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.t15 isoform g17015.t15 12162767 12163690
chr_4 g17015 g17015.t15 exon g17015.t15.exon1 12162767 12163690
chr_4 g17015 g17015.t15 cds g17015.t15.CDS1 12162896 12163690
chr_4 g17015 g17015.t15 TTS g17015.t15 12163773 12163773
chr_4 g17015 g17015.t15 TSS g17015.t15 NA NA

Sequences

>g17015.t15 Gene=g17015 Length=924
GGACGTAAGACCGAGAAGGAAAAGTTTGCTGGTGGTGATTTTACAACAACAGTTGAAGCT
TTTATTTCTGCAAGTGGTCGTGGAATTCAAGGTGCTACAAGTCACTTCCTTGGTCAAAAC
TTTTCAAAAATGTTTGAAATCATCTTTGAAAATCCAGAAACACAAGAAAAGGAATATGTT
TATCAAAATTCATGGGGAATTACTACCAGAACTATTGGTGTGATGGTGATGGTCCATGCT
GATAATCAAGGTCTTGTTTTGCCACCTCGAGTTGCTTATACTCAAGTTGTTATAGTTCCA
TGCGGTATTACTGCCACAACATCAGATACCGATCGTAAAAATCTCATTGACAGTTGTAAA
GAATTGGAAAAGCAACTGCAAGCATGCAATATTCGTGTTGAAGGTGATTATCGTGACAAT
TACTCTCCTGGTTGGAAATATAATCATTGGGAATTGAAAGGTGTTCCAATTCGCATTGAA
TTGGGACCAAAAGATTTGAAAGCTCAACAATTTGTTGCTGTACGTCGCGATAATTCTGAA
AAATTGACCATCAGTCGAAGCAAAGCTTCAACAGATATCCCAGAATTACTTGAAAAAATT
CATCAAAATATGTTGGCAAAAGCAACAAAAGATTTAACCGAACATTTAAAAACAACAAAA
GATTGGAAAGAATTTACATCATTTTTGGATACAAAAAATATTATAATGGCTCCATTCTGT
GGTGATATTCCTTGTGAGGAAAAGATCAAGGCAGATAGTGCACGTGAAGAAACTGATGAA
GCTGTTCAAGGACCTGCAATGGGAGCAAAATCCTTGTGCATTCCATTTGAACAACCAGCT
GAAATTCAAGCAAACGACAAATGCATTCATCCACAGTGCAACAACAAACCGAAATTCTAC
ACACTTTTTGGAAGAAGCTACTAA

>g17015.t15 Gene=g17015 Length=264
MFEIIFENPETQEKEYVYQNSWGITTRTIGVMVMVHADNQGLVLPPRVAYTQVVIVPCGI
TATTSDTDRKNLIDSCKELEKQLQACNIRVEGDYRDNYSPGWKYNHWELKGVPIRIELGP
KDLKAQQFVAVRRDNSEKLTISRSKASTDIPELLEKIHQNMLAKATKDLTEHLKTTKDWK
EFTSFLDTKNIIMAPFCGDIPCEEKIKADSAREETDEAVQGPAMGAKSLCIPFEQPAEIQ
ANDKCIHPQCNNKPKFYTLFGRSY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g17015.t15 CDD cd00862 ProRS_anticodon_zinc 41 264 3.15195E-90
12 g17015.t15 Coils Coil Coil 69 89 -
11 g17015.t15 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 1 45 4.9E-11
10 g17015.t15 Gene3D G3DSA:3.40.50.800 - 46 171 8.5E-45
9 g17015.t15 Gene3D G3DSA:3.30.110.30 - 173 263 1.3E-33
3 g17015.t15 PANTHER PTHR43382 PROLYL-TRNA SYNTHETASE 1 264 1.0E-123
4 g17015.t15 PANTHER PTHR43382:SF2 BIFUNCTIONAL GLUTAMATE/PROLINE–TRNA LIGASE 1 264 1.0E-123
2 g17015.t15 Pfam PF03129 Anticodon binding domain 52 150 9.0E-20
1 g17015.t15 Pfam PF09180 Prolyl-tRNA synthetase, C-terminal 179 264 3.3E-23
8 g17015.t15 SMART SM00946 ProRS_C_1_2 179 264 4.2E-31
5 g17015.t15 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 2 58 1.03E-6
7 g17015.t15 SUPERFAMILY SSF52954 Class II aaRS ABD-related 41 171 1.36E-31
6 g17015.t15 SUPERFAMILY SSF64586 C-terminal domain of ProRS 175 264 7.85E-18

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:0006433 prolyl-tRNA aminoacylation BP
GO:0005524 ATP binding MF
GO:0000166 nucleotide binding MF
GO:0005737 cytoplasm CC
GO:0004827 proline-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