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.t72 TTS g11474.t72 16437300 16437300
chr_1 g11474 g11474.t72 isoform g11474.t72 16437372 16438953
chr_1 g11474 g11474.t72 exon g11474.t72.exon1 16437372 16437863
chr_1 g11474 g11474.t72 cds g11474.t72.CDS1 16437372 16437863
chr_1 g11474 g11474.t72 exon g11474.t72.exon2 16437937 16438259
chr_1 g11474 g11474.t72 cds g11474.t72.CDS2 16437937 16438259
chr_1 g11474 g11474.t72 exon g11474.t72.exon3 16438549 16438720
chr_1 g11474 g11474.t72 cds g11474.t72.CDS3 16438549 16438720
chr_1 g11474 g11474.t72 exon g11474.t72.exon4 16438948 16438953
chr_1 g11474 g11474.t72 cds g11474.t72.CDS4 16438948 16438953
chr_1 g11474 g11474.t72 TSS g11474.t72 16438988 16438988

Sequences

>g11474.t72 Gene=g11474 Length=993
ATGAAGTTAAACGTCTCCTATCCCTCAACGGGAGCTCAGAAAACTTTTGAGGTCAACGAT
GACCACAAATTGCGATTGTTTTACGAGAAACGCATGGGCGCTGAAATTGAAGCTGATCAA
TTAGGCGATGAATGGAAAGGATATATTCTTAAAATCGCTGGTGGTAATGATAAACAAGGA
CATTCCTGTTATCGTCCAAGAAGAACTGGAGAACGTAAACGTAAATCAGTTCGTGGTTGC
ATTGTTGATCAAAACTTGTCAGCTCTCGCTTTGATCGTCGTACGTAAGGGTGAGAGTGAA
GTTGAAGGTTTAACTGATGTCACCGTTCCTCGTCGTCTCGGACCTAAACGTGCAAGCCAC
ATTCGTAAACTGTTTGCTTTGACAAAAGAGGATGATGTTCGCAAGTATGTCATTAAGAAG
CCTTTGCCACCAAAAGAGGGCAAAAAGCAACGTTTTCAAGCTCCTAGAATTCAACGTTTA
GTAACACCGGTCGTTTTACAGCGTAAAAGACATCGTTTGGCTCTTAAAAAACGCCGAGTT
GAATCACGCAAAGAAGCTGAAGCTGAATATGCAAAATTATTAGCTCAGCGTAGACGTGAA
GAAAAACTTCGTCGTCGTACACGTTCAGCATCTATTCGTGAATCAAAGAGCTCAATTTCA
TCAGATAAAGATAGCAAGAAAGAAGTTAAGAAGCCAGAAGTTGTCAAGAAAGTTGAAGCT
AAACCAGCAAAGAAGGTTGAAGAGAAGAAAAAGGTTGATGACAAAAAGAAACCAGCTGAA
AAGAAAGTTGAAACTAAAAAGGGTGATGCAAAAGCCGCCGCTGTAAAGAAGATTGAAGAA
AAGAAAAAGCCAGCCCAAGCTGAGAAGAAATCTGCAGACAAAAAACCAGCAGCTGCACCA
GCAAAGAAAGAGGCCCCAAAGCCTGCAACAGCACCATCAGCCAAGAAGGAAGCATCTAAA
CCAACAGATGCAAAGAAGCCCAAAAAAAAGTAA

>g11474.t72 Gene=g11474 Length=330
MKLNVSYPSTGAQKTFEVNDDHKLRLFYEKRMGAEIEADQLGDEWKGYILKIAGGNDKQG
HSCYRPRRTGERKRKSVRGCIVDQNLSALALIVVRKGESEVEGLTDVTVPRRLGPKRASH
IRKLFALTKEDDVRKYVIKKPLPPKEGKKQRFQAPRIQRLVTPVVLQRKRHRLALKKRRV
ESRKEAEAEYAKLLAQRRREEKLRRRTRSASIRESKSSISSDKDSKKEVKKPEVVKKVEA
KPAKKVEEKKKVDDKKKPAEKKVETKKGDAKAAAVKKIEEKKKPAQAEKKSADKKPAAAP
AKKEAPKPATAPSAKKEASKPTDAKKPKKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g11474.t72 Coils Coil Coil 183 203 -
5 g11474.t72 MobiDBLite mobidb-lite consensus disorder prediction 198 330 -
6 g11474.t72 MobiDBLite mobidb-lite consensus disorder prediction 198 301 -
3 g11474.t72 PANTHER PTHR11502 40S RIBOSOMAL PROTEIN S6 1 225 1.6E-90
1 g11474.t72 Pfam PF01092 Ribosomal protein S6e 1 61 2.1E-23
2 g11474.t72 Pfam PF01092 Ribosomal protein S6e 60 106 2.3E-17
4 g11474.t72 SMART SM01405 Ribosomal_S6e_2 1 106 2.5E-59

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.

Raw TPM values