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.t92 isoform g10408.t92 9592031 9593239
chr_1 g10408 g10408.t92 exon g10408.t92.exon1 9592031 9592052
chr_1 g10408 g10408.t92 cds g10408.t92.CDS1 9592031 9592052
chr_1 g10408 g10408.t92 exon g10408.t92.exon2 9592192 9592504
chr_1 g10408 g10408.t92 cds g10408.t92.CDS2 9592192 9592504
chr_1 g10408 g10408.t92 exon g10408.t92.exon3 9592605 9592899
chr_1 g10408 g10408.t92 cds g10408.t92.CDS3 9592605 9592899
chr_1 g10408 g10408.t92 exon g10408.t92.exon4 9592975 9593239
chr_1 g10408 g10408.t92 cds g10408.t92.CDS4 9592975 9593133
chr_1 g10408 g10408.t92 TTS g10408.t92 9593229 9593229
chr_1 g10408 g10408.t92 TSS g10408.t92 NA NA

Sequences

>g10408.t92 Gene=g10408 Length=895
ATGGCAGTCGGAAAAAATAAAGCCAAAGGTGGCAAGAAAGGAACCAAGAAGAAGATTGTG
GATCCCTTCACACGTAAGGACTGGTATGATATCAAAGCTCCATCAATGTTCACCACACGC
CAAGTGGGAAAGACATTGGTCAATCGTACACAAGGTACAAAAATTGCTAGCGAAGGCTTG
AAAGGTCGCGTGTTTGAAGTCTCATTAGCTGATTTACAAAACGACAATGATGCCGAGAGA
TCTTTCCGCAAATTCAAGCTTATCGCTGAAGACGTTCAAGGACGAAATGTCCTCACAAAT
TTCCATGGAATGGACTTAACAACTGATAAATTGAGATCGATGGTGAAGAAATGGCAAACA
TTGATTGAATGTCATGTTGATGTCAAAACAACCGATGGTTACGTTTTGCGTGTATTCTGC
ATTGGATTTACTGCAAAAGATAGTTCATCGCATCGCAAAACTTGTTACGCTCAAACCTCT
CAAATCAAAACAATTCGCAAAAAGATGACTGACATCATCACACGCGACATTTCAAGCTCT
GACTTGAAGGAAGTTGTCAACAAATTGTTGCCAGACTCAATTGCAAAGGATATTGAGAAG
GCCTGTCATGGAGTCTATCCTCTTCATGATGTCAAGGTATTGAAGAAGCCTCGTTTCGAC
CTCTCAAAATTACTTGAATTGCACGGCGATGGAGGAAAGTCAACAGAACCCACAGCAGCC
GCAGCTGCAGAAGGAGTTGCCGTTGAAAGACCAGAAGGATATGAACCACCAGTCCAAGCC
GCAGTTTAAGCAGTTATTATTCCATTAAAATGAAAGTTATGAATCCATCTAGAAATATAA
ATGGAAAATTAAAAAAAGAAATGCTTTCATAAGCCTTTGAACATCAAAAATTAAA

>g10408.t92 Gene=g10408 Length=262
MAVGKNKAKGGKKGTKKKIVDPFTRKDWYDIKAPSMFTTRQVGKTLVNRTQGTKIASEGL
KGRVFEVSLADLQNDNDAERSFRKFKLIAEDVQGRNVLTNFHGMDLTTDKLRSMVKKWQT
LIECHVDVKTTDGYVLRVFCIGFTAKDSSSHRKTCYAQTSQIKTIRKKMTDIITRDISSS
DLKEVVNKLLPDSIAKDIEKACHGVYPLHDVKVLKKPRFDLSKLLELHGDGGKSTEPTAA
AAAEGVAVERPEGYEPPVQAAV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g10408.t92 Hamap MF_03122 40S ribosomal protein S1 [RPS3A]. 1 262 38.694912
7 g10408.t92 MobiDBLite mobidb-lite consensus disorder prediction 232 262 -
2 g10408.t92 PANTHER PTHR11830 40S RIBOSOMAL PROTEIN S3A 1 261 3.9E-112
3 g10408.t92 PANTHER PTHR11830:SF22 40S RIBOSOMAL PROTEIN S3A 1 261 3.9E-112
1 g10408.t92 Pfam PF01015 Ribosomal S3Ae family 15 215 3.0E-81
6 g10408.t92 ProSitePatterns PS01191 Ribosomal protein S3Ae signature. 60 72 -
5 g10408.t92 SMART SM01397 Ribosomal_S3Ae_2 14 217 3.3E-131

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