Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t110 isoform g10408.t110 9592031 9594321
chr_1 g10408 g10408.t110 exon g10408.t110.exon1 9592031 9592052
chr_1 g10408 g10408.t110 exon g10408.t110.exon2 9592186 9592504
chr_1 g10408 g10408.t110 exon g10408.t110.exon3 9592605 9592678
chr_1 g10408 g10408.t110 cds g10408.t110.CDS1 9592643 9592678
chr_1 g10408 g10408.t110 exon g10408.t110.exon4 9592774 9592914
chr_1 g10408 g10408.t110 cds g10408.t110.CDS2 9592774 9592914
chr_1 g10408 g10408.t110 exon g10408.t110.exon5 9592975 9593241
chr_1 g10408 g10408.t110 cds g10408.t110.CDS3 9592975 9593133
chr_1 g10408 g10408.t110 exon g10408.t110.exon6 9593309 9593337
chr_1 g10408 g10408.t110 exon g10408.t110.exon7 9593745 9593817
chr_1 g10408 g10408.t110 exon g10408.t110.exon8 9594019 9594063
chr_1 g10408 g10408.t110 exon g10408.t110.exon9 9594269 9594321
chr_1 g10408 g10408.t110 TTS g10408.t110 9594355 9594355
chr_1 g10408 g10408.t110 TSS g10408.t110 NA NA

Sequences

>g10408.t110 Gene=g10408 Length=1023
ATGGCAGTCGGAAAAAATAAAGGTTTAGCCAAAGGTGGCAAGAAAGGAACCAAGAAGAAG
ATTGTGGATCCCTTCACACGTAAGGACTGGTATGATATCAAAGCTCCATCAATGTTCACC
ACACGCCAAGTGGGAAAGACATTGGTCAATCGTACACAAGGTACAAAAATTGCTAGCGAA
GGCTTGAAAGGTCGCGTGTTTGAAGTCTCATTAGCTGATTTACAAAACGACAATGATGCC
GAGAGATCTTTCCGCAAATTCAAGCTTATCGCTGAAGACGTTCAAGGACGAAATGTCCTC
ACAAATTTCCATGGAATGGACTTAACAACTGATAAATTGAGATCGATGGTGAAGAAATGG
CAAACATTGATTGAATGTCATGTTGATGTCAAAACAACCGATGGTTACGTTTTGCATGAC
TGACATCATCACACGCGACATTTCAAGCTCTGACTTGAAGGAAGTTGTCAACAAATTGTT
GCCAGACTCAATTGCAAAGGATATTGAGAAGGCCTGTCATGGAGTCTATCCTCTTCATGA
TGTGTACATTCGCAAGGTCAAGGTATTGAAGAAGCCTCGTTTCGACCTCTCAAAATTACT
TGAATTGCACGGCGATGGAGGAAAGTCAACAGAACCCACAGCAGCCGCAGCTGCAGAAGG
AGTTGCCGTTGAAAGACCAGAAGGATATGAACCACCAGTCCAAGCCGCAGTTTAAGCAGT
TATTATTCCATTAAAATGAAAGTTATGAATCCATCTAGAAATATAAATGGAAAATTAAAA
AAAGAAATGCTTTCATAAGCCTTTGAACATCAAAAATTAAACGATATTTCTTAAATTGAA
CATCAGTATTAGAAATTTTAATATTTTGTATAATCTTTGCAGGTTTCACAAATCTAATTT
CGTTATTTCAAGAGTCATTTTTCAGGTTTCTGAAGGTATTTTGAATGTTTCTCATCGTTA
TGTTTTACAGATGGTTACATTATATGTCAATGGAAGATGATAAAAAATGCAATAGCTTAA
ACG

>g10408.t110 Gene=g10408 Length=111
MLMSKQPMVTFCMTDIITRDISSSDLKEVVNKLLPDSIAKDIEKACHGVYPLHDVYIRKV
KVLKKPRFDLSKLLELHGDGGKSTEPTAAAAAEGVAVERPEGYEPPVQAAV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g10408.t110 MobiDBLite mobidb-lite consensus disorder prediction 82 111 -
2 g10408.t110 PANTHER PTHR11830:SF25 40S RIBOSOMAL PROTEIN S3A 20 111 2.5E-32
3 g10408.t110 PANTHER PTHR11830 40S RIBOSOMAL PROTEIN S3A 20 111 2.5E-32
1 g10408.t110 Pfam PF01015 Ribosomal S3Ae family 9 66 4.0E-17

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