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.t34 TTS g11474.t34 16437300 16437300
chr_1 g11474 g11474.t34 isoform g11474.t34 16437372 16438953
chr_1 g11474 g11474.t34 exon g11474.t34.exon1 16437372 16437863
chr_1 g11474 g11474.t34 cds g11474.t34.CDS1 16437372 16437863
chr_1 g11474 g11474.t34 exon g11474.t34.exon2 16437937 16438286
chr_1 g11474 g11474.t34 cds g11474.t34.CDS2 16437937 16438286
chr_1 g11474 g11474.t34 exon g11474.t34.exon3 16438516 16438711
chr_1 g11474 g11474.t34 cds g11474.t34.CDS3 16438516 16438711
chr_1 g11474 g11474.t34 exon g11474.t34.exon4 16438948 16438953
chr_1 g11474 g11474.t34 cds g11474.t34.CDS4 16438948 16438953
chr_1 g11474 g11474.t34 TSS g11474.t34 16438988 16438988

Sequences

>g11474.t34 Gene=g11474 Length=1044
ATGAAGTCCTATCCCTCAACGGGAGCTCAGAAAACTTTTGAGGTCAACGATGACCACAAA
TTGCGATTGTTTTACGAGAAACGCATGGGCGCTGAAATTGAAGCTGATCAATTAGGCGAT
GAATGGAAAGGATATATTCTTAAAATCGCTGGTGGTAATGATAAACAAGGTTTCCCAATG
AAACAGGGTGTTTTAACAAACACTCGTGTTCGTCTCTTGCTTAAAAAAGGACATTCCTGT
TATCGTCCAAGAAGAACTGGAGAACGTAAACGTAAATCAGTTCGTGGTTGCATTGTTGAT
CAAAACTTGTCAGCTCTCGCTTTGATCGTCGTACGTAAGGGTGAGAGTGAAGTTGAAGGT
TTAACTGATGTCACCGTTCCTCGTCGTCTCGGACCTAAACGTGCAAGCCACATTCGTAAA
CTGTTTGCTTTGACAAAAGAGGATGATGTTCGCAAGTATGTCATTAAGAAGCCTTTGCCA
CCAAAAGAGGGCAAAAAGCAACGTTTTCAAGCTCCTAGAATTCAACGTTTAGTAACACCG
GTCGTTTTACAGCGTAAAAGACATCGTTTGGCTCTTAAAAAACGCCGAGTTGAATCACGC
AAAGAAGCTGAAGCTGAATATGCAAAATTATTAGCTCAGCGTAGACGTGAAGAAAAACTT
CGTCGTCGTACACGTTCAGCATCTATTCGTGAATCAAAGAGCTCAATTTCATCAGATAAA
GATAGCAAGAAAGAAGTTAAGAAGCCAGAAGTTGTCAAGAAAGTTGAAGCTAAACCAGCA
AAGAAGGTTGAAGAGAAGAAAAAGGTTGATGACAAAAAGAAACCAGCTGAAAAGAAAGTT
GAAACTAAAAAGGGTGATGCAAAAGCCGCCGCTGTAAAGAAGATTGAAGAAAAGAAAAAG
CCAGCCCAAGCTGAGAAGAAATCTGCAGACAAAAAACCAGCAGCTGCACCAGCAAAGAAA
GAGGCCCCAAAGCCTGCAACAGCACCATCAGCCAAGAAGGAAGCATCTAAACCAACAGAT
GCAAAGAAGCCCAAAAAAAAGTAA

>g11474.t34 Gene=g11474 Length=347
MKSYPSTGAQKTFEVNDDHKLRLFYEKRMGAEIEADQLGDEWKGYILKIAGGNDKQGFPM
KQGVLTNTRVRLLLKKGHSCYRPRRTGERKRKSVRGCIVDQNLSALALIVVRKGESEVEG
LTDVTVPRRLGPKRASHIRKLFALTKEDDVRKYVIKKPLPPKEGKKQRFQAPRIQRLVTP
VVLQRKRHRLALKKRRVESRKEAEAEYAKLLAQRRREEKLRRRTRSASIRESKSSISSDK
DSKKEVKKPEVVKKVEAKPAKKVEEKKKVDDKKKPAEKKVETKKGDAKAAAVKKIEEKKK
PAQAEKKSADKKPAAAPAKKEAPKPATAPSAKKEASKPTDAKKPKKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g11474.t34 Coils Coil Coil 200 220 -
6 g11474.t34 MobiDBLite mobidb-lite consensus disorder prediction 215 347 -
7 g11474.t34 MobiDBLite mobidb-lite consensus disorder prediction 215 318 -
2 g11474.t34 PANTHER PTHR11502:SF6 40S RIBOSOMAL PROTEIN S6 3 242 2.9E-112
3 g11474.t34 PANTHER PTHR11502 40S RIBOSOMAL PROTEIN S6 3 242 2.9E-112
1 g11474.t34 Pfam PF01092 Ribosomal protein S6e 3 123 1.8E-55
5 g11474.t34 ProSitePatterns PS00578 Ribosomal protein S6e signature. 49 60 -
4 g11474.t34 SMART SM01405 Ribosomal_S6e_2 1 123 4.6E-78

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