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.t4 isoform g4365.t4 1577584 1579533
chr_2 g4365 g4365.t4 exon g4365.t4.exon1 1577584 1577615
chr_2 g4365 g4365.t4 exon g4365.t4.exon2 1578447 1578495
chr_2 g4365 g4365.t4 TSS g4365.t4 1578467 1578467
chr_2 g4365 g4365.t4 cds g4365.t4.CDS1 1578481 1578495
chr_2 g4365 g4365.t4 exon g4365.t4.exon3 1578887 1579012
chr_2 g4365 g4365.t4 cds g4365.t4.CDS2 1578887 1579012
chr_2 g4365 g4365.t4 exon g4365.t4.exon4 1579204 1579533
chr_2 g4365 g4365.t4 cds g4365.t4.CDS3 1579204 1579533
chr_2 g4365 g4365.t4 TTS g4365.t4 1579602 1579602

Sequences

>g4365.t4 Gene=g4365 Length=537
TTATATTTTATGTATAAGAATAGAATTTTACTTGGTACAAAACTACGTTCTTTCTTTTCG
CTCAACATGGCAGACCATCAGATTGAACGTGCTTTTCAAAAACAGAAAGGTGTTAATCTT
AACCGAAATGCAAAATTCGTTGGTAAGAAGGAGAAATCAATCCGTCTTCACCGTAATGTC
GGCTTAGGATTTAAAACTCCAAAAGAGGCAATCTCGGGACACTACATCGATAAGAAATGC
CCATTTACTGGTATGATTTCAATTCGTGGACGTATTTTGACCGGAGTAGTACGCAAGATG
AAGATGCAGCGAACAATTGTTATTCGTCGCGATTACCTTCATTTTGTTCCAAAATACAGT
CGTTTTGAAAAGAGACACAAAAACATGTCAGTACATTTGTCACCTTGCTTCCGTGATGTT
GAATTGGGTGATGTTGTGACAGTTGGAGAATGCCGACCACTTTCAAAGACCGTTAAATTT
AATGTATTGAAGGTCAGCAAAGTTGCTGGATCAAAGAAAAAGTTCCAGAAATTCTAA

>g4365.t4 Gene=g4365 Length=156
MADHQIERAFQKQKGVNLNRNAKFVGKKEKSIRLHRNVGLGFKTPKEAISGHYIDKKCPF
TGMISIRGRILTGVVRKMKMQRTIVIRRDYLHFVPKYSRFEKRHKNMSVHLSPCFRDVEL
GDVVTVGECRPLSKTVKFNVLKVSKVAGSKKKFQKF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g4365.t4 Gene3D G3DSA:2.40.50.1000 - 1 156 4.2E-78
3 g4365.t4 PANTHER PTHR10744:SF9 40S RIBOSOMAL PROTEIN S11 2 155 2.3E-66
4 g4365.t4 PANTHER PTHR10744 40S RIBOSOMAL PROTEIN S11 FAMILY MEMBER 2 155 2.3E-66
5 g4365.t4 PRINTS PR00973 Ribosomal protein S17 family signature 87 110 4.4E-13
6 g4365.t4 PRINTS PR00973 Ribosomal protein S17 family signature 121 131 4.4E-13
7 g4365.t4 PRINTS PR00973 Ribosomal protein S17 family signature 131 138 4.4E-13
1 g4365.t4 Pfam PF16205 Ribosomal_S17 N-terminal 5 71 1.3E-29
2 g4365.t4 Pfam PF00366 Ribosomal protein S17 73 142 7.8E-27
9 g4365.t4 ProSitePatterns PS00056 Ribosomal protein S17 signature. 121 133 -
8 g4365.t4 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 67 148 1.46E-27
11 g4365.t4 TIGRFAM TIGR03630 uS17_arch: ribosomal protein uS17 54 143 1.0E-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: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