Gene loci information

Transcript annotation

  • This transcript has been annotated as 40S ribosomal protein S18.

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 g10508 g10508.t2 isoform g10508.t2 10274875 10278050
chr_1 g10508 g10508.t2 exon g10508.t2.exon1 10274875 10274914
chr_1 g10508 g10508.t2 cds g10508.t2.CDS1 10274899 10274914
chr_1 g10508 g10508.t2 exon g10508.t2.exon2 10277507 10277706
chr_1 g10508 g10508.t2 cds g10508.t2.CDS2 10277507 10277706
chr_1 g10508 g10508.t2 exon g10508.t2.exon3 10277781 10278050
chr_1 g10508 g10508.t2 cds g10508.t2.CDS3 10277781 10278050
chr_1 g10508 g10508.t2 TTS g10508.t2 10278168 10278168
chr_1 g10508 g10508.t2 TSS g10508.t2 NA NA

Sequences

>g10508.t2 Gene=g10508 Length=510
ACAGTTTCAAAAGATGATCACGCGATGCCGTCACAAGCCAAAAATAATAAGATGTCTCTC
GTCATACCTGAGAAGTTTCAACATATTTTGCGTATTATGAGTACCAATATCGATGGTAAA
CGCAAAGTTCCGGTCGCAATGACTGCCATCAAGGGTGTCGGTCGTCGTTACTCACACGTA
GTCCTCAGAAAAGCCGATGTTGATGTTGACAAACGTGCCGGTGAATGTACTGAGGAAGAA
GTCGAAAAAATTGTCACAATTATTTCCAATCCACGTCAATATAAAATTCCAGATTGGTTT
CTTAACAGACAAAAGGATATCATCGATGGTAAATATTCACAATTGACCTCTTCACTCGTC
GATTCAAAATTGCGTGAAGATTTGGAACGACTTAAGAAAATCCGTGCTCATCGTGGTATG
CGTCATTACTGGGGTCTTCGCGTTCGTGGTCAGCACACAAAAACAACCGGTCGTCGCGGA
CGTACTGTTGGTGTGTCAAAGAAGAAGTAA

>g10508.t2 Gene=g10508 Length=161
MPSQAKNNKMSLVIPEKFQHILRIMSTNIDGKRKVPVAMTAIKGVGRRYSHVVLRKADVD
VDKRAGECTEEEVEKIVTIISNPRQYKIPDWFLNRQKDIIDGKYSQLTSSLVDSKLREDL
ERLKKIRAHRGMRHYWGLRVRGQHTKTTGRRGRTVGVSKKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g10508.t2 Gene3D G3DSA:1.10.8.50 - 10 89 1.3E-35
7 g10508.t2 Gene3D G3DSA:4.10.910.10 30s ribosomal protein s13 101 152 1.5E-26
4 g10508.t2 Hamap MF_01315 30S ribosomal protein S13 [rpsM]. 21 161 22.280617
2 g10508.t2 PANTHER PTHR10871 30S RIBOSOMAL PROTEIN S13/40S RIBOSOMAL PROTEIN S18 8 161 8.6E-116
3 g10508.t2 PANTHER PTHR10871:SF3 40S RIBOSOMAL PROTEIN S18-RELATED 8 161 8.6E-116
8 g10508.t2 PIRSF PIRSF002134 RPS13p_RPS13a_RPS18e_RPS13o 6 161 6.6E-37
1 g10508.t2 Pfam PF00416 Ribosomal protein S13/S18 23 151 1.7E-54
9 g10508.t2 ProSitePatterns PS00646 Ribosomal protein S13 signature. 130 143 -
10 g10508.t2 ProSiteProfiles PS50159 Ribosomal protein S13 family profile. 24 154 33.586
5 g10508.t2 SUPERFAMILY SSF46946 S13-like H2TH domain 22 161 2.35E-36

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:0003723 RNA binding MF
GO:0006412 translation BP
GO:0003735 structural constituent of ribosome MF
GO:0003676 nucleic acid binding 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