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.t20 TTS g14133.t20 34847948 34847948
chr_1 g14133 g14133.t20 isoform g14133.t20 34848031 34849291
chr_1 g14133 g14133.t20 exon g14133.t20.exon1 34848031 34848556
chr_1 g14133 g14133.t20 cds g14133.t20.CDS1 34848031 34848556
chr_1 g14133 g14133.t20 exon g14133.t20.exon2 34848855 34849072
chr_1 g14133 g14133.t20 cds g14133.t20.CDS2 34848855 34848880
chr_1 g14133 g14133.t20 exon g14133.t20.exon3 34849279 34849291
chr_1 g14133 g14133.t20 TSS g14133.t20 34849310 34849310

Sequences

>g14133.t20 Gene=g14133 Length=757
AGTGGCATTAAACGTTTAATCGTTGCTCTATAAAATAACGTACAATGTCGGGAGGACTTG
ATGTACTCGCTTTGCGCGATTCAGATGTAACAAAAATGCTTGCAGCAACTGCTCATCTCG
GTTCAGAGCATGTTAATTTCCAAATGGAACAATATGTTTTTAAGAGACGCTCTGATGGTG
CCCATATTATTAACTTGGGACGAACATGGGAGAAGCTTTTGTTGGCTGCTCTGCTGGCCG
TTTCACTCCTGGTGCATTCACCAATCAGCAACAAACAACTTTCCGTGAACCACGTCTATT
GATTGTTACTGACCCATTGTCAGATCATCAGCCAGTCACTGAAGCTTCATATGTCAATAT
TCCTGTCATTGCTTTTTGCAATACTGACAGTCCATTGAAATATGTCGATATTGCAATTCC
ATGTAATACAAAATCGACTCACTCAATTGGTTTAATGTGGTGGCTATTGGCACGTGAAGT
TTTACGTCTCCGTGGTCAAATTCCACGTGAACAACCATGGGAAGTTATGGTTGATTTGTT
CTTCTATCGTGACCCAGAGGAAGCTGAAAAGGAAGAGCAAGCCGCCAAGGAAGTTTTGCC
AGTTAAAGATTACGCTGAAGATATTGCTGAAGATCCAACTTATCCAGATGATCCATCAGG
CGCAATTATTCCTACACCAGCAGTTGCAACAGAAGATTGGAATGAAGACGAAACTGTTGT
GCAATCAGAATGGGGTGGTGCCAACTCTGGCTTCTAA

>g14133.t20 Gene=g14133 Length=183
MGEAFVGCSAGRFTPGAFTNQQQTTFREPRLLIVTDPLSDHQPVTEASYVNIPVIAFCNT
DSPLKYVDIAIPCNTKSTHSIGLMWWLLAREVLRLRGQIPREQPWEVMVDLFFYRDPEEA
EKEEQAAKEVLPVKDYAEDIAEDPTYPDDPSGAIIPTPAVATEDWNEDETVVQSEWGGAN
SGF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g14133.t20 CDD cd01425 RPS2 5 94 1.38435E-38
11 g14133.t20 Gene3D G3DSA:3.40.50.10490 - 5 130 3.6E-62
3 g14133.t20 PANTHER PTHR11489 40S RIBOSOMAL PROTEIN SA 9 176 2.3E-68
4 g14133.t20 PANTHER PTHR11489:SF9 40S RIBOSOMAL PROTEIN SA 9 176 2.3E-68
5 g14133.t20 PRINTS PR00395 Ribosomal protein S2 signature 4 21 5.3E-18
8 g14133.t20 PRINTS PR00395 Ribosomal protein S2 signature 29 46 5.3E-18
7 g14133.t20 PRINTS PR00395 Ribosomal protein S2 signature 46 57 5.3E-18
6 g14133.t20 PRINTS PR00395 Ribosomal protein S2 signature 67 81 5.3E-18
1 g14133.t20 Pfam PF00318 Ribosomal protein S2 23 92 3.3E-13
2 g14133.t20 Pfam PF16122 40S ribosomal protein SA C-terminus 112 172 4.6E-10
10 g14133.t20 ProSitePatterns PS00963 Ribosomal protein S2 signature 2. 29 53 -
9 g14133.t20 SUPERFAMILY SSF52313 Ribosomal protein S2 10 110 2.88E-40

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