Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t27 isoform g10508.t27 10276903 10278050
chr_1 g10508 g10508.t27 exon g10508.t27.exon1 10276903 10277118
chr_1 g10508 g10508.t27 exon g10508.t27.exon2 10277594 10277706
chr_1 g10508 g10508.t27 cds g10508.t27.CDS1 10277605 10277706
chr_1 g10508 g10508.t27 exon g10508.t27.exon3 10277781 10278050
chr_1 g10508 g10508.t27 cds g10508.t27.CDS2 10277781 10278050
chr_1 g10508 g10508.t27 TTS g10508.t27 10278168 10278168
chr_1 g10508 g10508.t27 TSS g10508.t27 NA NA

Sequences

>g10508.t27 Gene=g10508 Length=599
ATGAAATTATTAAAAATAAAAAATTATTGTTTGCCAGAAAATACTTCCGCGCGTCAATAT
GGAAAAAATTTCTTTTCAAAAAGATGCGAAACAACAAATTTTTTGACGCAAAAAGTTGAC
TCTTTCTTTTTCGCATCTTTTATTGAGCAGGCGTGCAAAAGTAAGTAAAAAATTATTAAA
AAACACAGTAAAATAGATTCAAAGTGACCTAAAATATTCCGGTCGCAATGACTGCCATCA
AGGGTGTCGGTCGTCGTTACTCACACGTAGTCCTCAGAAAAGCCGATGTTGATGTTGACA
AACGTGCCGGTGAATGTACTGAGGAAGAAGTCGAAAAAATTGTCACAATTATTTCCAATC
CACGTCAATATAAAATTCCAGATTGGTTTCTTAACAGACAAAAGGATATCATCGATGGTA
AATATTCACAATTGACCTCTTCACTCGTCGATTCAAAATTGCGTGAAGATTTGGAACGAC
TTAAGAAAATCCGTGCTCATCGTGGTATGCGTCATTACTGGGGTCTTCGCGTTCGTGGTC
AGCACACAAAAACAACCGGTCGTCGCGGACGTACTGTTGGTGTGTCAAAGAAGAAGTAA

>g10508.t27 Gene=g10508 Length=123
MTAIKGVGRRYSHVVLRKADVDVDKRAGECTEEEVEKIVTIISNPRQYKIPDWFLNRQKD
IIDGKYSQLTSSLVDSKLREDLERLKKIRAHRGMRHYWGLRVRGQHTKTTGRRGRTVGVS
KKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g10508.t27 Gene3D G3DSA:1.10.8.50 - 1 51 1.9E-20
6 g10508.t27 Gene3D G3DSA:4.10.910.10 30s ribosomal protein s13 63 114 8.5E-27
9 g10508.t27 MobiDBLite mobidb-lite consensus disorder prediction 104 123 -
2 g10508.t27 PANTHER PTHR10871 30S RIBOSOMAL PROTEIN S13/40S RIBOSOMAL PROTEIN S18 1 123 3.9E-92
3 g10508.t27 PANTHER PTHR10871:SF3 40S RIBOSOMAL PROTEIN S18-RELATED 1 123 3.9E-92
7 g10508.t27 PIRSF PIRSF002134 RPS13p_RPS13a_RPS18e_RPS13o 1 123 4.1E-30
1 g10508.t27 Pfam PF00416 Ribosomal protein S13/S18 1 113 3.7E-48
8 g10508.t27 ProSitePatterns PS00646 Ribosomal protein S13 signature. 92 105 -
10 g10508.t27 ProSiteProfiles PS50159 Ribosomal protein S13 family profile. 1 116 29.195
4 g10508.t27 SUPERFAMILY SSF46946 S13-like H2TH domain 1 123 6.47E-31

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. There were no conditions that were differentially expressed