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.t11 TTS g14133.t11 34847948 34847948
chr_1 g14133 g14133.t11 isoform g14133.t11 34848031 34849072
chr_1 g14133 g14133.t11 exon g14133.t11.exon1 34848031 34848633
chr_1 g14133 g14133.t11 cds g14133.t11.CDS1 34848031 34848633
chr_1 g14133 g14133.t11 exon g14133.t11.exon2 34848840 34849072
chr_1 g14133 g14133.t11 cds g14133.t11.CDS2 34848840 34848932
chr_1 g14133 g14133.t11 TSS g14133.t11 34849310 34849310

Sequences

>g14133.t11 Gene=g14133 Length=836
GTTTAATCGTTGCTCTATAAAATAACGTACAATGTCGGGAGGACTTGATGTACTCGCTTT
GCGCGATTCAGATGTAACAAAAATGCTTGCAGCAACTGCTCATCTCGGTTCAGAGCATGT
TAATTTCCAAATGGAACAATATGTTTTTAAGAGACGCTCTGATGGTGCCCATATTATTAA
CTTGGGACGAACATGGGAGAAGCTTTTGTTGGCTGCTCGTGCGATTGCTGCTAATCTATG
CTATCTCATCACGAGCTTATGGACAGCGTGCTGTCTTGAAATTTGCTCATTATACTGGAG
CTACACCAATTGCTGGCCGTTTCACTCCTGGTGCATTCACCAATCAGCAACAAACAACTT
TCCGTGAACCACGTCTATTGATTGTTACTGACCCATTGTCAGATCATCAGCCAGTCACTG
AAGCTTCATATGTCAATATTCCTGTCATTGCTTTTTGCAATACTGACAGTCCATTGAAAT
ATGTCGATATTGCAATTCCATGTAATACAAAATCGACTCACTCAATTGGTTTAATGTGGT
GGCTATTGGCACGTGAAGTTTTACGTCTCCGTGGTCAAATTCCACGTGAACAACCATGGG
AAGTTATGGTTGATTTGTTCTTCTATCGTGACCCAGAGGAAGCTGAAAAGGAAGAGCAAG
CCGCCAAGGAAGTTTTGCCAGTTAAAGATTACGCTGAAGATATTGCTGAAGATCCAACTT
ATCCAGATGATCCATCAGGCGCAATTATTCCTACACCAGCAGTTGCAACAGAAGATTGGA
ATGAAGACGAAACTGTTGTGCAATCAGAATGGGGTGGTGCCAACTCTGGCTTCTAA

>g14133.t11 Gene=g14133 Length=231
MFLRDALMVPILLTWDEHGRSFCWLLVRLLLIYAISSRAYGQRAVLKFAHYTGATPIAGR
FTPGAFTNQQQTTFREPRLLIVTDPLSDHQPVTEASYVNIPVIAFCNTDSPLKYVDIAIP
CNTKSTHSIGLMWWLLAREVLRLRGQIPREQPWEVMVDLFFYRDPEEAEKEEQAAKEVLP
VKDYAEDIAEDPTYPDDPSGAIIPTPAVATEDWNEDETVVQSEWGGANSGF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g14133.t11 CDD cd01425 RPS2 32 142 9.94183E-48
10 g14133.t11 Gene3D G3DSA:3.40.50.10490 - 30 178 4.9E-74
3 g14133.t11 PANTHER PTHR11489 40S RIBOSOMAL PROTEIN SA 32 224 1.7E-82
4 g14133.t11 PANTHER PTHR11489:SF9 40S RIBOSOMAL PROTEIN SA 32 224 1.7E-82
7 g14133.t11 PRINTS PR00395 Ribosomal protein S2 signature 52 69 1.2E-21
8 g14133.t11 PRINTS PR00395 Ribosomal protein S2 signature 77 94 1.2E-21
6 g14133.t11 PRINTS PR00395 Ribosomal protein S2 signature 94 105 1.2E-21
5 g14133.t11 PRINTS PR00395 Ribosomal protein S2 signature 115 129 1.2E-21
1 g14133.t11 Pfam PF00318 Ribosomal protein S2 75 140 1.1E-12
2 g14133.t11 Pfam PF16122 40S ribosomal protein SA C-terminus 160 220 7.3E-10
11 g14133.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 20 -
13 g14133.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 21 40 -
12 g14133.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 41 231 -
15 g14133.t11 ProSitePatterns PS00963 Ribosomal protein S2 signature 2. 77 101 -
9 g14133.t11 SUPERFAMILY SSF52313 Ribosomal protein S2 32 158 7.85E-49

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