Gene loci information

Transcript annotation

  • This transcript has been annotated as 40S ribosomal protein S3a.

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 g10408 g10408.t276 TSS g10408.t276 9592185 9592185
chr_1 g10408 g10408.t276 isoform g10408.t276 9592423 9594359
chr_1 g10408 g10408.t276 exon g10408.t276.exon1 9592423 9592504
chr_1 g10408 g10408.t276 cds g10408.t276.CDS1 9592479 9592504
chr_1 g10408 g10408.t276 exon g10408.t276.exon2 9592605 9592914
chr_1 g10408 g10408.t276 cds g10408.t276.CDS2 9592605 9592914
chr_1 g10408 g10408.t276 exon g10408.t276.exon3 9592975 9593241
chr_1 g10408 g10408.t276 cds g10408.t276.CDS3 9592975 9593133
chr_1 g10408 g10408.t276 exon g10408.t276.exon4 9593309 9593337
chr_1 g10408 g10408.t276 exon g10408.t276.exon5 9593745 9593817
chr_1 g10408 g10408.t276 exon g10408.t276.exon6 9594236 9594359
chr_1 g10408 g10408.t276 TTS g10408.t276 9594355 9594355

Sequences

>g10408.t276 Gene=g10408 Length=885
TCAAGCTTATCGCTGAAGACGTTCAAGGACGAAATGTCCTCACAAATTTCCATGGAATGG
ACTTAACAACTGATAAATTGAGATCGATGGTGAAGAAATGGCAAACATTGATTGAATGTC
ATGTTGATGTCAAAACAACCGATGGTTACGTTTTGCGTGTATTCTGCATTGGATTTACTG
CAAAAGATAGTTCATCGCATCGCAAAACTTGTTACGCTCAAACCTCTCAAATCAAAACAA
TTCGCAAAAAGATGACTGACATCATCACACGCGACATTTCAAGCTCTGACTTGAAGGAAG
TTGTCAACAAATTGTTGCCAGACTCAATTGCAAAGGATATTGAGAAGGCCTGTCATGGAG
TCTATCCTCTTCATGATGTGTACATTCGCAAGGTCAAGGTATTGAAGAAGCCTCGTTTCG
ACCTCTCAAAATTACTTGAATTGCACGGCGATGGAGGAAAGTCAACAGAACCCACAGCAG
CCGCAGCTGCAGAAGGAGTTGCCGTTGAAAGACCAGAAGGATATGAACCACCAGTCCAAG
CCGCAGTTTAAGCAGTTATTATTCCATTAAAATGAAAGTTATGAATCCATCTAGAAATAT
AAATGGAAAATTAAAAAAAGAAATGCTTTCATAAGCCTTTGAACATCAAAAATTAAACGA
TATTTCTTAAATTGAACATCAGTATTAGAAATTTTAATATTTTGTATAATCTTTGCAGGT
TTCACAAATCTAATTTCGTTATTTCAAGAGTCATTTTTCAGGATTCTAATGTTTATATTT
TAATTTATTTACAGATGGTTACATTATATGTCAATGGAAGATGATAAAAAATGCAATAGC
TTAAACGCTAAACAGAAAAATATATTTTGAATTTAAAACATCAAA

>g10408.t276 Gene=g10408 Length=164
MDLTTDKLRSMVKKWQTLIECHVDVKTTDGYVLRVFCIGFTAKDSSSHRKTCYAQTSQIK
TIRKKMTDIITRDISSSDLKEVVNKLLPDSIAKDIEKACHGVYPLHDVYIRKVKVLKKPR
FDLSKLLELHGDGGKSTEPTAAAAAEGVAVERPEGYEPPVQAAV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g10408.t276 MobiDBLite mobidb-lite consensus disorder prediction 136 164 -
2 g10408.t276 PANTHER PTHR11830 40S RIBOSOMAL PROTEIN S3A 1 163 5.0E-62
3 g10408.t276 PANTHER PTHR11830:SF28 40S RIBOSOMAL PROTEIN S3A 1 163 5.0E-62
1 g10408.t276 Pfam PF01015 Ribosomal S3Ae family 1 119 5.5E-47
4 g10408.t276 SMART SM01397 Ribosomal_S3Ae_2 1 119 2.2E-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

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. There were no conditions that were differentially expressed