Gene loci information

Transcript annotation

  • This transcript has been annotated as 40S ribosomal protein S6.

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 g11474 g11474.t74 TTS g11474.t74 16437300 16437300
chr_1 g11474 g11474.t74 isoform g11474.t74 16437372 16438953
chr_1 g11474 g11474.t74 exon g11474.t74.exon1 16437372 16437855
chr_1 g11474 g11474.t74 cds g11474.t74.CDS1 16437838 16437855
chr_1 g11474 g11474.t74 exon g11474.t74.exon2 16437937 16438286
chr_1 g11474 g11474.t74 cds g11474.t74.CDS2 16437937 16438286
chr_1 g11474 g11474.t74 exon g11474.t74.exon3 16438516 16438953
chr_1 g11474 g11474.t74 cds g11474.t74.CDS3 16438516 16438633
chr_1 g11474 g11474.t74 TSS g11474.t74 16438988 16438988

Sequences

>g11474.t74 Gene=g11474 Length=1272
ATGAAGGTGAATAAATTAAAAATTCTAAGATAAATCTTGAAATTCAATTGAAATGATATT
TTCATAATAAGTATAAGTGTTTAATGAATGAAAAACACTCAAAATATTGCACAGAAATAC
ACAAAATTAATAAATAATTGTGAAAATATTTTTTCCCGATGTTAAAAAATTCTTCCATGT
GTATATTGTATTGAAAAATTCTAATGGTTTTTTATTTTTCTATTTTATTTTAGTTAAACG
TCTCCTATCCCTCAACGGGAGCTCAGAAAACTTTTGAGGTCAACGATGACCACAAATTGC
GATTGTTTTACGAGAAACGCATGGGCGCTGAAATTGAAGCTGATCAATTAGGCGATGAAT
GGAAAGGATATATTCTTAAAATCGCTGGTGGTAATGATAAACAAGGTTTCCCAATGAAAC
AGGGTGTTTTAACAAACACTCGTGTTCGTCTCTTGCTTAAAAAAGGACATTCCTGTTATC
GTCCAAGAAGAACTGGAGAACGTAAACGTAAATCAGTTCGTGGTTGCATTGTTGATCAAA
ACTTGTCAGCTCTCGCTTTGATCGTCGTACGTAAGGGTGAGAGTGAAGTTGAAGGTTTAA
CTGATGTCACCGTTCCTCGTCGTCTCGGACCTAAACGTGCAAGCCACATTCGTAAACTGT
TTGCTTTGACAAAAGAGGATGATGTTCGCAAGTATGTCATTAAGAAGCCTTTGCCACCAA
AAGAGGGCAAAAAGCAACGTTTTCAAGCTCCTAGAATTCAACGTTTAGTAACACCGGTCG
TTTTACAGACATCGTTTGGCTCTTAAAAAACGCCGAGTTGAATCACGCAAAGAAGCTGAA
GCTGAATATGCAAAATTATTAGCTCAGCGTAGACGTGAAGAAAAACTTCGTCGTCGTACA
CGTTCAGCATCTATTCGTGAATCAAAGAGCTCAATTTCATCAGATAAAGATAGCAAGAAA
GAAGTTAAGAAGCCAGAAGTTGTCAAGAAAGTTGAAGCTAAACCAGCAAAGAAGGTTGAA
GAGAAGAAAAAGGTTGATGACAAAAAGAAACCAGCTGAAAAGAAAGTTGAAACTAAAAAG
GGTGATGCAAAAGCCGCCGCTGTAAAGAAGATTGAAGAAAAGAAAAAGCCAGCCCAAGCT
GAGAAGAAATCTGCAGACAAAAAACCAGCAGCTGCACCAGCAAAGAAAGAGGCCCCAAAG
CCTGCAACAGCACCATCAGCCAAGAAGGAAGCATCTAAACCAACAGATGCAAAGAAGCCC
AAAAAAAAGTAA

>g11474.t74 Gene=g11474 Length=161
MGAEIEADQLGDEWKGYILKIAGGNDKQGFPMKQGVLTNTRVRLLLKKGHSCYRPRRTGE
RKRKSVRGCIVDQNLSALALIVVRKGESEVEGLTDVTVPRRLGPKRASHIRKLFALTKED
DVRKYVIKKPLPPKEGKKQRFQAPRIQRLVTPVVLQTSFGS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g11474.t74 PANTHER PTHR11502:SF6 40S RIBOSOMAL PROTEIN S6 1 157 1.5E-86
3 g11474.t74 PANTHER PTHR11502 40S RIBOSOMAL PROTEIN S6 1 157 1.5E-86
1 g11474.t74 Pfam PF01092 Ribosomal protein S6e 1 95 4.6E-45
5 g11474.t74 ProSitePatterns PS00578 Ribosomal protein S6e signature. 21 32 -
4 g11474.t74 SMART SM01405 Ribosomal_S6e_2 1 95 2.9E-50

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

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