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.t11 TSS g17015.t11 12156272 12156272
chr_4 g17015 g17015.t11 isoform g17015.t11 12156510 12157593
chr_4 g17015 g17015.t11 exon g17015.t11.exon1 12156510 12157593
chr_4 g17015 g17015.t11 cds g17015.t11.CDS1 12157071 12157592
chr_4 g17015 g17015.t11 TTS g17015.t11 12158328 12158328

Sequences

>g17015.t11 Gene=g17015 Length=1084
GGTGCTTTGGTTGTTGCCGAAATTATTAAATCAACTGATCCAGTTGTAATTGAATGGAGC
GATAAAGAAGCATCTATCAATTTTGGTAACAATTCACTTTCATGTGTGAGCAACAACGAC
CTTTTAAGAGCTCTAGCTCGACAAGCCGGAAGTTATCAGCTTTATGGAAAAACTCCGATT
GAAAGAACTCAAATTGATCATTGGTTGACTTACTGCCTCAATTATGATGCTCATATTGAT
GAAGCAATTCAATATTTGAATAAATGTTTAGCTCCATTGACTTATTTAGTGTCAAATAAG
CTGACAATTGCTGATTTAGCTGTGTTCAATGAATTTTTTGTCAAGTATGATCTTTTGAAG
AAATCTGGTTTGCCTAGTCATGTTCAACGCTGGTATAACCTCATCAGTTCATTGCCAACA
GTTCAAACTGTGCTTTCATCACTTCCAAAAGATGGTAAATCTACAAAATCAAAGAAACAA
GAAAAACAAGAATTTTCAGCAGCTCTTGGTGTTGGCGATAGAAAGCAAGAAGGAAAATTT
GTCGATCTTCCAGGAGCTGAAATGGGAAAAGTTGTTGTTCGCTTTCCTCCTGAAGCATCA
GGGTATTTGCACATTGGTCATGCTAAAGCAGCTCTTTTAAATCAATATTATCAGCAAGCA
TTTGATGGAAAATTGATTATGAGATTTGATGACACCAATCCAGCTAAAGAAAATGTTCAT
TTTGAGGAAGTCATTTTGGAAGATGTAGAAATGCTTCAAATTAAACCTGATGCATTCACT
TACACCTCAGATTATTTTGATATCATGCTTAAATATTGTGAGCAATTAATGAAAGAAGGA
AAAGCATATGCTGATGATACTGATCCTGAATTGATGAAACAAGAACGTGAACAGAAAGTT
GAGTCAAAGAACCGAAATAATTCGGTTGAAAAGAATTTTGAAATGTGGAAAGAAATGTTG
GCTGGCACAGAAAAAGGACAAAAATGTTGTATTCGAGCAAAAATTGACATGTCATCACCA
AATGGATGCCTTCGTGATCCAACAATTTATCGTTGCAAAAATGAACCACATCCACGTACT
GGAA

>g17015.t11 Gene=g17015 Length=174
MGKVVVRFPPEASGYLHIGHAKAALLNQYYQQAFDGKLIMRFDDTNPAKENVHFEEVILE
DVEMLQIKPDAFTYTSDYFDIMLKYCEQLMKEGKAYADDTDPELMKQEREQKVESKNRNN
SVEKNFEMWKEMLAGTEKGQKCCIRAKIDMSSPNGCLRDPTIYRCKNEPHPRTG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g17015.t11 Coils Coil Coil 105 125 -
8 g17015.t11 Gene3D G3DSA:3.40.50.620 HUPs 4 75 3.6E-68
9 g17015.t11 Gene3D G3DSA:3.90.800.10 - 76 174 3.6E-68
2 g17015.t11 PANTHER PTHR43382 PROLYL-TRNA SYNTHETASE 1 174 4.5E-107
5 g17015.t11 PRINTS PR00987 Glutamyl-tRNA synthetase signature 7 19 1.7E-11
4 g17015.t11 PRINTS PR00987 Glutamyl-tRNA synthetase signature 21 32 1.7E-11
3 g17015.t11 PRINTS PR00987 Glutamyl-tRNA synthetase signature 36 49 1.7E-11
1 g17015.t11 Pfam PF00749 tRNA synthetases class I (E and Q), catalytic domain 3 174 4.1E-65
7 g17015.t11 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature. 10 21 -
6 g17015.t11 SUPERFAMILY SSF52374 Nucleotidylyl transferase 3 173 1.45E-49

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:0043039 tRNA aminoacylation BP
GO:0004812 aminoacyl-tRNA ligase activity 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