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.t5 TSS g17015.t5 12156272 12156272
chr_4 g17015 g17015.t5 isoform g17015.t5 12156363 12157920
chr_4 g17015 g17015.t5 exon g17015.t5.exon1 12156363 12156405
chr_4 g17015 g17015.t5 exon g17015.t5.exon2 12156511 12156830
chr_4 g17015 g17015.t5 exon g17015.t5.exon3 12157141 12157603
chr_4 g17015 g17015.t5 cds g17015.t5.CDS1 12157188 12157603
chr_4 g17015 g17015.t5 exon g17015.t5.exon4 12157660 12157920
chr_4 g17015 g17015.t5 cds g17015.t5.CDS2 12157660 12157918
chr_4 g17015 g17015.t5 TTS g17015.t5 12158328 12158328

Sequences

>g17015.t5 Gene=g17015 Length=1087
ATGCCAATCAAAGTAATTTGTGATTTAAAGAATCCACCAATTGGTGCTTTGGTTGTTGCC
GAAATTATTAAATCAACTGATCCAGTTGTAATTGAATGGAGCGATAAAGAAGCATCTATC
AATTTTGGTAACAATTCACTTTCATGTGTGAGCAACAACGACCTTTTAAGAGCTCTAGCT
CGACAAGCCGGAAGTTATCAGCTTTATGGAAAAACTCCGATTGAAAGAACTCAAATTGAT
CATTGGTTGACTTACTGCCTCAATTATGATGCTCATATTGATGAAGCAATTCAATATTTG
AATAAATGTTTAGCTCCATTGACTTATTTAGTGTCAAATAAGCTGACAATTGCTGATTTA
GCTCTCTTTTAAATCAATATTATCAGCAAGCATTTGATGGAAAATTGATTATGAGATTTG
ATGACACCAATCCAGCTAAAGAAAATGTTCATTTTGAGGAAGTCATTTTGGAAGATGTAG
AAATGCTTCAAATTAAACCTGATGCATTCACTTACACCTCAGATTATTTTGATATCATGC
TTAAATATTGTGAGCAATTAATGAAAGAAGGAAAAGCATATGCTGATGATACTGATCCTG
AATTGATGAAACAAGAACGTGAACAGAAAGTTGAGTCAAAGAACCGAAATAATTCGGTTG
AAAAGAATTTTGAAATGTGGAAAGAAATGTTGGCTGGCACAGAAAAAGGACAAAAATGTT
GTATTCGAGCAAAAATTGACATGTCATCACCAAATGGATGCCTTCGTGATCCAACAATTT
ATCGTTGCAAAAATGAACCACATCCACGTACTGGAACTAATTACAAAGTTTATCCAACTT
ATGATTTTGCTTGTCCTATTGTTGATGCAATTGAAAATGTGACTCATACTCTTCGTACAA
TGGAATATCACGATCGTGATGATCAATTTTATTGGTTTATTGATGCATTGAAACTTCGTA
AACCATACATTTGGGAATATTCACGTTTAAATATGACTAACACTGTTCTATCTAAACGTA
AATTGACTTGGTTTGTTGAAAACGGTCTGGTTGATGGCTGGGATGATCCTCGTTTTCCTA
CAGTTCG

>g17015.t5 Gene=g17015 Length=225
MRFDDTNPAKENVHFEEVILEDVEMLQIKPDAFTYTSDYFDIMLKYCEQLMKEGKAYADD
TDPELMKQEREQKVESKNRNNSVEKNFEMWKEMLAGTEKGQKCCIRAKIDMSSPNGCLRD
PTIYRCKNEPHPRTGTNYKVYPTYDFACPIVDAIENVTHTLRTMEYHDRDDQFYWFIDAL
KLRKPYIWEYSRLNMTNTVLSKRKLTWFVENGLVDGWDDPRFPTV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g17015.t5 Coils Coil Coil 66 86 -
4 g17015.t5 Gene3D G3DSA:3.40.50.620 HUPs 1 180 1.9E-74
6 g17015.t5 Gene3D G3DSA:3.90.800.10 - 37 141 1.9E-74
5 g17015.t5 Gene3D G3DSA:1.10.1160.10 - 192 225 1.7E-14
2 g17015.t5 PANTHER PTHR43382 PROLYL-TRNA SYNTHETASE 1 225 5.2E-142
1 g17015.t5 Pfam PF00749 tRNA synthetases class I (E and Q), catalytic domain 1 225 4.0E-84
3 g17015.t5 SUPERFAMILY SSF52374 Nucleotidylyl transferase 1 216 1.05E-56

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: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