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.t28 TTS g14133.t28 34847948 34847948
chr_1 g14133 g14133.t28 isoform g14133.t28 34848031 34849291
chr_1 g14133 g14133.t28 exon g14133.t28.exon1 34848031 34848224
chr_1 g14133 g14133.t28 cds g14133.t28.CDS1 34848221 34848224
chr_1 g14133 g14133.t28 exon g14133.t28.exon2 34848332 34848633
chr_1 g14133 g14133.t28 cds g14133.t28.CDS2 34848332 34848633
chr_1 g14133 g14133.t28 exon g14133.t28.exon3 34848823 34849072
chr_1 g14133 g14133.t28 cds g14133.t28.CDS3 34848823 34849041
chr_1 g14133 g14133.t28 exon g14133.t28.exon4 34849279 34849291
chr_1 g14133 g14133.t28 TSS g14133.t28 34849310 34849310

Sequences

>g14133.t28 Gene=g14133 Length=759
AGTGGCATTAAACGTTTAATCGTTGCTCTATAAAATAACGTACAATGTCGGGAGGACTTG
ATGTACTCGCTTTGCGCGATTCAGATGTAACAAAAATGCTTGCAGCAACTGCTCATCTCG
GTTCAGAGCATGTTAATTTCCAAATGGAACAATATGTTTTTAAGAGACGCTCTGATGGTG
CCCATATTATTAACTTGGGACGAACATGGGAGAAGCTTTTGTTGGCTGCTCGTGCGATTG
CTGCTATTGAACATCCACAAGAGATCTATGCTATCTCATCACGAGCTTATGGACAGCGTG
CTGTCTTGAAATTTGCTCATTATACTGGAGCTACACCAATTGCTGGCCGTTTCACTCCTG
GTGCATTCACCAATCAGCAACAAACAACTTTCCGTGAACCACGTCTATTGATTGTTACTG
ACCCATTGTCAGATCATCAGCCAGTCACTGAAGCTTCATATGTCAATATTCCTGTCATTG
CTTTTTGCAATACTGACAGTCCATTGAAATATGTCGATATTGCAATTCCATGTAATACAA
AATCGACTCACTCAATTGGTTTAATCTGAAAAGGAAGAGCAAGCCGCCAAGGAAGTTTTG
CCAGTTAAAGATTACGCTGAAGATATTGCTGAAGATCCAACTTATCCAGATGATCCATCA
GGCGCAATTATTCCTACACCAGCAGTTGCAACAGAAGATTGGAATGAAGACGAAACTGTT
GTGCAATCAGAATGGGGTGGTGCCAACTCTGGCTTCTAA

>g14133.t28 Gene=g14133 Length=174
MSGGLDVLALRDSDVTKMLAATAHLGSEHVNFQMEQYVFKRRSDGAHIINLGRTWEKLLL
AARAIAAIEHPQEIYAISSRAYGQRAVLKFAHYTGATPIAGRFTPGAFTNQQQTTFREPR
LLIVTDPLSDHQPVTEASYVNIPVIAFCNTDSPLKYVDIAIPCNTKSTHSIGLI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g14133.t28 CDD cd01425 RPS2 18 174 4.76789E-56
12 g14133.t28 Gene3D G3DSA:3.40.50.10490 - 14 174 3.5E-81
3 g14133.t28 PANTHER PTHR11489 40S RIBOSOMAL PROTEIN SA 8 174 2.2E-87
4 g14133.t28 PANTHER PTHR11489:SF9 40S RIBOSOMAL PROTEIN SA 8 174 2.2E-87
9 g14133.t28 PRINTS PR00395 Ribosomal protein S2 signature 15 33 1.0E-31
8 g14133.t28 PRINTS PR00395 Ribosomal protein S2 signature 45 54 1.0E-31
6 g14133.t28 PRINTS PR00395 Ribosomal protein S2 signature 94 111 1.0E-31
5 g14133.t28 PRINTS PR00395 Ribosomal protein S2 signature 119 136 1.0E-31
7 g14133.t28 PRINTS PR00395 Ribosomal protein S2 signature 136 147 1.0E-31
10 g14133.t28 PRINTS PR00395 Ribosomal protein S2 signature 157 171 1.0E-31
2 g14133.t28 Pfam PF00318 Ribosomal protein S2 18 113 5.5E-11
1 g14133.t28 Pfam PF00318 Ribosomal protein S2 117 174 1.1E-11
14 g14133.t28 ProSitePatterns PS00962 Ribosomal protein S2 signature 1. 15 26 -
15 g14133.t28 ProSitePatterns PS00963 Ribosomal protein S2 signature 2. 119 143 -
11 g14133.t28 SUPERFAMILY SSF52313 Ribosomal protein S2 12 174 6.93E-64
16 g14133.t28 TIGRFAM TIGR01012 uS2_euk_arch: ribosomal protein uS2 13 174 3.0E-70

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