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.t31 TTS g14133.t31 34847948 34847948
chr_1 g14133 g14133.t31 isoform g14133.t31 34848031 34849386
chr_1 g14133 g14133.t31 exon g14133.t31.exon1 34848031 34848633
chr_1 g14133 g14133.t31 cds g14133.t31.CDS1 34848031 34848633
chr_1 g14133 g14133.t31 exon g14133.t31.exon2 34848823 34849072
chr_1 g14133 g14133.t31 cds g14133.t31.CDS2 34848823 34849041
chr_1 g14133 g14133.t31 exon g14133.t31.exon3 34849291 34849386
chr_1 g14133 g14133.t31 TSS g14133.t31 NA NA

Sequences

>g14133.t31 Gene=g14133 Length=949
TAATTTTAAAACTTTATTTTCAATCTCGTGTTTTTGTTTTTGAATTTATTTACAAATTCG
CTCTACTGAATTCGCCCTTTTTCAACTCGCTCTCAAGTTTAATCGTTGCTCTATAAAATA
ACGTACAATGTCGGGAGGACTTGATGTACTCGCTTTGCGCGATTCAGATGTAACAAAAAT
GCTTGCAGCAACTGCTCATCTCGGTTCAGAGCATGTTAATTTCCAAATGGAACAATATGT
TTTTAAGAGACGCTCTGATGGTGCCCATATTATTAACTTGGGACGAACATGGGAGAAGCT
TTTGTTGGCTGCTCGTGCGATTGCTGCTATTGAACATCCACAAGAGATCTATGCTATCTC
ATCACGAGCTTATGGACAGCGTGCTGTCTTGAAATTTGCTCATTATACTGGAGCTACACC
AATTGCTGGCCGTTTCACTCCTGGTGCATTCACCAATCAGCAACAAACAACTTTCCGTGA
ACCACGTCTATTGATTGTTACTGACCCATTGTCAGATCATCAGCCAGTCACTGAAGCTTC
ATATGTCAATATTCCTGTCATTGCTTTTTGCAATACTGACAGTCCATTGAAATATGTCGA
TATTGCAATTCCATGTAATACAAAATCGACTCACTCAATTGGTTTAATGTGGTGGCTATT
GGCACGTGAAGTTTTACGTCTCCGTGGTCAAATTCCACGTGAACAACCATGGGAAGTTAT
GGTTGATTTGTTCTTCTATCGTGACCCAGAGGAAGCTGAAAAGGAAGAGCAAGCCGCCAA
GGAAGTTTTGCCAGTTAAAGATTACGCTGAAGATATTGCTGAAGATCCAACTTATCCAGA
TGATCCATCAGGCGCAATTATTCCTACACCAGCAGTTGCAACAGAAGATTGGAATGAAGA
CGAAACTGTTGTGCAATCAGAATGGGGTGGTGCCAACTCTGGCTTCTAA

>g14133.t31 Gene=g14133 Length=273
MSGGLDVLALRDSDVTKMLAATAHLGSEHVNFQMEQYVFKRRSDGAHIINLGRTWEKLLL
AARAIAAIEHPQEIYAISSRAYGQRAVLKFAHYTGATPIAGRFTPGAFTNQQQTTFREPR
LLIVTDPLSDHQPVTEASYVNIPVIAFCNTDSPLKYVDIAIPCNTKSTHSIGLMWWLLAR
EVLRLRGQIPREQPWEVMVDLFFYRDPEEAEKEEQAAKEVLPVKDYAEDIAEDPTYPDDP
SGAIIPTPAVATEDWNEDETVVQSEWGGANSGF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g14133.t31 CDD cd01425 RPS2 18 184 1.36226E-61
14 g14133.t31 Gene3D G3DSA:3.40.50.10490 - 14 220 1.7E-105
6 g14133.t31 Hamap MF_03015 40S ribosomal protein SA [rps-0]. 2 269 53.734024
4 g14133.t31 PANTHER PTHR11489 40S RIBOSOMAL PROTEIN SA 8 266 8.2E-117
5 g14133.t31 PANTHER PTHR11489:SF9 40S RIBOSOMAL PROTEIN SA 8 266 8.2E-117
11 g14133.t31 PRINTS PR00395 Ribosomal protein S2 signature 15 33 7.7E-31
10 g14133.t31 PRINTS PR00395 Ribosomal protein S2 signature 45 54 7.7E-31
8 g14133.t31 PRINTS PR00395 Ribosomal protein S2 signature 94 111 7.7E-31
7 g14133.t31 PRINTS PR00395 Ribosomal protein S2 signature 119 136 7.7E-31
9 g14133.t31 PRINTS PR00395 Ribosomal protein S2 signature 136 147 7.7E-31
12 g14133.t31 PRINTS PR00395 Ribosomal protein S2 signature 157 171 7.7E-31
2 g14133.t31 Pfam PF00318 Ribosomal protein S2 18 113 1.6E-10
1 g14133.t31 Pfam PF00318 Ribosomal protein S2 117 182 1.4E-12
3 g14133.t31 Pfam PF16122 40S ribosomal protein SA C-terminus 202 262 9.8E-10
16 g14133.t31 ProSitePatterns PS00962 Ribosomal protein S2 signature 1. 15 26 -
17 g14133.t31 ProSitePatterns PS00963 Ribosomal protein S2 signature 2. 119 143 -
13 g14133.t31 SUPERFAMILY SSF52313 Ribosomal protein S2 12 200 3.27E-72
18 g14133.t31 TIGRFAM TIGR01012 uS2_euk_arch: ribosomal protein uS2 13 205 2.3E-85

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

Pathway

  • This transcript belongs to the following pathways

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