Gene loci information

Transcript annotation

  • This transcript has been annotated as Methionine–tRNA ligase, mitochondrial.

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_3 g1890 g1890.t1 isoform g1890.t1 13710020 13712075
chr_3 g1890 g1890.t1 exon g1890.t1.exon1 13710020 13710101
chr_3 g1890 g1890.t1 cds g1890.t1.CDS1 13710020 13710101
chr_3 g1890 g1890.t1 exon g1890.t1.exon2 13710160 13711125
chr_3 g1890 g1890.t1 cds g1890.t1.CDS2 13710160 13711125
chr_3 g1890 g1890.t1 exon g1890.t1.exon3 13711181 13711600
chr_3 g1890 g1890.t1 cds g1890.t1.CDS3 13711181 13711600
chr_3 g1890 g1890.t1 exon g1890.t1.exon4 13711956 13711970
chr_3 g1890 g1890.t1 cds g1890.t1.CDS4 13711956 13711970
chr_3 g1890 g1890.t1 exon g1890.t1.exon5 13712047 13712075
chr_3 g1890 g1890.t1 cds g1890.t1.CDS5 13712047 13712075
chr_3 g1890 g1890.t1 TSS g1890.t1 NA NA
chr_3 g1890 g1890.t1 TTS g1890.t1 NA NA

Sequences

>g1890.t1 Gene=g1890 Length=1512
ATGAATAAGATAATATTTAGAAAATTTTCAAATTTATCAAATGGATTCTTTATAACAACT
CCAATCTATTATGTTAACGCATCGCCTCATTTGGGACATTTATATACTTCTTTGATTGCC
GACACTATAAATCGGTTTGAAAAATTAACTGCAACACATAGTGATTATATATTTAGCACT
GGAACTGATGAACATGGTGAAAAGGTTTTACGAGCTGCAAAGCAAAATAATTCATCAGTT
ACTGAATATTGCAAAAATATTTCAGAGAAATACAAAAGTTTATTTAGAAAATGCGATATT
GAATTTACTGATTATGTGAGAACCACAGAAGACCGTCATTCAAAAGCAGTTACTTCATTT
TGGAGTACTTTAGTGAATAATAAAGCAATTTATAAAGCAGATTATTCTGGTTGGTATTGT
GTTCCTGATGAAACATTTTTGACTGAATCACAGCTGATTACTGACAATTCAGGCAAGAAA
TTTTCACTCGAAAGTGGTCATCCGGTTGAGTGGACAAGTGAAGAAAATTATATGTTCAAA
TTAAGCAAATATCAAGATGAAATAATTTATTGGGCGAGACAAGACAATCGTGTTATTCCA
ACAAAATTTAATAAAATCCTTCTTGATATGCTTTATCAAGAAATACTGCCAGACCTCTCA
GTTTCAAGACCATCAACCAGAATGTCTTGGGGTATATCGGTGCCTAATGATGATTCACAA
AACATATATGTTTGGCTCGACGCACTCGTCAACTATTTGACAGTTGCTGGTTATCCTGAT
CAATTGCGTTTGTGGCCTCCAAATGTGCAAGTTATAGGAAAAGATATTTTAAAATTTCAT
GGGATATATTGGCCTGCATTTCTTATAGCTGCAAATATCAATTCATTACCTGAACAGCTC
TTAGTACATTCGCATTGGACTGTTGAAGGGCAAAAGATGTCAAAGAGTAAAATGAATGTA
ATTGATCCAAATGAAAGAGCAAGTTTATATACAATGGAGGGTATTCGATACTTTTTACTT
CGCGAAGGAACTTTTCATAACGATGGAAATTATAGTGACACAAAAATAACAAGAATACTA
AATTCAGAGCTTGCAGATACGATGGGAAATCTTTTATCGAGAGCATGTGCAAAGTCATTA
AATCCAAAACAACAGTTTCCACAAGTGCATCAAGATCAATTAAGTGAGCTTATCAAATTA
GATTCATGTAAAATGCTCTTTGAAAAATTATCTGAAATGCCTGATAAATGCCGTCAACAT
TATACTGAATATAATTTTCATTTTGTCGTTGATACGATTATGTCCACATTACATGCAGCA
AATGGATTTTTCGAAACAACAAAACCGTGGCTGCTCAAAAACAGTGTCGACAAATCACAA
CAAAAAAGACTAGAGACGATAATTGCTATAACTTTCGAGTGTCTTCGAATATGTGGAATT
GCACTGCAACCAATTGTTCCCAGTTACATGAAATTTAATAAAAAATTAAGATTAGACTCT
GGATGCCGATAA

>g1890.t1 Gene=g1890 Length=503
MNKIIFRKFSNLSNGFFITTPIYYVNASPHLGHLYTSLIADTINRFEKLTATHSDYIFST
GTDEHGEKVLRAAKQNNSSVTEYCKNISEKYKSLFRKCDIEFTDYVRTTEDRHSKAVTSF
WSTLVNNKAIYKADYSGWYCVPDETFLTESQLITDNSGKKFSLESGHPVEWTSEENYMFK
LSKYQDEIIYWARQDNRVIPTKFNKILLDMLYQEILPDLSVSRPSTRMSWGISVPNDDSQ
NIYVWLDALVNYLTVAGYPDQLRLWPPNVQVIGKDILKFHGIYWPAFLIAANINSLPEQL
LVHSHWTVEGQKMSKSKMNVIDPNERASLYTMEGIRYFLLREGTFHNDGNYSDTKITRIL
NSELADTMGNLLSRACAKSLNPKQQFPQVHQDQLSELIKLDSCKMLFEKLSEMPDKCRQH
YTEYNFHFVVDTIMSTLHAANGFFETTKPWLLKNSVDKSQQKRLETIIAITFECLRICGI
ALQPIVPSYMKFNKKLRLDSGCR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g1890.t1 CDD cd00814 MetRS_core 16 351 0.0e+00
13 g1890.t1 Gene3D G3DSA:3.40.50.620 HUPs 16 348 0.0e+00
12 g1890.t1 Gene3D G3DSA:2.170.220.10 - 129 244 0.0e+00
14 g1890.t1 Gene3D G3DSA:1.10.730.10 - 352 501 0.0e+00
3 g1890.t1 PANTHER PTHR43326 METHIONYL-TRNA SYNTHETASE 13 491 0.0e+00
6 g1890.t1 PRINTS PR01041 Methionyl-tRNA synthetase signature 18 31 0.0e+00
5 g1890.t1 PRINTS PR01041 Methionyl-tRNA synthetase signature 52 66 0.0e+00
8 g1890.t1 PRINTS PR01041 Methionyl-tRNA synthetase signature 100 111 0.0e+00
7 g1890.t1 PRINTS PR01041 Methionyl-tRNA synthetase signature 242 253 0.0e+00
4 g1890.t1 PRINTS PR01041 Methionyl-tRNA synthetase signature 270 285 0.0e+00
9 g1890.t1 PRINTS PR01041 Methionyl-tRNA synthetase signature 363 374 0.0e+00
2 g1890.t1 Pfam PF09334 tRNA synthetases class I (M) 17 375 0.0e+00
1 g1890.t1 Pfam PF08264 Anticodon-binding domain of tRNA ligase 407 488 3.3e-06
10 g1890.t1 SUPERFAMILY SSF52374 Nucleotidylyl transferase 15 362 0.0e+00
11 g1890.t1 SUPERFAMILY SSF47323 Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 369 490 0.0e+00
15 g1890.t1 TIGRFAM TIGR00398 metG: methionine–tRNA ligase 16 491 0.0e+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: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