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.t4 TSS g17015.t4 12156272 12156272
chr_4 g17015 g17015.t4 isoform g17015.t4 12156363 12157661
chr_4 g17015 g17015.t4 exon g17015.t4.exon1 12156363 12157603
chr_4 g17015 g17015.t4 cds g17015.t4.CDS1 12156363 12157603
chr_4 g17015 g17015.t4 exon g17015.t4.exon2 12157660 12157661
chr_4 g17015 g17015.t4 cds g17015.t4.CDS2 12157660 12157660
chr_4 g17015 g17015.t4 TTS g17015.t4 12158328 12158328

Sequences

>g17015.t4 Gene=g17015 Length=1243
ATGCCAATCAAAGTAATTTGTGATTTAAAGAATCCACCAATTGGTAAGTTACAGATTAAT
CATAAAATTACTTCTGCAGAAAGCTTAAAATTCAAAATTTTAAATTTTCATGAAATATTT
TTAATTTTTTATGAAATCAAATTTGCAGGTGCTTTGGTTGTTGCCGAAATTATTAAATCA
ACTGATCCAGTTGTAATTGAATGGAGCGATAAAGAAGCATCTATCAATTTTGGTAACAAT
TCACTTTCATGTGTGAGCAACAACGACCTTTTAAGAGCTCTAGCTCGACAAGCCGGAAGT
TATCAGCTTTATGGAAAAACTCCGATTGAAAGAACTCAAATTGATCATTGGTTGACTTAC
TGCCTCAATTATGATGCTCATATTGATGAAGCAATTCAATATTTGAATAAATGTTTAGCT
CCATTGACTTATTTAGTGTCAAATAAGCTGACAATTGCTGATTTAGCTGTGTTCAATGAA
TTTTTTGTCAAGTATGATCTTTTGAAGAAATCTGGTTTGCCTAGTCATGTTCAACGCTGG
TATAACCTCATCAGTTCATTGCCAACAGTTCAAACTGTGCTTTCATCACTTCCAAAAGAT
GGTAAATCTACAAAATCAAAGAAACAAGAAAAACAAGAATTTTCAGCAGCTCTTGGTGTT
GGCGATAGAAAGCAAGAAGGAAAATTTGTCGATCTTCCAGGAGCTGAAATGGGAAAAGTT
GTTGTTCGCTTTCCTCCTGAAGCATCAGGGTATTTGCACATTGGTCATGCTAAAGCAGCT
CTTTTAAATCAATATTATCAGCAAGCATTTGATGGAAAATTGATTATGAGATTTGATGAC
ACCAATCCAGCTAAAGAAAATGTTCATTTTGAGGAAGTCATTTTGGAAGATGTAGAAATG
CTTCAAATTAAACCTGATGCATTCACTTACACCTCAGATTATTTTGATATCATGCTTAAA
TATTGTGAGCAATTAATGAAAGAAGGAAAAGCATATGCTGATGATACTGATCCTGAATTG
ATGAAACAAGAACGTGAACAGAAAGTTGAGTCAAAGAACCGAAATAATTCGGTTGAAAAG
AATTTTGAAATGTGGAAAGAAATGTTGGCTGGCACAGAAAAAGGACAAAAATGTTGTATT
CGAGCAAAAATTGACATGTCATCACCAAATGGATGCCTTCGTGATCCAACAATTTATCGT
TGCAAAAATGAACCACATCCACGTACTGGAACTAATTACAAAG

>g17015.t4 Gene=g17015 Length=414
MPIKVICDLKNPPIGKLQINHKITSAESLKFKILNFHEIFLIFYEIKFAGALVVAEIIKS
TDPVVIEWSDKEASINFGNNSLSCVSNNDLLRALARQAGSYQLYGKTPIERTQIDHWLTY
CLNYDAHIDEAIQYLNKCLAPLTYLVSNKLTIADLAVFNEFFVKYDLLKKSGLPSHVQRW
YNLISSLPTVQTVLSSLPKDGKSTKSKKQEKQEFSAALGVGDRKQEGKFVDLPGAEMGKV
VVRFPPEASGYLHIGHAKAALLNQYYQQAFDGKLIMRFDDTNPAKENVHFEEVILEDVEM
LQIKPDAFTYTSDYFDIMLKYCEQLMKEGKAYADDTDPELMKQEREQKVESKNRNNSVEK
NFEMWKEMLAGTEKGQKCCIRAKIDMSSPNGCLRDPTIYRCKNEPHPRTGTNYK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g17015.t4 Coils Coil Coil 341 361 -
13 g17015.t4 Coils Coil Coil 413 414 -
11 g17015.t4 Gene3D G3DSA:1.20.1050.130 - 46 205 1.7E-36
10 g17015.t4 Gene3D G3DSA:3.40.50.620 HUPs 240 311 1.6E-72
12 g17015.t4 Gene3D G3DSA:3.90.800.10 - 312 414 1.6E-72
3 g17015.t4 PANTHER PTHR43382 PROLYL-TRNA SYNTHETASE 51 414 1.8E-150
5 g17015.t4 PRINTS PR00987 Glutamyl-tRNA synthetase signature 243 255 1.3E-10
6 g17015.t4 PRINTS PR00987 Glutamyl-tRNA synthetase signature 257 268 1.3E-10
4 g17015.t4 PRINTS PR00987 Glutamyl-tRNA synthetase signature 272 285 1.3E-10
2 g17015.t4 Pfam PF14497 Glutathione S-transferase, C-terminal domain 126 196 7.7E-5
1 g17015.t4 Pfam PF00749 tRNA synthetases class I (E and Q), catalytic domain 239 413 1.2E-64
9 g17015.t4 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature. 246 257 -
8 g17015.t4 SUPERFAMILY SSF47616 GST C-terminal domain-like 89 192 1.53E-16
7 g17015.t4 SUPERFAMILY SSF52374 Nucleotidylyl transferase 239 412 5.36E-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