Gene loci information

Transcript annotation

  • This transcript has been annotated as 40S ribosomal protein S8.

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_3 g4086 g4086.t7 isoform g4086.t7 30509271 30510484
chr_3 g4086 g4086.t7 exon g4086.t7.exon1 30509271 30509440
chr_3 g4086 g4086.t7 TTS g4086.t7 30509274 30509274
chr_3 g4086 g4086.t7 cds g4086.t7.CDS1 30509322 30509440
chr_3 g4086 g4086.t7 exon g4086.t7.exon2 30509682 30510093
chr_3 g4086 g4086.t7 cds g4086.t7.CDS2 30509682 30510093
chr_3 g4086 g4086.t7 exon g4086.t7.exon3 30510213 30510319
chr_3 g4086 g4086.t7 cds g4086.t7.CDS3 30510213 30510319
chr_3 g4086 g4086.t7 exon g4086.t7.exon4 30510481 30510484
chr_3 g4086 g4086.t7 cds g4086.t7.CDS4 30510481 30510484
chr_3 g4086 g4086.t7 TSS g4086.t7 30510508 30510508

Sequences

>g4086.t7 Gene=g4086 Length=693
ATGGGTATTTCTCGCGATTCATTTCATAAACGCCGTGCGACTGGAGGCAAGAAGGCCCAG
ATTCGCAAGAAGCGAAAGTACGAATTGGGACGTCCACCAAGCAACACAAAGATCGGCGCT
CATCGCGTACATTTTGTAAGAACCCGTGGTGGTAACAGAAAATTCCGTGCCCTTCGTTTA
GACGGTGGTAATTTTGCATGGGCTTCACAAGGAGCTGCACGCAAAACTAGAATTCTCGAT
GTCGTCTACAATGCATCAAACAACGAACTCGTTCGTACAAAGACATTGGTAAAGAATTGC
ATTGTTTCCATTGATGCTACACCATTCAAGCAGTTCTACGAAAGTCATTACTTGCTTCCA
CTTGGTCGCAAGAAGGATCACAAAGTGCAACTTGCAGAAGGTGAGGAAGATCCACTGACA
AAGAAACGTAGCAAAGATGCATTGAAGAAATACGAAGAACGTCAAAAGTATGCTAAAGTT
GAACCAGCTTTAGAAGAACAATTCTTGCAAGGACGTTTATTAGACCAGGACAATGTGGTC
GTGCTGATGGATATATTTTGGAAGGCAAGGAACTCGAGTTCTACGTTAAGAAAATCAAAT
CTAAGAAATCAAAGTAATTTTGATGAAAGTAAACAAATGTGAAATGTATGCATTCAAAAA
AACATCAATAAAAATCCATATTGAATAATGAAA

>g4086.t7 Gene=g4086 Length=213
MGISRDSFHKRRATGGKKAQIRKKRKYELGRPPSNTKIGAHRVHFVRTRGGNRKFRALRL
DGGNFAWASQGAARKTRILDVVYNASNNELVRTKTLVKNCIVSIDATPFKQFYESHYLLP
LGRKKDHKVQLAEGEEDPLTKKRSKDALKKYEERQKYAKVEPALEEQFLQGRLLDQDNVV
VLMDIFWKARNSSSTLRKSNLRNQSNFDESKQM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g4086.t7 CDD cd11382 Ribosomal_S8e 5 105 4.20352E-55
8 g4086.t7 Gene3D G3DSA:2.40.10.450 - 32 110 3.7E-28
7 g4086.t7 Gene3D G3DSA:1.10.168.20 - 111 171 1.6E-23
6 g4086.t7 MobiDBLite mobidb-lite consensus disorder prediction 1 34 -
5 g4086.t7 MobiDBLite mobidb-lite consensus disorder prediction 11 25 -
2 g4086.t7 PANTHER PTHR10394 40S RIBOSOMAL PROTEIN S8 1 174 2.0E-77
3 g4086.t7 PANTHER PTHR10394:SF3 40S RIBOSOMAL PROTEIN S8 1 174 2.0E-77
1 g4086.t7 Pfam PF01201 Ribosomal protein S8e 1 174 2.5E-44
4 g4086.t7 ProSitePatterns PS01193 Ribosomal protein S8e signature. 11 30 -
9 g4086.t7 TIGRFAM TIGR00307 eS8: ribosomal protein eS8 1 107 6.5E-42

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