Gene loci information

Transcript annotation

  • This transcript has been annotated as Bifunctional glutamate/proline–tRNA ligase.

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_4 g17015 g17015.t12 isoform g17015.t12 12160085 12161191
chr_4 g17015 g17015.t12 exon g17015.t12.exon1 12160085 12160863
chr_4 g17015 g17015.t12 cds g17015.t12.CDS1 12160093 12160863
chr_4 g17015 g17015.t12 exon g17015.t12.exon2 12161139 12161191
chr_4 g17015 g17015.t12 cds g17015.t12.CDS2 12161139 12161189
chr_4 g17015 g17015.t12 TTS g17015.t12 12161168 12161168
chr_4 g17015 g17015.t12 TSS g17015.t12 NA NA

Sequences

>g17015.t12 Gene=g17015 Length=832
GTCGTGGTATGACTGTTGAAGGTCTAAAACAATTCATTATTGCACAAGGTTCTAGTAAAG
CTGTAGTATTTATGGAATGGGATAAAATTTGGGCTTTCAATAAGAAAGTCATTGATCCAA
TTGCACCTAGATATACAGCATTAGAAAATGACAATCGTATTATTGTTAAAGTCGCTAATG
CAAAATTGCAAGCACTTGAAGTTCCAAAACATCCCAAAAATGAGGAAGTTGGCACAAAAA
CTATTTGGGTTGGTCCAGAAATTTATATTGACTATGCTGATGCTGAATGTTTAAAAGAAG
GTGAAAATGCGACATTTATAAATTGGGGTAATTTGAGAATCAAGAAAATTCATAAAGAAG
GAGAAAAAATTACTTCAGTCGATGCTGAATTGAATTTGGGTGACACTGATTTCAAAAAGA
CGTTAAAACTTACATGGCTTTGTAAACAAGATCCATCAGAATATCCACCAACTTATTGTG
TTTATTTTGATCATATTATAAACAAATCTGTTCTTGGTAAAGATGAAGACTTTAAATCAT
ACATCGGACATGAGACTAGAAAAGAAACAAAAATGTTTGGTGATCCTGAATTGAAAAAAT
GTCAAAAAGGCGACATCATTCAACTACAACGACGTGGATTTTTCAAAGTTGATCAAGCTT
ATGCTCCAGCTAGTGAAATTTCAGGAGTTGAACGTCCAATTGTTTTGTTCTTTATTCCTG
ATGGTCATAAAAAAGAAATGCCCACGTCTGGTCTTTCAAAGAAACTTCAAGCAGCAGAGG
AAAAATCAAACAACAGTGCATCAGTGATTAAAAAATCATCATCTGTTGGACA

>g17015.t12 Gene=g17015 Length=274
MTVEGLKQFIIAQGSSKAVVFMEWDKIWAFNKKVIDPIAPRYTALENDNRIIVKVANAKL
QALEVPKHPKNEEVGTKTIWVGPEIYIDYADAECLKEGENATFINWGNLRIKKIHKEGEK
ITSVDAELNLGDTDFKKTLKLTWLCKQDPSEYPPTYCVYFDHIINKSVLGKDEDFKSYIG
HETRKETKMFGDPELKKCQKGDIIQLQRRGFFKVDQAYAPASEISGVERPIVLFFIPDGH
KKEMPTSGLSKKLQAAEEKSNNSASVIKKSSSVG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g17015.t12 Gene3D G3DSA:2.40.240.10 Ribosomal Protein L25; Chain P 40 218 5.2E-24
7 g17015.t12 Gene3D G3DSA:2.40.240.10 Ribosomal Protein L25; Chain P 47 149 5.2E-24
5 g17015.t12 MobiDBLite mobidb-lite consensus disorder prediction 243 274 -
4 g17015.t12 MobiDBLite mobidb-lite consensus disorder prediction 253 274 -
2 g17015.t12 PANTHER PTHR43382 PROLYL-TRNA SYNTHETASE 1 271 2.6E-108
1 g17015.t12 Pfam PF03950 tRNA synthetases class I (E and Q), anti-codon binding domain 39 215 1.1E-32
3 g17015.t12 SUPERFAMILY SSF50715 Ribosomal protein L25-like 39 241 2.04E-45

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:0005524 ATP binding MF
GO:0006418 tRNA aminoacylation for protein translation BP
GO:0000166 nucleotide binding MF
GO:0006412 translation BP
GO:0004812 aminoacyl-tRNA ligase activity MF
GO:0005737 cytoplasm CC

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