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.t67 isoform g10408.t67 9592031 9593133
chr_1 g10408 g10408.t67 exon g10408.t67.exon1 9592031 9592072
chr_1 g10408 g10408.t67 cds g10408.t67.CDS1 9592031 9592072
chr_1 g10408 g10408.t67 exon g10408.t67.exon2 9592218 9592504
chr_1 g10408 g10408.t67 cds g10408.t67.CDS2 9592218 9592504
chr_1 g10408 g10408.t67 exon g10408.t67.exon3 9592605 9592914
chr_1 g10408 g10408.t67 cds g10408.t67.CDS3 9592605 9592914
chr_1 g10408 g10408.t67 exon g10408.t67.exon4 9592975 9593133
chr_1 g10408 g10408.t67 cds g10408.t67.CDS4 9592975 9593133
chr_1 g10408 g10408.t67 TTS g10408.t67 9593229 9593229
chr_1 g10408 g10408.t67 TSS g10408.t67 NA NA

Sequences

>g10408.t67 Gene=g10408 Length=798
ATGGCAGTCGGAAAAAATAAAGGTAGTTTAAAATTTGATAGGAAGAAGATTGTGGATCCC
TTCACACGTAAGGACTGGTATGATATCAAAGCTCCATCAATGTTCACCACACGCCAAGTG
GGAAAGACATTGGTCAATCGTACACAAGGTACAAAAATTGCTAGCGAAGGCTTGAAAGGT
CGCGTGTTTGAAGTCTCATTAGCTGATTTACAAAACGACAATGATGCCGAGAGATCTTTC
CGCAAATTCAAGCTTATCGCTGAAGACGTTCAAGGACGAAATGTCCTCACAAATTTCCAT
GGAATGGACTTAACAACTGATAAATTGAGATCGATGGTGAAGAAATGGCAAACATTGATT
GAATGTCATGTTGATGTCAAAACAACCGATGGTTACGTTTTGCGTGTATTCTGCATTGGA
TTTACTGCAAAAGATAGTTCATCGCATCGCAAAACTTGTTACGCTCAAACCTCTCAAATC
AAAACAATTCGCAAAAAGATGACTGACATCATCACACGCGACATTTCAAGCTCTGACTTG
AAGGAAGTTGTCAACAAATTGTTGCCAGACTCAATTGCAAAGGATATTGAGAAGGCCTGT
CATGGAGTCTATCCTCTTCATGATGTGTACATTCGCAAGGTCAAGGTATTGAAGAAGCCT
CGTTTCGACCTCTCAAAATTACTTGAATTGCACGGCGATGGAGGAAAGTCAACAGAACCC
ACAGCAGCCGCAGCTGCAGAAGGAGTTGCCGTTGAAAGACCAGAAGGATATGAACCACCA
GTCCAAGCCGCAGTTTAA

>g10408.t67 Gene=g10408 Length=265
MAVGKNKGSLKFDRKKIVDPFTRKDWYDIKAPSMFTTRQVGKTLVNRTQGTKIASEGLKG
RVFEVSLADLQNDNDAERSFRKFKLIAEDVQGRNVLTNFHGMDLTTDKLRSMVKKWQTLI
ECHVDVKTTDGYVLRVFCIGFTAKDSSSHRKTCYAQTSQIKTIRKKMTDIITRDISSSDL
KEVVNKLLPDSIAKDIEKACHGVYPLHDVYIRKVKVLKKPRFDLSKLLELHGDGGKSTEP
TAAAAAEGVAVERPEGYEPPVQAAV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g10408.t67 Hamap MF_03122 40S ribosomal protein S1 [RPS3A]. 1 265 39.792477
7 g10408.t67 MobiDBLite mobidb-lite consensus disorder prediction 237 265 -
2 g10408.t67 PANTHER PTHR11830 40S RIBOSOMAL PROTEIN S3A 1 264 3.1E-113
3 g10408.t67 PANTHER PTHR11830:SF22 40S RIBOSOMAL PROTEIN S3A 1 264 3.1E-113
1 g10408.t67 Pfam PF01015 Ribosomal S3Ae family 14 220 4.1E-86
6 g10408.t67 ProSitePatterns PS01191 Ribosomal protein S3Ae signature. 58 70 -
5 g10408.t67 SMART SM01397 Ribosomal_S3Ae_2 12 220 1.8E-136

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