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.t155 isoform g10408.t155 9592031 9594359
chr_1 g10408 g10408.t155 exon g10408.t155.exon1 9592031 9592052
chr_1 g10408 g10408.t155 cds g10408.t155.CDS1 9592031 9592052
chr_1 g10408 g10408.t155 exon g10408.t155.exon2 9592186 9592504
chr_1 g10408 g10408.t155 cds g10408.t155.CDS2 9592186 9592504
chr_1 g10408 g10408.t155 exon g10408.t155.exon3 9592605 9592901
chr_1 g10408 g10408.t155 cds g10408.t155.CDS3 9592605 9592901
chr_1 g10408 g10408.t155 exon g10408.t155.exon4 9592975 9593330
chr_1 g10408 g10408.t155 cds g10408.t155.CDS4 9592975 9592987
chr_1 g10408 g10408.t155 exon g10408.t155.exon5 9594269 9594359
chr_1 g10408 g10408.t155 TTS g10408.t155 9594355 9594355
chr_1 g10408 g10408.t155 TSS g10408.t155 NA NA

Sequences

>g10408.t155 Gene=g10408 Length=1085
ATGGCAGTCGGAAAAAATAAAGGTTTAGCCAAAGGTGGCAAGAAAGGAACCAAGAAGAAG
ATTGTGGATCCCTTCACACGTAAGGACTGGTATGATATCAAAGCTCCATCAATGTTCACC
ACACGCCAAGTGGGAAAGACATTGGTCAATCGTACACAAGGTACAAAAATTGCTAGCGAA
GGCTTGAAAGGTCGCGTGTTTGAAGTCTCATTAGCTGATTTACAAAACGACAATGATGCC
GAGAGATCTTTCCGCAAATTCAAGCTTATCGCTGAAGACGTTCAAGGACGAAATGTCCTC
ACAAATTTCCATGGAATGGACTTAACAACTGATAAATTGAGATCGATGGTGAAGAAATGG
CAAACATTGATTGAATGTCATGTTGATGTCAAAACAACCGATGGTTACGTTTTGCGTGTA
TTCTGCATTGGATTTACTGCAAAAGATAGTTCATCGCATCGCAAAACTTGTTACGCTCAA
ACCTCTCAAATCAAAACAATTCGCAAAAAGATGACTGACATCATCACACGCGACATTTCA
AGCTCTGACTTGAAGGAAGTTGTCAACAAATTGTTGCCAGACTCAATTGCAAAGGATATT
GAGAAGGCCTGTCATGGAGTCTATCCTCTTCATGATGTGTCAAGGTATTGAAGAAGCCTC
GTTTCGACCTCTCAAAATTACTTGAATTGCACGGCGATGGAGGAAAGTCAACAGAACCCA
CAGCAGCCGCAGCTGCAGAAGGAGTTGCCGTTGAAAGACCAGAAGGATATGAACCACCAG
TCCAAGCCGCAGTTTAAGCAGTTATTATTCCATTAAAATGAAAGTTATGAATCCATCTAG
AAATATAAATGGAAAATTAAAAAAAGAAATGCTTTCATAAGCCTTTGAACATCAAAAATT
AAACGGTTTATCAATACAGAAATTTCTGTAACTTCTTTTATTATATTATATTAATCATTT
TCATAATTTTAGATATTTCTTAAATTGAACATCAATGGTTACATTATATGTCAATGGAAG
ATGATAAAAAATGCAATAGCTTAAACGCTAAACAGAAAAATATATTTTGAATTTAAAACA
TCAAA

>g10408.t155 Gene=g10408 Length=216
MAVGKNKGLAKGGKKGTKKKIVDPFTRKDWYDIKAPSMFTTRQVGKTLVNRTQGTKIASE
GLKGRVFEVSLADLQNDNDAERSFRKFKLIAEDVQGRNVLTNFHGMDLTTDKLRSMVKKW
QTLIECHVDVKTTDGYVLRVFCIGFTAKDSSSHRKTCYAQTSQIKTIRKKMTDIITRDIS
SSDLKEVVNKLLPDSIAKDIEKACHGVYPLHDVSRY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g10408.t155 Hamap MF_03122 40S ribosomal protein S1 [RPS3A]. 1 216 32.381359
2 g10408.t155 PANTHER PTHR11830 40S RIBOSOMAL PROTEIN S3A 1 213 1.7E-98
3 g10408.t155 PANTHER PTHR11830:SF28 40S RIBOSOMAL PROTEIN S3A 1 213 1.7E-98
1 g10408.t155 Pfam PF01015 Ribosomal S3Ae family 17 213 1.2E-80
6 g10408.t155 ProSitePatterns PS01191 Ribosomal protein S3Ae signature. 62 74 -
5 g10408.t155 SMART SM01397 Ribosomal_S3Ae_2 16 216 3.2E-125

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