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.t38 TSS g10508.t38 10277506 10277506
chr_1 g10508 g10508.t38 isoform g10508.t38 10277507 10278050
chr_1 g10508 g10508.t38 exon g10508.t38.exon1 10277507 10277728
chr_1 g10508 g10508.t38 cds g10508.t38.CDS1 10277518 10277728
chr_1 g10508 g10508.t38 exon g10508.t38.exon2 10277833 10278050
chr_1 g10508 g10508.t38 cds g10508.t38.CDS2 10277833 10278050
chr_1 g10508 g10508.t38 TTS g10508.t38 10278168 10278168

Sequences

>g10508.t38 Gene=g10508 Length=440
AAAATAATAAGATGTCTCTCGTCATACCTGAGAAGTTTCAACATATTTTGCGTATTATGA
GTACCAATATCGATGGTAAACGCAAAGTTCCGGTCGCAATGACTGCCATCAAGGGTGTCG
GTCGTCGTTACTCACACGTAGTCCTCAGAAAAGCCGATGTTGATGTTGACAAACGTGCCG
GTGAATGTACTGAGGAAGAAGTGAGTGAATTTAGGAAAATACATTGGTTTCTTAACAGAC
AAAAGGATATCATCGATGGTAAATATTCACAATTGACCTCTTCACTCGTCGATTCAAAAT
TGCGTGAAGATTTGGAACGACTTAAGAAAATCCGTGCTCATCGTGGTATGCGTCATTACT
GGGGTCTTCGCGTTCGTGGTCAGCACACAAAAACAACCGGTCGTCGCGGACGTACTGTTG
GTGTGTCAAAGAAGAAGTAA

>g10508.t38 Gene=g10508 Length=142
MSLVIPEKFQHILRIMSTNIDGKRKVPVAMTAIKGVGRRYSHVVLRKADVDVDKRAGECT
EEEVSEFRKIHWFLNRQKDIIDGKYSQLTSSLVDSKLREDLERLKKIRAHRGMRHYWGLR
VRGQHTKTTGRRGRTVGVSKKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g10508.t38 Coils Coil Coil 139 142 -
8 g10508.t38 Gene3D G3DSA:1.10.8.50 - 1 77 1.9E-27
9 g10508.t38 Gene3D G3DSA:4.10.910.10 30s ribosomal protein s13 82 133 1.2E-26
6 g10508.t38 Hamap MF_01315 30S ribosomal protein S13 [rpsM]. 12 142 22.094532
3 g10508.t38 PANTHER PTHR10871 30S RIBOSOMAL PROTEIN S13/40S RIBOSOMAL PROTEIN S18 1 64 2.5E-90
5 g10508.t38 PANTHER PTHR10871:SF3 40S RIBOSOMAL PROTEIN S18-RELATED 1 64 2.5E-90
2 g10508.t38 PANTHER PTHR10871 30S RIBOSOMAL PROTEIN S13/40S RIBOSOMAL PROTEIN S18 72 142 2.5E-90
4 g10508.t38 PANTHER PTHR10871:SF3 40S RIBOSOMAL PROTEIN S18-RELATED 72 142 2.5E-90
11 g10508.t38 PIRSF PIRSF002134 RPS13p_RPS13a_RPS18e_RPS13o 5 142 1.2E-34
1 g10508.t38 Pfam PF00416 Ribosomal protein S13/S18 14 132 4.0E-44
12 g10508.t38 ProSitePatterns PS00646 Ribosomal protein S13 signature. 111 124 -
13 g10508.t38 ProSiteProfiles PS50159 Ribosomal protein S13 family profile. 15 135 32.122
7 g10508.t38 SUPERFAMILY SSF46946 S13-like H2TH domain 13 142 1.81E-33

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

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