Gene loci information

Transcript annotation

  • This transcript has been annotated as 40S ribosomal protein S12.

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 g2608 g2608.t17 TSS g2608.t17 19031543 19031543
chr_3 g2608 g2608.t17 isoform g2608.t17 19031621 19032276
chr_3 g2608 g2608.t17 exon g2608.t17.exon1 19031621 19031634
chr_3 g2608 g2608.t17 exon g2608.t17.exon2 19031749 19031869
chr_3 g2608 g2608.t17 cds g2608.t17.CDS1 19031772 19031869
chr_3 g2608 g2608.t17 exon g2608.t17.exon3 19032009 19032276
chr_3 g2608 g2608.t17 cds g2608.t17.CDS2 19032009 19032276
chr_3 g2608 g2608.t17 TTS g2608.t17 19032355 19032355

Sequences

>g2608.t17 Gene=g2608 Length=403
ATGTCAGATACTGATTGCTGTCTCATTGGATGGCGCTATGGACTTAAATACTGCTCTTCA
GGAAGTTTTGAAGCAATCACTTGTTAGTGATGGTTTAGTTCATGGAATTCATCAGGCATG
CAAAGTTTTGGACAAACGCCAAGCCGTATTGTGTATTCTCTCTGAGAGCTGTGATGAGCC
TCAATACAAACAACTCATTACTGCTTTGTGCAACGAGCATCAAATCCCATTGATTCGTGT
CGATAGCAGCAAAAAATTAGGTGAATGGTCAGGTCTTTGCAAGATCGACAAAGAGGGCAA
ACCAAGAAAGATTTGCGGATGTTCCTGTGTCGTTATTAAAAACTTTGGTCAAGAAACACC
AGCTTTGGACATTGTCAAGCAGCACTTGCGTTCATCAGCTTAA

>g2608.t17 Gene=g2608 Length=121
MDLNTALQEVLKQSLVSDGLVHGIHQACKVLDKRQAVLCILSESCDEPQYKQLITALCNE
HQIPLIRVDSSKKLGEWSGLCKIDKEGKPRKICGCSCVVIKNFGQETPALDIVKQHLRSS
A

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g2608.t17 Gene3D G3DSA:3.30.1330.30 - 1 120 2.3E-58
2 g2608.t17 PANTHER PTHR11843 40S RIBOSOMAL PROTEIN S12 1 120 2.4E-50
5 g2608.t17 PRINTS PR00972 Ribosomal protein S12E family signature 10 23 1.4E-27
3 g2608.t17 PRINTS PR00972 Ribosomal protein S12E family signature 24 40 1.4E-27
6 g2608.t17 PRINTS PR00972 Ribosomal protein S12E family signature 65 86 1.4E-27
4 g2608.t17 PRINTS PR00972 Ribosomal protein S12E family signature 90 103 1.4E-27
1 g2608.t17 Pfam PF01248 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family 6 99 4.7E-27
8 g2608.t17 ProSitePatterns PS01189 Ribosomal protein S12e signature. 6 24 -
7 g2608.t17 SUPERFAMILY SSF55315 L30e-like 1 117 2.36E-30

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: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. There were no conditions that were differentially expressed