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.t40 TSS g10508.t40 10277506 10277506
chr_1 g10508 g10508.t40 isoform g10508.t40 10277507 10281056
chr_1 g10508 g10508.t40 exon g10508.t40.exon1 10277507 10277706
chr_1 g10508 g10508.t40 cds g10508.t40.CDS1 10277518 10277706
chr_1 g10508 g10508.t40 exon g10508.t40.exon2 10277781 10278127
chr_1 g10508 g10508.t40 cds g10508.t40.CDS2 10277781 10278050
chr_1 g10508 g10508.t40 exon g10508.t40.exon3 10281042 10281056
chr_1 g10508 g10508.t40 TTS g10508.t40 NA NA

Sequences

>g10508.t40 Gene=g10508 Length=562
AAAATAATAAGATGTCTCTCGTCATACCTGAGAAGTTTCAACATATTTTGCGTATTATGA
GTACCAATATCGATGGTAAACGCAAAGTTCCGGTCGCAATGACTGCCATCAAGGGTGTCG
GTCGTCGTTACTCACACGTAGTCCTCAGAAAAGCCGATGTTGATGTTGACAAACGTGCCG
GTGAATGTACTGAGGAAGAAGTCGAAAAAATTGTCACAATTATTTCCAATCCACGTCAAT
ATAAAATTCCAGATTGGTTTCTTAACAGACAAAAGGATATCATCGATGGTAAATATTCAC
AATTGACCTCTTCACTCGTCGATTCAAAATTGCGTGAAGATTTGGAACGACTTAAGAAAA
TCCGTGCTCATCGTGGTATGCGTCATTACTGGGGTCTTCGCGTTCGTGGTCAGCACACAA
AAACAACCGGTCGTCGCGGACGTACTGTTGGTGTGTCAAAGAAGAAGTAAACATTCTAAT
ATATGCATACAAAATTTATGCATATGCATCTTTATAATTGCATAATTCGATCTTATGTTT
TTATGAATGCTATTAAAAAATT

>g10508.t40 Gene=g10508 Length=152
MSLVIPEKFQHILRIMSTNIDGKRKVPVAMTAIKGVGRRYSHVVLRKADVDVDKRAGECT
EEEVEKIVTIISNPRQYKIPDWFLNRQKDIIDGKYSQLTSSLVDSKLREDLERLKKIRAH
RGMRHYWGLRVRGQHTKTTGRRGRTVGVSKKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g10508.t40 Gene3D G3DSA:1.10.8.50 - 1 80 1.1E-35
7 g10508.t40 Gene3D G3DSA:4.10.910.10 30s ribosomal protein s13 92 143 1.3E-26
4 g10508.t40 Hamap MF_01315 30S ribosomal protein S13 [rpsM]. 12 152 22.280617
10 g10508.t40 MobiDBLite mobidb-lite consensus disorder prediction 133 152 -
2 g10508.t40 PANTHER PTHR10871 30S RIBOSOMAL PROTEIN S13/40S RIBOSOMAL PROTEIN S18 1 152 8.9E-116
3 g10508.t40 PANTHER PTHR10871:SF3 40S RIBOSOMAL PROTEIN S18-RELATED 1 152 8.9E-116
8 g10508.t40 PIRSF PIRSF002134 RPS13p_RPS13a_RPS18e_RPS13o 5 152 4.5E-37
1 g10508.t40 Pfam PF00416 Ribosomal protein S13/S18 14 142 1.4E-54
9 g10508.t40 ProSitePatterns PS00646 Ribosomal protein S13 signature. 121 134 -
11 g10508.t40 ProSiteProfiles PS50159 Ribosomal protein S13 family profile. 15 145 33.586
5 g10508.t40 SUPERFAMILY SSF46946 S13-like H2TH domain 13 152 1.63E-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