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.t55 isoform g10408.t55 9592031 9593133
chr_1 g10408 g10408.t55 exon g10408.t55.exon1 9592031 9592052
chr_1 g10408 g10408.t55 cds g10408.t55.CDS1 9592031 9592052
chr_1 g10408 g10408.t55 exon g10408.t55.exon2 9592186 9592399
chr_1 g10408 g10408.t55 cds g10408.t55.CDS2 9592186 9592399
chr_1 g10408 g10408.t55 exon g10408.t55.exon3 9592605 9592914
chr_1 g10408 g10408.t55 cds g10408.t55.CDS3 9592605 9592914
chr_1 g10408 g10408.t55 exon g10408.t55.exon4 9592975 9593133
chr_1 g10408 g10408.t55 cds g10408.t55.CDS4 9592975 9593133
chr_1 g10408 g10408.t55 TTS g10408.t55 9593229 9593229
chr_1 g10408 g10408.t55 TSS g10408.t55 NA NA

Sequences

>g10408.t55 Gene=g10408 Length=705
ATGGCAGTCGGAAAAAATAAAGGTTTAGCCAAAGGTGGCAAGAAAGGAACCAAGAAGAAG
ATTGTGGATCCCTTCACACGTAAGGACTGGTATGATATCAAAGCTCCATCAATGTTCACC
ACACGCCAAGTGGGAAAGACATTGGTCAATCGTACACAAGGTACAAAAATTGCTAGCGAA
GGCTTGAAAGGTCGCGTGTTTGAAGTCTCATTAGCTGATTTACAAAACGACAATGAATCG
ATGGTGAAGAAATGGCAAACATTGATTGAATGTCATGTTGATGTCAAAACAACCGATGGT
TACGTTTTGCGTGTATTCTGCATTGGATTTACTGCAAAAGATAGTTCATCGCATCGCAAA
ACTTGTTACGCTCAAACCTCTCAAATCAAAACAATTCGCAAAAAGATGACTGACATCATC
ACACGCGACATTTCAAGCTCTGACTTGAAGGAAGTTGTCAACAAATTGTTGCCAGACTCA
ATTGCAAAGGATATTGAGAAGGCCTGTCATGGAGTCTATCCTCTTCATGATGTGTACATT
CGCAAGGTCAAGGTATTGAAGAAGCCTCGTTTCGACCTCTCAAAATTACTTGAATTGCAC
GGCGATGGAGGAAAGTCAACAGAACCCACAGCAGCCGCAGCTGCAGAAGGAGTTGCCGTT
GAAAGACCAGAAGGATATGAACCACCAGTCCAAGCCGCAGTTTAA

>g10408.t55 Gene=g10408 Length=234
MAVGKNKGLAKGGKKGTKKKIVDPFTRKDWYDIKAPSMFTTRQVGKTLVNRTQGTKIASE
GLKGRVFEVSLADLQNDNESMVKKWQTLIECHVDVKTTDGYVLRVFCIGFTAKDSSSHRK
TCYAQTSQIKTIRKKMTDIITRDISSSDLKEVVNKLLPDSIAKDIEKACHGVYPLHDVYI
RKVKVLKKPRFDLSKLLELHGDGGKSTEPTAAAAAEGVAVERPEGYEPPVQAAV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g10408.t55 Hamap MF_03122 40S ribosomal protein S1 [RPS3A]. 1 234 32.083889
10 g10408.t55 MobiDBLite mobidb-lite consensus disorder prediction 206 234 -
3 g10408.t55 PANTHER PTHR11830 40S RIBOSOMAL PROTEIN S3A 1 78 2.8E-97
5 g10408.t55 PANTHER PTHR11830:SF28 40S RIBOSOMAL PROTEIN S3A 1 78 2.8E-97
4 g10408.t55 PANTHER PTHR11830 40S RIBOSOMAL PROTEIN S3A 80 233 2.8E-97
6 g10408.t55 PANTHER PTHR11830:SF28 40S RIBOSOMAL PROTEIN S3A 80 233 2.8E-97
1 g10408.t55 Pfam PF01015 Ribosomal S3Ae family 17 78 5.4E-21
2 g10408.t55 Pfam PF01015 Ribosomal S3Ae family 80 189 6.3E-42
9 g10408.t55 ProSitePatterns PS01191 Ribosomal protein S3Ae signature. 62 74 -
8 g10408.t55 SMART SM01397 Ribosomal_S3Ae_2 16 189 1.3E-101

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