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.t258 TSS g10408.t258 9592185 9592185
chr_1 g10408 g10408.t258 isoform g10408.t258 9592186 9594359
chr_1 g10408 g10408.t258 exon g10408.t258.exon1 9592186 9592504
chr_1 g10408 g10408.t258 cds g10408.t258.CDS1 9592275 9592504
chr_1 g10408 g10408.t258 exon g10408.t258.exon2 9592605 9592914
chr_1 g10408 g10408.t258 cds g10408.t258.CDS2 9592605 9592914
chr_1 g10408 g10408.t258 exon g10408.t258.exon3 9592975 9593241
chr_1 g10408 g10408.t258 cds g10408.t258.CDS3 9592975 9593133
chr_1 g10408 g10408.t258 exon g10408.t258.exon4 9594006 9594063
chr_1 g10408 g10408.t258 exon g10408.t258.exon5 9594269 9594359
chr_1 g10408 g10408.t258 TTS g10408.t258 9594355 9594355

Sequences

>g10408.t258 Gene=g10408 Length=1045
GTTTAGCCAAAGGTGGCAAGAAAGGAACCAAGAAGAAGATTGTGGATCCCTTCACACGTA
AGGACTGGTATGATATCAAAGCTCCATCAATGTTCACCACACGCCAAGTGGGAAAGACAT
TGGTCAATCGTACACAAGGTACAAAAATTGCTAGCGAAGGCTTGAAAGGTCGCGTGTTTG
AAGTCTCATTAGCTGATTTACAAAACGACAATGATGCCGAGAGATCTTTCCGCAAATTCA
AGCTTATCGCTGAAGACGTTCAAGGACGAAATGTCCTCACAAATTTCCATGGAATGGACT
TAACAACTGATAAATTGAGATCGATGGTGAAGAAATGGCAAACATTGATTGAATGTCATG
TTGATGTCAAAACAACCGATGGTTACGTTTTGCGTGTATTCTGCATTGGATTTACTGCAA
AAGATAGTTCATCGCATCGCAAAACTTGTTACGCTCAAACCTCTCAAATCAAAACAATTC
GCAAAAAGATGACTGACATCATCACACGCGACATTTCAAGCTCTGACTTGAAGGAAGTTG
TCAACAAATTGTTGCCAGACTCAATTGCAAAGGATATTGAGAAGGCCTGTCATGGAGTCT
ATCCTCTTCATGATGTGTACATTCGCAAGGTCAAGGTATTGAAGAAGCCTCGTTTCGACC
TCTCAAAATTACTTGAATTGCACGGCGATGGAGGAAAGTCAACAGAACCCACAGCAGCCG
CAGCTGCAGAAGGAGTTGCCGTTGAAAGACCAGAAGGATATGAACCACCAGTCCAAGCCG
CAGTTTAAGCAGTTATTATTCCATTAAAATGAAAGTTATGAATCCATCTAGAAATATAAA
TGGAAAATTAAAAAAAGAAATGCTTTCATAAGCCTTTGAACATCAAAAATTAAACGTCTT
TATTTGCAGGTTTCTGAAGGTATTTTGAATGTTTCTCATCGTTATGTTTTACAGATGGTT
ACATTATATGTCAATGGAAGATGATAAAAAATGCAATAGCTTAAACGCTAAACAGAAAAA
TATATTTTGAATTTAAAACATCAAA

>g10408.t258 Gene=g10408 Length=232
MFTTRQVGKTLVNRTQGTKIASEGLKGRVFEVSLADLQNDNDAERSFRKFKLIAEDVQGR
NVLTNFHGMDLTTDKLRSMVKKWQTLIECHVDVKTTDGYVLRVFCIGFTAKDSSSHRKTC
YAQTSQIKTIRKKMTDIITRDISSSDLKEVVNKLLPDSIAKDIEKACHGVYPLHDVYIRK
VKVLKKPRFDLSKLLELHGDGGKSTEPTAAAAAEGVAVERPEGYEPPVQAAV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g10408.t258 Hamap MF_03122 40S ribosomal protein S1 [RPS3A]. 1 232 31.237637
7 g10408.t258 MobiDBLite mobidb-lite consensus disorder prediction 204 232 -
2 g10408.t258 PANTHER PTHR11830 40S RIBOSOMAL PROTEIN S3A 1 231 3.4E-98
3 g10408.t258 PANTHER PTHR11830:SF28 40S RIBOSOMAL PROTEIN S3A 1 231 3.4E-98
1 g10408.t258 Pfam PF01015 Ribosomal S3Ae family 1 187 2.2E-74
6 g10408.t258 ProSitePatterns PS01191 Ribosomal protein S3Ae signature. 25 37 -
5 g10408.t258 SMART SM01397 Ribosomal_S3Ae_2 1 187 1.9E-114

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