Gene loci information

Transcript annotation

  • This transcript has been annotated as 40S ribosomal protein S11.

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_2 g4365 g4365.t6 TSS g4365.t6 1578467 1578467
chr_2 g4365 g4365.t6 isoform g4365.t6 1578481 1579533
chr_2 g4365 g4365.t6 exon g4365.t6.exon1 1578481 1578495
chr_2 g4365 g4365.t6 cds g4365.t6.CDS1 1578481 1578495
chr_2 g4365 g4365.t6 exon g4365.t6.exon2 1578911 1579012
chr_2 g4365 g4365.t6 cds g4365.t6.CDS2 1578911 1579012
chr_2 g4365 g4365.t6 exon g4365.t6.exon3 1579204 1579533
chr_2 g4365 g4365.t6 cds g4365.t6.CDS3 1579204 1579533
chr_2 g4365 g4365.t6 TTS g4365.t6 1579602 1579602

Sequences

>g4365.t6 Gene=g4365 Length=447
ATGGCAGACCATCAGAAAGGTGTTAATCTTAACCGAAATGCAAAATTCGTTGGTAAGAAG
GAGAAATCAATCCGTCTTCACCGTAATGTCGGCTTAGGATTTAAAACTCCAAAAGAGGCA
ATCTCGGGACACTACATCGATAAGAAATGCCCATTTACTGGTATGATTTCAATTCGTGGA
CGTATTTTGACCGGAGTAGTACGCAAGATGAAGATGCAGCGAACAATTGTTATTCGTCGC
GATTACCTTCATTTTGTTCCAAAATACAGTCGTTTTGAAAAGAGACACAAAAACATGTCA
GTACATTTGTCACCTTGCTTCCGTGATGTTGAATTGGGTGATGTTGTGACAGTTGGAGAA
TGCCGACCACTTTCAAAGACCGTTAAATTTAATGTATTGAAGGTCAGCAAAGTTGCTGGA
TCAAAGAAAAAGTTCCAGAAATTCTAA

>g4365.t6 Gene=g4365 Length=148
MADHQKGVNLNRNAKFVGKKEKSIRLHRNVGLGFKTPKEAISGHYIDKKCPFTGMISIRG
RILTGVVRKMKMQRTIVIRRDYLHFVPKYSRFEKRHKNMSVHLSPCFRDVELGDVVTVGE
CRPLSKTVKFNVLKVSKVAGSKKKFQKF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g4365.t6 Gene3D G3DSA:2.40.50.1000 - 2 148 4.1E-72
3 g4365.t6 PANTHER PTHR10744:SF9 40S RIBOSOMAL PROTEIN S11 6 147 7.2E-63
4 g4365.t6 PANTHER PTHR10744 40S RIBOSOMAL PROTEIN S11 FAMILY MEMBER 6 147 7.2E-63
6 g4365.t6 PRINTS PR00973 Ribosomal protein S17 family signature 79 102 4.0E-13
7 g4365.t6 PRINTS PR00973 Ribosomal protein S17 family signature 113 123 4.0E-13
5 g4365.t6 PRINTS PR00973 Ribosomal protein S17 family signature 123 130 4.0E-13
1 g4365.t6 Pfam PF16205 Ribosomal_S17 N-terminal 4 63 5.9E-25
2 g4365.t6 Pfam PF00366 Ribosomal protein S17 65 134 6.9E-27
9 g4365.t6 ProSitePatterns PS00056 Ribosomal protein S17 signature. 113 125 -
8 g4365.t6 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 59 140 1.24E-27
11 g4365.t6 TIGRFAM TIGR03630 uS17_arch: ribosomal protein uS17 46 135 8.5E-32

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.

Raw TPM values