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.t49 TTS g11474.t49 16437300 16437300
chr_1 g11474 g11474.t49 isoform g11474.t49 16437372 16438953
chr_1 g11474 g11474.t49 exon g11474.t49.exon1 16437372 16437863
chr_1 g11474 g11474.t49 cds g11474.t49.CDS1 16437372 16437863
chr_1 g11474 g11474.t49 exon g11474.t49.exon2 16437937 16438286
chr_1 g11474 g11474.t49 cds g11474.t49.CDS2 16437937 16438286
chr_1 g11474 g11474.t49 exon g11474.t49.exon3 16438531 16438720
chr_1 g11474 g11474.t49 cds g11474.t49.CDS3 16438531 16438720
chr_1 g11474 g11474.t49 exon g11474.t49.exon4 16438948 16438953
chr_1 g11474 g11474.t49 cds g11474.t49.CDS4 16438948 16438953
chr_1 g11474 g11474.t49 TSS g11474.t49 16438988 16438988

Sequences

>g11474.t49 Gene=g11474 Length=1038
ATGAAGTTAAACGTCTCCTATCCCTCAACGGGAGCTCAGAAAACTTTTGAGGTCAACGAT
GACCACAAATTGCGATTGTTTTACGAGAAACGCATGGGCGCTGAAATTGAAGCTGATCAA
TTAGGCGATGAATGGAAAGGATATATTCTTAAAATCGCTGGTGGTAATGATAAACAAGGT
TTCCCAATGAAACAGGCTCGTGTTCGTCTCTTGCTTAAAAAAGGACATTCCTGTTATCGT
CCAAGAAGAACTGGAGAACGTAAACGTAAATCAGTTCGTGGTTGCATTGTTGATCAAAAC
TTGTCAGCTCTCGCTTTGATCGTCGTACGTAAGGGTGAGAGTGAAGTTGAAGGTTTAACT
GATGTCACCGTTCCTCGTCGTCTCGGACCTAAACGTGCAAGCCACATTCGTAAACTGTTT
GCTTTGACAAAAGAGGATGATGTTCGCAAGTATGTCATTAAGAAGCCTTTGCCACCAAAA
GAGGGCAAAAAGCAACGTTTTCAAGCTCCTAGAATTCAACGTTTAGTAACACCGGTCGTT
TTACAGCGTAAAAGACATCGTTTGGCTCTTAAAAAACGCCGAGTTGAATCACGCAAAGAA
GCTGAAGCTGAATATGCAAAATTATTAGCTCAGCGTAGACGTGAAGAAAAACTTCGTCGT
CGTACACGTTCAGCATCTATTCGTGAATCAAAGAGCTCAATTTCATCAGATAAAGATAGC
AAGAAAGAAGTTAAGAAGCCAGAAGTTGTCAAGAAAGTTGAAGCTAAACCAGCAAAGAAG
GTTGAAGAGAAGAAAAAGGTTGATGACAAAAAGAAACCAGCTGAAAAGAAAGTTGAAACT
AAAAAGGGTGATGCAAAAGCCGCCGCTGTAAAGAAGATTGAAGAAAAGAAAAAGCCAGCC
CAAGCTGAGAAGAAATCTGCAGACAAAAAACCAGCAGCTGCACCAGCAAAGAAAGAGGCC
CCAAAGCCTGCAACAGCACCATCAGCCAAGAAGGAAGCATCTAAACCAACAGATGCAAAG
AAGCCCAAAAAAAAGTAA

>g11474.t49 Gene=g11474 Length=345
MKLNVSYPSTGAQKTFEVNDDHKLRLFYEKRMGAEIEADQLGDEWKGYILKIAGGNDKQG
FPMKQARVRLLLKKGHSCYRPRRTGERKRKSVRGCIVDQNLSALALIVVRKGESEVEGLT
DVTVPRRLGPKRASHIRKLFALTKEDDVRKYVIKKPLPPKEGKKQRFQAPRIQRLVTPVV
LQRKRHRLALKKRRVESRKEAEAEYAKLLAQRRREEKLRRRTRSASIRESKSSISSDKDS
KKEVKKPEVVKKVEAKPAKKVEEKKKVDDKKKPAEKKVETKKGDAKAAAVKKIEEKKKPA
QAEKKSADKKPAAAPAKKEAPKPATAPSAKKEASKPTDAKKPKKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g11474.t49 Coils Coil Coil 198 218 -
6 g11474.t49 MobiDBLite mobidb-lite consensus disorder prediction 213 316 -
7 g11474.t49 MobiDBLite mobidb-lite consensus disorder prediction 213 345 -
2 g11474.t49 PANTHER PTHR11502:SF6 40S RIBOSOMAL PROTEIN S6 1 240 4.1E-108
3 g11474.t49 PANTHER PTHR11502 40S RIBOSOMAL PROTEIN S6 1 240 4.1E-108
1 g11474.t49 Pfam PF01092 Ribosomal protein S6e 1 121 2.1E-53
5 g11474.t49 ProSitePatterns PS00578 Ribosomal protein S6e signature. 52 63 -
4 g11474.t49 SMART SM01405 Ribosomal_S6e_2 1 121 4.2E-76

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