 33 6.7E-11
8 g14133.t26 PRINTS PR00395 Ribosomal protein S2 signature 45 54 6.7E-11
7 g14133.t26 PRINTS PR00395 Ribosomal protein S2 signature 94 111 6.7E-11
2 g14133.t26 Pfam PF00318 Ribosomal protein S2 18 114 1.0E-10
1 g14133.t26 Pfam PF00318 Ribosomal protein S2 118 160 3.0E-6
3 g14133.t26 Pfam PF16122 40S ribosomal protein SA C-terminus 180 240 8.5E-10
13 g14133.t26 ProSitePatterns PS00962 Ribosomal protein S2 signature 1. 15 26 -
10 g14133.t26 SUPERFAMILY SSF52313 Ribosomal protein S2 12 178 5.1E-58

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