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.t79 isoform g10408.t79 9592031 9593233
chr_1 g10408 g10408.t79 exon g10408.t79.exon1 9592031 9592052
chr_1 g10408 g10408.t79 cds g10408.t79.CDS1 9592031 9592052
chr_1 g10408 g10408.t79 exon g10408.t79.exon2 9592186 9592358
chr_1 g10408 g10408.t79 cds g10408.t79.CDS2 9592186 9592358
chr_1 g10408 g10408.t79 exon g10408.t79.exon3 9592428 9592504
chr_1 g10408 g10408.t79 cds g10408.t79.CDS3 9592428 9592504
chr_1 g10408 g10408.t79 exon g10408.t79.exon4 9592605 9592914
chr_1 g10408 g10408.t79 cds g10408.t79.CDS4 9592605 9592914
chr_1 g10408 g10408.t79 exon g10408.t79.exon5 9592975 9593233
chr_1 g10408 g10408.t79 cds g10408.t79.CDS5 9592975 9593133
chr_1 g10408 g10408.t79 TTS g10408.t79 9593229 9593229
chr_1 g10408 g10408.t79 TSS g10408.t79 NA NA

Sequences

>g10408.t79 Gene=g10408 Length=841
ATGGCAGTCGGAAAAAATAAAGGTTTAGCCAAAGGTGGCAAGAAAGGAACCAAGAAGAAG
ATTGTGGATCCCTTCACACGTAAGGACTGGTATGATATCAAAGCTCCATCAATGTTCACC
ACACGCCAAGTGGGAAAGACATTGGTCAATCGTACACAAGGTACAAAAATTGCTAGCGAA
GGCTTGAAAGGTCGCCTTATCGCTGAAGACGTTCAAGGACGAAATGTCCTCACAAATTTC
CATGGAATGGACTTAACAACTGATAAATTGAGATCGATGGTGAAGAAATGGCAAACATTG
ATTGAATGTCATGTTGATGTCAAAACAACCGATGGTTACGTTTTGCGTGTATTCTGCATT
GGATTTACTGCAAAAGATAGTTCATCGCATCGCAAAACTTGTTACGCTCAAACCTCTCAA
ATCAAAACAATTCGCAAAAAGATGACTGACATCATCACACGCGACATTTCAAGCTCTGAC
TTGAAGGAAGTTGTCAACAAATTGTTGCCAGACTCAATTGCAAAGGATATTGAGAAGGCC
TGTCATGGAGTCTATCCTCTTCATGATGTGTACATTCGCAAGGTCAAGGTATTGAAGAAG
CCTCGTTTCGACCTCTCAAAATTACTTGAATTGCACGGCGATGGAGGAAAGTCAACAGAA
CCCACAGCAGCCGCAGCTGCAGAAGGAGTTGCCGTTGAAAGACCAGAAGGATATGAACCA
CCAGTCCAAGCCGCAGTTTAAGCAGTTATTATTCCATTAAAATGAAAGTTATGAATCCAT
CTAGAAATATAAATGGAAAATTAAAAAAAGAAATGCTTTCATAAGCCTTTGAACATCAAA
A

>g10408.t79 Gene=g10408 Length=246
MAVGKNKGLAKGGKKGTKKKIVDPFTRKDWYDIKAPSMFTTRQVGKTLVNRTQGTKIASE
GLKGRLIAEDVQGRNVLTNFHGMDLTTDKLRSMVKKWQTLIECHVDVKTTDGYVLRVFCI
GFTAKDSSSHRKTCYAQTSQIKTIRKKMTDIITRDISSSDLKEVVNKLLPDSIAKDIEKA
CHGVYPLHDVYIRKVKVLKKPRFDLSKLLELHGDGGKSTEPTAAAAAEGVAVERPEGYEP
PVQAAV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g10408.t79 Hamap MF_03122 40S ribosomal protein S1 [RPS3A]. 1 246 35.361195
9 g10408.t79 MobiDBLite mobidb-lite consensus disorder prediction 218 246 -
3 g10408.t79 PANTHER PTHR11830 40S RIBOSOMAL PROTEIN S3A 1 66 2.5E-102
5 g10408.t79 PANTHER PTHR11830:SF22 40S RIBOSOMAL PROTEIN S3A 1 66 2.5E-102
4 g10408.t79 PANTHER PTHR11830 40S RIBOSOMAL PROTEIN S3A 65 245 2.5E-102
6 g10408.t79 PANTHER PTHR11830:SF22 40S RIBOSOMAL PROTEIN S3A 65 245 2.5E-102
1 g10408.t79 Pfam PF01015 Ribosomal S3Ae family 17 67 2.5E-13
2 g10408.t79 Pfam PF01015 Ribosomal S3Ae family 66 201 2.7E-56
8 g10408.t79 SMART SM01397 Ribosomal_S3Ae_2 16 201 1.1E-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.

Raw TPM values