Gene loci information

Transcript annotation

  • This transcript has been annotated as 40S ribosomal protein S13.

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_3 g565 g565.t11 isoform g565.t11 4159776 4160610
chr_3 g565 g565.t11 exon g565.t11.exon1 4159776 4160165
chr_3 g565 g565.t11 TTS g565.t11 4159781 4159781
chr_3 g565 g565.t11 cds g565.t11.CDS1 4159867 4160165
chr_3 g565 g565.t11 exon g565.t11.exon2 4160243 4160370
chr_3 g565 g565.t11 cds g565.t11.CDS2 4160243 4160370
chr_3 g565 g565.t11 exon g565.t11.exon3 4160588 4160610
chr_3 g565 g565.t11 cds g565.t11.CDS3 4160588 4160610
chr_3 g565 g565.t11 TSS g565.t11 4160636 4160636

Sequences

>g565.t11 Gene=g565 Length=541
ATGGGTCGTATGCACGCGCCTGGTAAAGGTATTTCGCAATCTGCGTTACCTTATCGTCGA
TCAGTTCCATCATGGCTTAAACTCAACGCTGAAGATGTCAAAGAACAAATCAAAAAGCTC
GGAAAAAAGGGAATGACTCCATCTCAAATTGTTCTCCGAGACAGTCATGGAGTCGCTCAG
GTGCGTTTTGTTAATGGAAATAAAATCCTCAGAATCATGAAAGCAGTCGGTTTGAAGCCA
GACATTCCTGAAGACTTGTATTTCCTCATCAAGCGTGCCGTCAGCATCCGTAAGCATTTA
GAAAGAAATCGCAAGGATATTGACTCAAAATTCAGATTGATTTTGGTGGAATCAAGAATT
CATCGCTTGGCTCGCTATTACAAAAACAAAGCCGTTCTTCCACCAACATGGAAATATGAA
TCAGCAACTGCCTCAGCTTTAGTTGCTTAAGTGAAACAACCAAGAAATAAGATCAGTTTT
ATTCTTTAAAATAACGTGAATAAATGGAAGTTTCATAATAAGAAATTGGAAAAATTAAAA
A

>g565.t11 Gene=g565 Length=149
MGRMHAPGKGISQSALPYRRSVPSWLKLNAEDVKEQIKKLGKKGMTPSQIVLRDSHGVAQ
VRFVNGNKILRIMKAVGLKPDIPEDLYFLIKRAVSIRKHLERNRKDIDSKFRLILVESRI
HRLARYYKNKAVLPPTWKYESATASALVA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g565.t11 CDD cd00353 Ribosomal_S15p_S13e 68 143 1.36735E-25
7 g565.t11 Gene3D G3DSA:1.10.8.1030 - 35 80 8.0E-21
6 g565.t11 Gene3D G3DSA:1.10.287.10 - 81 149 3.5E-37
4 g565.t11 Hamap MF_01343_A 30S ribosomal protein S15 [rpsO]. 3 147 28.841486
3 g565.t11 PANTHER PTHR11885 RIBOSOMAL PROTEIN S15P/S13E 1 149 7.8E-74
2 g565.t11 Pfam PF08069 Ribosomal S13/S15 N-terminal domain 1 58 2.8E-25
1 g565.t11 Pfam PF00312 Ribosomal protein S15 72 144 1.4E-15
9 g565.t11 ProSitePatterns PS00362 Ribosomal protein S15 signature. 96 126 -
10 g565.t11 SMART SM01386 Ribosomal_S13_N_2 1 58 1.9E-32
11 g565.t11 SMART SM01387 Ribosomal_S15_2 68 147 7.1E-15
5 g565.t11 SUPERFAMILY SSF47060 S15/NS1 RNA-binding domain 64 140 6.77E-22

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g565/g565.t11; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g565.t11.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005840 ribosome CC
GO:0006412 translation BP
GO:0003735 structural constituent of ribosome MF

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