Gene loci information

Transcript annotation

  • This transcript has been annotated as Methionine–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_1 g14086 g14086.t5 TTS g14086.t5 34523708 34523708
chr_1 g14086 g14086.t5 isoform g14086.t5 34523794 34524848
chr_1 g14086 g14086.t5 exon g14086.t5.exon1 34523794 34523926
chr_1 g14086 g14086.t5 cds g14086.t5.CDS1 34523794 34523926
chr_1 g14086 g14086.t5 exon g14086.t5.exon2 34523986 34524848
chr_1 g14086 g14086.t5 cds g14086.t5.CDS2 34523986 34524674
chr_1 g14086 g14086.t5 TSS g14086.t5 NA NA

Sequences

>g14086.t5 Gene=g14086 Length=996
AGAGATCTAAAATGGGGTATCCCAGTTCCATTAAAAGGTTTCGAGAGCAAAGTATTTTAT
GTGTGGTTTGATGCACCAATTGGTTATATTTCAATCACTAGCAAATATACAAAAGAATGG
CGAAAATGGTGGCAACCAGCAGATCCATCAACAAAGGTTGAACTATTTCAATTTATGGCA
AAGGACAATGTACCTTTCCATTCAGTCATGTTCCCAGCGACACTTATTGGCGTTAATAAA
GGCTACACTCTCGTTTCACGTATCCTTTCGATTGAATATTTGAACTATGAGGATGGAAAA
TTCAGTAAAAGTCGTGGAATTGGAGTTTTTGGAAATGATGCACAAGATACTGGTATCGAA
TCTGATATTTGGCGTTTCTATCTCGCCTCAGCACGACCAGAAGGTCAAGATTCTAGCTTC
AGTTGGAGTGAATTGGCTTCTAGAAATAATTCTGAATTGCTCAACAACCTGGGTAATTTC
ATTAATCGTGCTTTAGTGTTCTGTGAGAAGAACTTCAATTCAACTATTTCGAATATTACA
TTGAACCATGATGATGCTGTTTTATTAGCTGTTATTAACAGAGAAATTAGAGAGTATGTT
AATTCCATGGAAAAAACAAGATTCCGTGATGGTATTCGTCACATTTTGGCGATTTCAAGA
CAAGGAAACTTATACATGCAGAATGAGAAGCCATGGGTCCTTCTTAAAGGAACTGCCGAA
CAAAAAACAAGAGCTCATAGTGTTATCAGTTTAAGTTGTAACATTGCATGTTTGTTAGCT
AATCTTCTCTATCCGTTTATGCCAGCAACATCAAGAAAGATTTTCACACAACTCAACTTT
GCAGGCGGTGCAATTAATCCAACGAAACCACATTTGACAGTTCTTCTTCAAACTGGACAT
CAAATTGGAAAACCATCTCCACTGTTTGCTAAAATTGACCAGGCTACTGTTGATCAATTG
AAAGCCAAGTACTCAGGTGTTCAAGTTACAGCTTAA

>g14086.t5 Gene=g14086 Length=273
MAKDNVPFHSVMFPATLIGVNKGYTLVSRILSIEYLNYEDGKFSKSRGIGVFGNDAQDTG
IESDIWRFYLASARPEGQDSSFSWSELASRNNSELLNNLGNFINRALVFCEKNFNSTISN
ITLNHDDAVLLAVINREIREYVNSMEKTRFRDGIRHILAISRQGNLYMQNEKPWVLLKGT
AEQKTRAHSVISLSCNIACLLANLLYPFMPATSRKIFTQLNFAGGAINPTKPHLTVLLQT
GHQIGKPSPLFAKIDQATVDQLKAKYSGVQVTA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g14086.t5 CDD cd07957 Anticodon_Ia_Met 91 220 0e+00
6 g14086.t5 Gene3D G3DSA:3.40.50.620 HUPs 1 97 0e+00
7 g14086.t5 Gene3D G3DSA:1.10.730.10 - 98 253 0e+00
3 g14086.t5 PANTHER PTHR45765 METHIONINE–TRNA LIGASE 1 270 0e+00
2 g14086.t5 Pfam PF09334 tRNA synthetases class I (M) 1 106 0e+00
1 g14086.t5 Pfam PF08264 Anticodon-binding domain of tRNA ligase 127 219 7e-07
4 g14086.t5 SUPERFAMILY SSF52374 Nucleotidylyl transferase 2 94 0e+00
5 g14086.t5 SUPERFAMILY SSF47323 Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 95 254 0e+00

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: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