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.t1 TTS g14086.t1 34523708 34523708
chr_1 g14086 g14086.t1 isoform g14086.t1 34523794 34526379
chr_1 g14086 g14086.t1 exon g14086.t1.exon1 34523794 34523926
chr_1 g14086 g14086.t1 cds g14086.t1.CDS1 34523794 34523926
chr_1 g14086 g14086.t1 exon g14086.t1.exon2 34523986 34526215
chr_1 g14086 g14086.t1 cds g14086.t1.CDS2 34523986 34526215
chr_1 g14086 g14086.t1 exon g14086.t1.exon3 34526277 34526379
chr_1 g14086 g14086.t1 cds g14086.t1.CDS3 34526277 34526379
chr_1 g14086 g14086.t1 TSS g14086.t1 34526497 34526497

Sequences

>g14086.t1 Gene=g14086 Length=2466
ATGATAATTTATACGAATGAATCAAATCCACTTGGTTTAAAGCTCTTGTTGATTAGCAAA
TTTGCTAAGAAAAACGTGGAACTAAAAATAGTTAATTTAAATGATCCGAATGTAAAAGAG
CCAAAACATCTGCCTTGTCTTGAACTAGACAGTGGCAATCAGTTCTTTATGACTGACGCG
GCAGTAAAATATTTGATGCACGGAATCGAACAAGAGTCAATAACTCGCAGTCAATGGCTT
GAATGGTCAACTTCTCGATTAGCTCCAGCATTAGCTCAATTTCTTACAACCGGTCATCGA
GTTGATCCTCATGTCACAGAAACATTAAATTCATTAGTAAAATTACTCGATGACACACTC
GCAAAATCTGCTTACTTGACAGGCGATAAAATTGCATCAGCTGATCTTGCAGTTTGGTGT
CTTCTTACACCGGATGGAACATTAAAGGGTTCGCATGATATAAACAATGTTATGAGATGG
TACAAAACAATTGCTGAAATGCCAGAAGTAAAAGAATCATTGAAAATATTTGGACCAGTT
AAAAATATTCATTTTGCATCACTTTTGCAATGTAACCGCTTTGGTGGATTGCATCATGTT
GAAATGCGCCCACATATTGCTGAAATTGAGACAAAAGTTCTCGCGGAGACACCAACTACT
CTTGCTGAAACAGTTTTGCCCAATGAAATTGAAGATGCTAAACAATTCTTTGTATATGTG
GCACCAGAAAAAAGGGTTGAAGCAAAAACAGTTCTACCTAAACCAAATGAACGCAATATT
CTTATCACATCTGCTCTTCCTTATGTTAACAATGTTCCACACTTGGGTAACATTATCGGT
TGTGTTTTATCTGCAGATATTTTTGCAAGATATTCACGCATGTGTGGCTATAATACACTT
TATGTTTGCGGTACTGATGAATATGGAACTGCCACAGAGACAAAAGCAATTGCTGAGAAT
CTAACATGTAAGCAAATTTGTGACAAATATTTTGAAATGCACAATTCAATTTATCGTTGG
TTTGGAATTGGATTTGATTATTTTGGTCGAACAACAACAAATGAGCAAACTGAAATTGTT
CAAGAACTTTTCTTAGATCTTCATAAACAAAATTTAATTGAAACTCAAGCTGTCGAACAG
TTACTGTGTCAAAAGTGCGATAGATTTCTTGCAGATAGATTTGTCGAAGGAACTTGTCCA
CATCCAGGCTGTAATTATGAAGACGCTAGAGGTGATCAATGTGACAATTGTGGAAAATTA
ATAAATGCTGTTGAACTTATTCGTCCACGATGTAAATTGTGTAGCACAGCGCCAGTTGTT
CGCGAGTCAAATCAATTGTTCCTTAATTTACCAAAAATCGAGTCAAAACTTCGAAATTGG
ATTGATTCAGTTGATAGTTTGTGGACAAATAATGCTCGAACAATTACAAAATCATGGCTT
AAAGAAGGTTTAAAAACAAGATGCATTACGAGAGATCTAAAATGGGGTATCCCAGTTCCA
TTAAAAGGTTTCGAGAGCAAAGTATTTTATGTGTGGTTTGATGCACCAATTGGTTATATT
TCAATCACTAGCAAATATACAAAAGAATGGCGAAAATGGTGGCAACCAGCAGATCCATCA
ACAAAGGTTGAACTATTTCAATTTATGGCAAAGGACAATGTACCTTTCCATTCAGTCATG
TTCCCAGCGACACTTATTGGCGTTAATAAAGGCTACACTCTCGTTTCACGTATCCTTTCG
ATTGAATATTTGAACTATGAGGATGGAAAATTCAGTAAAAGTCGTGGAATTGGAGTTTTT
GGAAATGATGCACAAGATACTGGTATCGAATCTGATATTTGGCGTTTCTATCTCGCCTCA
GCACGACCAGAAGGTCAAGATTCTAGCTTCAGTTGGAGTGAATTGGCTTCTAGAAATAAT
TCTGAATTGCTCAACAACCTGGGTAATTTCATTAATCGTGCTTTAGTGTTCTGTGAGAAG
AACTTCAATTCAACTATTTCGAATATTACATTGAACCATGATGATGCTGTTTTATTAGCT
GTTATTAACAGAGAAATTAGAGAGTATGTTAATTCCATGGAAAAAACAAGATTCCGTGAT
GGTATTCGTCACATTTTGGCGATTTCAAGACAAGGAAACTTATACATGCAGAATGAGAAG
CCATGGGTCCTTCTTAAAGGAACTGCCGAACAAAAAACAAGAGCTCATAGTGTTATCAGT
TTAAGTTGTAACATTGCATGTTTGTTAGCTAATCTTCTCTATCCGTTTATGCCAGCAACA
TCAAGAAAGATTTTCACACAACTCAACTTTGCAGGCGGTGCAATTAATCCAACGAAACCA
CATTTGACAGTTCTTCTTCAAACTGGACATCAAATTGGAAAACCATCTCCACTGTTTGCT
AAAATTGACCAGGCTACTGTTGATCAATTGAAAGCCAAGTACTCAGGTGTTCAAGTTACA
GCTTAA

>g14086.t1 Gene=g14086 Length=821
MIIYTNESNPLGLKLLLISKFAKKNVELKIVNLNDPNVKEPKHLPCLELDSGNQFFMTDA
AVKYLMHGIEQESITRSQWLEWSTSRLAPALAQFLTTGHRVDPHVTETLNSLVKLLDDTL
AKSAYLTGDKIASADLAVWCLLTPDGTLKGSHDINNVMRWYKTIAEMPEVKESLKIFGPV
KNIHFASLLQCNRFGGLHHVEMRPHIAEIETKVLAETPTTLAETVLPNEIEDAKQFFVYV
APEKRVEAKTVLPKPNERNILITSALPYVNNVPHLGNIIGCVLSADIFARYSRMCGYNTL
YVCGTDEYGTATETKAIAENLTCKQICDKYFEMHNSIYRWFGIGFDYFGRTTTNEQTEIV
QELFLDLHKQNLIETQAVEQLLCQKCDRFLADRFVEGTCPHPGCNYEDARGDQCDNCGKL
INAVELIRPRCKLCSTAPVVRESNQLFLNLPKIESKLRNWIDSVDSLWTNNARTITKSWL
KEGLKTRCITRDLKWGIPVPLKGFESKVFYVWFDAPIGYISITSKYTKEWRKWWQPADPS
TKVELFQFMAKDNVPFHSVMFPATLIGVNKGYTLVSRILSIEYLNYEDGKFSKSRGIGVF
GNDAQDTGIESDIWRFYLASARPEGQDSSFSWSELASRNNSELLNNLGNFINRALVFCEK
NFNSTISNITLNHDDAVLLAVINREIREYVNSMEKTRFRDGIRHILAISRQGNLYMQNEK
PWVLLKGTAEQKTRAHSVISLSCNIACLLANLLYPFMPATSRKIFTQLNFAGGAINPTKP
HLTVLLQTGHQIGKPSPLFAKIDQATVDQLKAKYSGVQVTA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
26 g14086.t1 CDD cd00814 MetRS_core 259 630 7.2672E-156
25 g14086.t1 CDD cd07957 Anticodon_Ia_Met 639 768 2.58135E-42
21 g14086.t1 Gene3D G3DSA:3.40.30.10 Glutaredoxin 1 177 1.0E-26
17 g14086.t1 Gene3D G3DSA:1.20.1050.10 - 69 167 1.0E-26
18 g14086.t1 Gene3D G3DSA:3.40.50.620 HUPs 260 637 1.7E-161
19 g14086.t1 Gene3D G3DSA:2.20.28.20 - 395 431 1.7E-161
20 g14086.t1 Gene3D G3DSA:1.10.730.10 - 638 807 1.6E-44
6 g14086.t1 Hamap MF_00098 Methionine–tRNA ligase [metG]. 258 813 36.062954
5 g14086.t1 PANTHER PTHR45765 METHIONINE–TRNA LIGASE 249 818 4.0E-275
7 g14086.t1 PRINTS PR01041 Methionyl-tRNA synthetase signature 262 275 2.2E-30
12 g14086.t1 PRINTS PR01041 Methionyl-tRNA synthetase signature 295 309 2.2E-30
9 g14086.t1 PRINTS PR01041 Methionyl-tRNA synthetase signature 343 354 2.2E-30
11 g14086.t1 PRINTS PR01041 Methionyl-tRNA synthetase signature 509 520 2.2E-30
8 g14086.t1 PRINTS PR01041 Methionyl-tRNA synthetase signature 547 562 2.2E-30
10 g14086.t1 PRINTS PR01041 Methionyl-tRNA synthetase signature 642 653 2.2E-30
1 g14086.t1 Pfam PF18485 Glutathione S-transferase, N-terminal domain 1 66 1.7E-11
3 g14086.t1 Pfam PF14497 Glutathione S-transferase, C-terminal domain 102 172 4.7E-6
4 g14086.t1 Pfam PF09334 tRNA synthetases class I (M) 260 654 1.1E-149
2 g14086.t1 Pfam PF08264 Anticodon-binding domain of tRNA ligase 675 767 4.7E-6
23 g14086.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 734 -
24 g14086.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 735 754 -
22 g14086.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 755 821 -
27 g14086.t1 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature. 267 278 -
29 g14086.t1 ProSiteProfiles PS50405 Soluble glutathione S-transferase C-terminal domain profile. 69 194 10.99
15 g14086.t1 SUPERFAMILY SSF47616 GST C-terminal domain-like 77 178 2.23E-13
14 g14086.t1 SUPERFAMILY SSF52374 Nucleotidylyl transferase 258 642 1.16E-95
13 g14086.t1 SUPERFAMILY SSF57770 Methionyl-tRNA synthetase (MetRS), Zn-domain 395 431 1.96E-9
16 g14086.t1 SUPERFAMILY SSF47323 Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 643 802 2.43E-37
28 g14086.t1 TIGRFAM TIGR00398 metG: methionine–tRNA ligase 260 803 2.3E-168

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

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.

Raw TPM values