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.t4 isoform g14086.t4 34518706 34526379
chr_1 g14086 g14086.t4 exon g14086.t4.exon1 34518706 34518843
chr_1 g14086 g14086.t4 cds g14086.t4.CDS1 34518836 34518843
chr_1 g14086 g14086.t4 exon g14086.t4.exon2 34524848 34526215
chr_1 g14086 g14086.t4 cds g14086.t4.CDS2 34524848 34526215
chr_1 g14086 g14086.t4 exon g14086.t4.exon3 34526277 34526379
chr_1 g14086 g14086.t4 cds g14086.t4.CDS3 34526277 34526379
chr_1 g14086 g14086.t4 TSS g14086.t4 34526497 34526497
chr_1 g14086 g14086.t4 TTS g14086.t4 NA NA

Sequences

>g14086.t4 Gene=g14086 Length=1609
ATGATAATTTATACGAATGAATCAAATCCACTTGGTTTAAAGCTCTTGTTGATTAGCAAA
TTTGCTAAGAAAAACGTGGAACTAAAAATAGTTAATTTAAATGATCCGAATGTAAAAGAG
CCAAAACATCTGCCTTGTCTTGAACTAGACAGTGGCAATCAGTTCTTTATGACTGACGCG
GCAGTAAAATATTTGATGCACGGAATCGAACAAGAGTCAATAACTCGCAGTCAATGGCTT
GAATGGTCAACTTCTCGATTAGCTCCAGCATTAGCTCAATTTCTTACAACCGGTCATCGA
GTTGATCCTCATGTCACAGAAACATTAAATTCATTAGTAAAATTACTCGATGACACACTC
GCAAAATCTGCTTACTTGACAGGCGATAAAATTGCATCAGCTGATCTTGCAGTTTGGTGT
CTTCTTACACCGGATGGAACATTAAAGGGTTCGCATGATATAAACAATGTTATGAGATGG
TACAAAACAATTGCTGAAATGCCAGAAGTAAAAGAATCATTGAAAATATTTGGACCAGTT
AAAAATATTCATTTTGCATCACTTTTGCAATGTAACCGCTTTGGTGGATTGCATCATGTT
GAAATGCGCCCACATATTGCTGAAATTGAGACAAAAGTTCTCGCGGAGACACCAACTACT
CTTGCTGAAACAGTTTTGCCCAATGAAATTGAAGATGCTAAACAATTCTTTGTATATGTG
GCACCAGAAAAAAGGGTTGAAGCAAAAACAGTTCTACCTAAACCAAATGAACGCAATATT
CTTATCACATCTGCTCTTCCTTATGTTAACAATGTTCCACACTTGGGTAACATTATCGGT
TGTGTTTTATCTGCAGATATTTTTGCAAGATATTCACGCATGTGTGGCTATAATACACTT
TATGTTTGCGGTACTGATGAATATGGAACTGCCACAGAGACAAAAGCAATTGCTGAGAAT
CTAACATGTAAGCAAATTTGTGACAAATATTTTGAAATGCACAATTCAATTTATCGTTGG
TTTGGAATTGGATTTGATTATTTTGGTCGAACAACAACAAATGAGCAAACTGAAATTGTT
CAAGAACTTTTCTTAGATCTTCATAAACAAAATTTAATTGAAACTCAAGCTGTCGAACAG
TTACTGTGTCAAAAGTGCGATAGATTTCTTGCAGATAGATTTGTCGAAGGAACTTGTCCA
CATCCAGGCTGTAATTATGAAGACGCTAGAGGTGATCAATGTGACAATTGTGGAAAATTA
ATAAATGCTGTTGAACTTATTCGTCCACGATGTAAATTGTGTAGCACAGCGCCAGTTGTT
CGCGAGTCAAATCAATTGTTCCTTAATTTACCAAAAATCGAGTCAAAACTTCGAAATTGG
ATTGATTCAGTTGATAGTTTGTGGACAAATAATGCTCGAACAATTACAAAATCATGGCTT
AAAGAAGGTTTAAAAACAAGATGCATTACGAATCGCTAATAAAACGTTCATTCCATTTGA
TGCAAAACAATAATATTTTGATGGAAAAGAAAAGTAGATATTTAAGAACGTGGCATGATC
ATCAAAATAATGAGAAAAGAGAAATTTATTACTGGCGTCACGAGATAGA

>g14086.t4 Gene=g14086 Length=492
MIIYTNESNPLGLKLLLISKFAKKNVELKIVNLNDPNVKEPKHLPCLELDSGNQFFMTDA
AVKYLMHGIEQESITRSQWLEWSTSRLAPALAQFLTTGHRVDPHVTETLNSLVKLLDDTL
AKSAYLTGDKIASADLAVWCLLTPDGTLKGSHDINNVMRWYKTIAEMPEVKESLKIFGPV
KNIHFASLLQCNRFGGLHHVEMRPHIAEIETKVLAETPTTLAETVLPNEIEDAKQFFVYV
APEKRVEAKTVLPKPNERNILITSALPYVNNVPHLGNIIGCVLSADIFARYSRMCGYNTL
YVCGTDEYGTATETKAIAENLTCKQICDKYFEMHNSIYRWFGIGFDYFGRTTTNEQTEIV
QELFLDLHKQNLIETQAVEQLLCQKCDRFLADRFVEGTCPHPGCNYEDARGDQCDNCGKL
INAVELIRPRCKLCSTAPVVRESNQLFLNLPKIESKLRNWIDSVDSLWTNNARTITKSWL
KEGLKTRCITNR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g14086.t4 Gene3D G3DSA:3.40.30.10 Glutaredoxin 1 177 4.0E-27
13 g14086.t4 Gene3D G3DSA:1.20.1050.10 - 69 167 4.0E-27
14 g14086.t4 Gene3D G3DSA:2.20.28.20 - 396 431 1.0E-10
4 g14086.t4 PANTHER PTHR45765:SF1 METHIONINE–TRNA LIGASE, CYTOPLASMIC 249 491 1.9E-126
5 g14086.t4 PANTHER PTHR45765 METHIONINE–TRNA LIGASE 249 491 1.9E-126
6 g14086.t4 PRINTS PR01041 Methionyl-tRNA synthetase signature 262 275 1.7E-13
8 g14086.t4 PRINTS PR01041 Methionyl-tRNA synthetase signature 295 309 1.7E-13
7 g14086.t4 PRINTS PR01041 Methionyl-tRNA synthetase signature 343 354 1.7E-13
1 g14086.t4 Pfam PF18485 Glutathione S-transferase, N-terminal domain 1 66 8.3E-12
2 g14086.t4 Pfam PF14497 Glutathione S-transferase, C-terminal domain 102 172 2.2E-6
3 g14086.t4 Pfam PF09334 tRNA synthetases class I (M) 260 491 4.7E-83
12 g14086.t4 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature. 267 278 -
16 g14086.t4 ProSiteProfiles PS50405 Soluble glutathione S-transferase C-terminal domain profile. 69 194 10.99
11 g14086.t4 SUPERFAMILY SSF47616 GST C-terminal domain-like 77 178 1.03E-13
10 g14086.t4 SUPERFAMILY SSF52374 Nucleotidylyl transferase 258 490 8.94E-56
9 g14086.t4 SUPERFAMILY SSF57770 Methionyl-tRNA synthetase (MetRS), Zn-domain 395 431 9.81E-10

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:0006431 methionyl-tRNA aminoacylation BP
GO:0004825 methionine-tRNA ligase activity 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