Gene loci information

Transcript annotation

  • This transcript has been annotated as Leucine–tRNA ligase, cytoplasmic.

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_2 g4655 g4655.t3 isoform g4655.t3 3964597 3965678
chr_2 g4655 g4655.t3 exon g4655.t3.exon1 3964597 3965412
chr_2 g4655 g4655.t3 cds g4655.t3.CDS1 3964597 3965412
chr_2 g4655 g4655.t3 exon g4655.t3.exon2 3965494 3965577
chr_2 g4655 g4655.t3 cds g4655.t3.CDS2 3965494 3965577
chr_2 g4655 g4655.t3 exon g4655.t3.exon3 3965676 3965678
chr_2 g4655 g4655.t3 cds g4655.t3.CDS3 3965676 3965678
chr_2 g4655 g4655.t3 TSS g4655.t3 3965812 3965812
chr_2 g4655 g4655.t3 TTS g4655.t3 NA NA

Sequences

>g4655.t3 Gene=g4655 Length=903
ATGGCTACTGAAAGGAAAGGAACATTTAAAGTTGAGTTTCTGCAAAAGATAGAACGTGAA
ATTCAAGAAAAATGGGAACGAGAGAAGATTCACGACTCGGATGCACCAAAAGAAGCTCGC
AAATCTCTCGATGAAAAATTCTTTGTCACTTTTCCTTATCCTTACATGAATGGACGTCTT
CATTTAGGTCATACTTTCTCTTTATCAAAAGCTGAATTTGGTGTTCGTTATTTTCGATTG
AAAGGAAAGAATGTTTTATTTCCACTTGGATTTCATTGTACTGGAATGCCAATCAAGGCT
TGTGCTGATAAGTTGAAACGTGAAATTGAGACATTTGGCTATCCTCCAAACTTTCCAATT
GAAGAAGAAACAACAGCTGTTGAAGTTGAACGCGATGTTGTGCCAAAAGATAAGTCAAAA
AGTAAAAAGAGCAAAGCTGTCGCAAAAGCTGGATCAACTAAATATCAATGGCAAATTATG
CAAAGTCTTGGTCTTGAAGATGAAGAGATTAAAAAGTTTGCTGACACCGATCATTGGCTT
GAATATTTCCCTCCTCTCGCTATTCAAGATTTAAAAAAGATGGGATCGCACATTGATTTT
CGTCGAACATTCGTTACAACTGATGTCAATCCATTCTATGATTCGTTTGTTCGATGGCAA
TTTTGTCTATTAAAGGAACGTGGAAAAATTATGTACGGAAAACGTCATACAATCTTCTCA
CCAAAAGATGGTCAACCCTGTATGGACCATGATCGTTCTTCAGGTGAAGGTGTTGGACCA
CAAGAGTATACTCTTATCAAAATGAAAGTTATTGGAAATATTCCAGAGAAATTGAAAAAT
GTCAAAACTGAAATTTTCATGGTTGCAGCAACTCTTCGTCCTGAAACAATGTATGGTCAA
ACA

>g4655.t3 Gene=g4655 Length=301
MATERKGTFKVEFLQKIEREIQEKWEREKIHDSDAPKEARKSLDEKFFVTFPYPYMNGRL
HLGHTFSLSKAEFGVRYFRLKGKNVLFPLGFHCTGMPIKACADKLKREIETFGYPPNFPI
EEETTAVEVERDVVPKDKSKSKKSKAVAKAGSTKYQWQIMQSLGLEDEEIKKFADTDHWL
EYFPPLAIQDLKKMGSHIDFRRTFVTTDVNPFYDSFVRWQFCLLKERGKIMYGKRHTIFS
PKDGQPCMDHDRSSGEGVGPQEYTLIKMKVIGNIPEKLKNVKTEIFMVAATLRPETMYGQ
T

Protein features from InterProScan

Transcript Database ID Name Start End E.value
3 g4655.t3 PANTHER PTHR45794 LEUCYL-TRNA SYNTHETASE 4 301 1.3E-138
4 g4655.t3 PANTHER PTHR45794:SF1 LEUCINE–TRNA LIGASE, CYTOPLASMIC 4 301 1.3E-138
2 g4655.t3 Pfam PF00133 tRNA synthetases class I (I, L, M and V) 21 104 2.4E-12
1 g4655.t3 Pfam PF00133 tRNA synthetases class I (I, L, M and V) 178 300 2.4E-5
6 g4655.t3 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature. 54 65 -
5 g4655.t3 SUPERFAMILY SSF52374 Nucleotidylyl transferase 9 254 1.69E-42

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:0004823 leucine-tRNA ligase activity MF
GO:0005524 ATP binding MF
GO:0006418 tRNA aminoacylation for protein translation BP
GO:0000166 nucleotide binding MF
GO:0006429 leucyl-tRNA aminoacylation BP
GO:0004812 aminoacyl-tRNA ligase activity MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

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. There were no conditions that were differentially expressed