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.t47 TTS g11474.t47 16437300 16437300
chr_1 g11474 g11474.t47 isoform g11474.t47 16437372 16438953
chr_1 g11474 g11474.t47 exon g11474.t47.exon1 16437372 16437589
chr_1 g11474 g11474.t47 cds g11474.t47.CDS1 16437539 16437589
chr_1 g11474 g11474.t47 exon g11474.t47.exon2 16437663 16437863
chr_1 g11474 g11474.t47 cds g11474.t47.CDS2 16437663 16437863
chr_1 g11474 g11474.t47 exon g11474.t47.exon3 16437937 16438286
chr_1 g11474 g11474.t47 cds g11474.t47.CDS3 16437937 16438286
chr_1 g11474 g11474.t47 exon g11474.t47.exon4 16438516 16438720
chr_1 g11474 g11474.t47 cds g11474.t47.CDS4 16438516 16438720
chr_1 g11474 g11474.t47 exon g11474.t47.exon5 16438948 16438953
chr_1 g11474 g11474.t47 cds g11474.t47.CDS5 16438948 16438953
chr_1 g11474 g11474.t47 TSS g11474.t47 16438988 16438988

Sequences

>g11474.t47 Gene=g11474 Length=980
ATGAAGTTAAACGTCTCCTATCCCTCAACGGGAGCTCAGAAAACTTTTGAGGTCAACGAT
GACCACAAATTGCGATTGTTTTACGAGAAACGCATGGGCGCTGAAATTGAAGCTGATCAA
TTAGGCGATGAATGGAAAGGATATATTCTTAAAATCGCTGGTGGTAATGATAAACAAGGT
TTCCCAATGAAACAGGGTGTTTTAACAAACACTCGTGTTCGTCTCTTGCTTAAAAAAGGA
CATTCCTGTTATCGTCCAAGAAGAACTGGAGAACGTAAACGTAAATCAGTTCGTGGTTGC
ATTGTTGATCAAAACTTGTCAGCTCTCGCTTTGATCGTCGTACGTAAGGGTGAGAGTGAA
GTTGAAGGTTTAACTGATGTCACCGTTCCTCGTCGTCTCGGACCTAAACGTGCAAGCCAC
ATTCGTAAACTGTTTGCTTTGACAAAAGAGGATGATGTTCGCAAGTATGTCATTAAGAAG
CCTTTGCCACCAAAAGAGGGCAAAAAGCAACGTTTTCAAGCTCCTAGAATTCAACGTTTA
GTAACACCGGTCGTTTTACAGCGTAAAAGACATCGTTTGGCTCTTAAAAAACGCCGAGTT
GAATCACGCAAAGAAGCTGAAGCTGAATATGCAAAATTATTAGCTCAGCGTAGACGTGAA
GAAAAACTTCGTCGTCGTACACGTTCAGCATCTATTCGTGAATCAAAGAGCTCAATTTCA
TCAGATAAAGATAGCAAGAAAGAAGTTAAGAAGCCAGAAGTTCTGAAAAGAAAGTTGAAA
CTAAAAAGGGTGATGCAAAAGCCGCCGCTGTAAAGAAGATTGAAGAAAAGAAAAAGCCAG
CCCAAGCTGAGAAGAAATCTGCAGACAAAAAACCAGCAGCTGCACCAGCAAAGAAAGAGG
CCCCAAAGCCTGCAACAGCACCATCAGCCAAGAAGGAAGCATCTAAACCAACAGATGCAA
AGAAGCCCAAAAAAAAGTAA

>g11474.t47 Gene=g11474 Length=270
MKLNVSYPSTGAQKTFEVNDDHKLRLFYEKRMGAEIEADQLGDEWKGYILKIAGGNDKQG
FPMKQGVLTNTRVRLLLKKGHSCYRPRRTGERKRKSVRGCIVDQNLSALALIVVRKGESE
VEGLTDVTVPRRLGPKRASHIRKLFALTKEDDVRKYVIKKPLPPKEGKKQRFQAPRIQRL
VTPVVLQRKRHRLALKKRRVESRKEAEAEYAKLLAQRRREEKLRRRTRSASIRESKSSIS
SDKDSKKEVKKPEVLKRKLKLKRVMQKPPL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g11474.t47 Coils Coil Coil 203 223 -
6 g11474.t47 MobiDBLite mobidb-lite consensus disorder prediction 218 255 -
7 g11474.t47 MobiDBLite mobidb-lite consensus disorder prediction 218 270 -
2 g11474.t47 PANTHER PTHR11502:SF6 40S RIBOSOMAL PROTEIN S6 1 245 5.6E-116
3 g11474.t47 PANTHER PTHR11502 40S RIBOSOMAL PROTEIN S6 1 245 5.6E-116
9 g11474.t47 PIRSF PIRSF002129 RPS6e 1 251 9.2E-123
1 g11474.t47 Pfam PF01092 Ribosomal protein S6e 1 126 3.2E-59
5 g11474.t47 ProSitePatterns PS00578 Ribosomal protein S6e signature. 52 63 -
4 g11474.t47 SMART SM01405 Ribosomal_S6e_2 1 126 4.9E-83

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