General information for g1890.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Methionine–tRNA ligase, mitochondrial.
Parent gene
- The parent gene g1890 is located on chr_3: 13710020..13712075 (+ strand)
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.t4 | isoform | g1890.t4 | 13710020 | 13712075 |
| chr_3 | g1890 | g1890.t4 | exon | g1890.t4.exon1 | 13710020 | 13711125 |
| chr_3 | g1890 | g1890.t4 | cds | g1890.t4.CDS1 | 13710141 | 13711125 |
| chr_3 | g1890 | g1890.t4 | exon | g1890.t4.exon2 | 13711181 | 13712075 |
| chr_3 | g1890 | g1890.t4 | cds | g1890.t4.CDS2 | 13711181 | 13711749 |
| chr_3 | g1890 | g1890.t4 | TSS | g1890.t4 | NA | NA |
| chr_3 | g1890 | g1890.t4 | TTS | g1890.t4 | NA | NA |
Sequences
>g1890.t4 Gene=g1890 Length=2001
ATGAATAAGATAATATTTAGAAAATTTTCAAATTTATCAAATGGATTCTTTATAACAACT
CCAATCTATTATGTTAACGCATGTGAGTTAACTTATATAATTATTAAAATACAATATTTG
TATGGTTTATTTCGTTTTAGCGCCTCATTTGGGACATTTATATACTTCTTTGATTGCCGA
CACTATAAATCGGTTTGAAAAATTAACTGCAACACATAGTGATTATATATTTAGCACTGG
AACTGATGAACATGGTGAAAAGGTTTTACGAGCTGCAAAGCAAAATAATTCATCAGTTAC
TGAATATTGCAAAAATATTTCAGAGAAATACAAAAGTTTATTTAGAAAATGCGATATTGA
ATTTACTGATTATGTGAGAACCACAGAAGACCGTCATTCAAAAGCAGTTACTTCATTTTG
GAGTACTTTAGTGAATAATAAAGCAATTTATAAAGCAGATTATTCTGGTTGGTATTGTGT
TCCTGATGAAACATTTTTGACTGAATCACAGCTGATTACTGACAATTCAGGCAAGAAATT
TTCACTCGAAAGTGGTCATCCGGTTGAGTGGACAAGTGAAGAAAATTATATGTTCAAATT
AAGCAAATATCAAGATGAAATAATTTATTGGGCGAGACAAGACAATCGTGTTATTCCAAC
AAAATTTAATAAAATCCTTCTTGATATGCTTTATCAAGAAATACTGCCAGACCTCTCAGT
TTCAAGACCATCAACCAGAATGTCTTGGGGTATATCGGTGCCTAATGATGATTCACAAAA
CATATATGTTTGGCTCGACGCACTCGTCAACTATTTGACAGTTGCTGGTTATCCTGATCA
ATTGCGTTTGTGGCCTCCAAATGTGCAAGTTATAGGAAAAGATATTTTAAAATTTCATGG
GATATATTGGCCTGCATTTCTTATAGCTGCAAATATCAATTCATTACCTGAACAGCTCTT
AGTACATTCGCATTGGACTGTTGAAGGGCAAAAGATGTCAAAGAGTAAAATGAATGTAAT
TGATCCAAATGAAAGAGCAAGTTTATATACAATGGAGGGTATTCGATACTTTTTACTTCG
CGAAGGAACTTTTCATAACGATGGAAATTATAGTGACACAAAAATAACAAGAATACTAAA
TTCAGAGCTTGCAGATACGATGGGAAATCTTTTATCGAGAGCATGTGCAAAGTCATTAAA
TCCAAAACAACAGTTTCCACAAGTGCATCAAGATCAATTAAGTGAGCTTATCAAATTAGA
TTCATGTAAAATGCTCTTTGAAAAATTATCTGAAATGCCTGATAAATGCCGTCAACATTA
TACTGAATATAATTTTCATTTTGTCGTTGATACGATTATGTCCACATTACATGCAGCAAA
TGGATTTTTCGAAACAACAAAACCGTGGCTGCTCAAAAACAGTGTCGACAAATCACAACA
AAAAAGACTAGAGACGATAATTGCTATAACTTTCGAGTGTCTTCGAATATGTGGAATTGC
ACTGCAACCAATTGTTCCCAGTTACAGTAAAAATCTCTTAGATCGTTTGAATGTTTCAAA
TGAGTTGAGATTTTGGAAAGACACTAAACTAAGTCTTTCTAAAGTATCTAAGCCATTAGT
AGACTTAGGATCAAATGTCTTATTTAAAAGAATTTTGACAAGCGAGAAAAAATAATATAA
TAAATAGACAAATGCTATAGCAATACACATCACTGGTCTTAACGGATTTTAAAAATTCAA
AAAATTTCAAAACAACTAAATTCTCTGAAAAATTCCAAAATTCTTTTTATTAAAAATTAT
TAAATTTACCTCATAATAAGATTACATTTCTATTTAAAAACAACTTGAGAATTGATAAAG
TGTCATAGTTTTGTACAACAGTGAAATTTAATAAAAGTAAGTCTTTCTTAATCAAATAAG
GTGAAATTCACCTTTGACACAAAGAATTTCAAAATTTTCTTAAATCTTACAGAATTAAGA
TTAGACTCTGGATGCCGATAA
>g1890.t4 Gene=g1890 Length=517
MVYFVLAPHLGHLYTSLIADTINRFEKLTATHSDYIFSTGTDEHGEKVLRAAKQNNSSVT
EYCKNISEKYKSLFRKCDIEFTDYVRTTEDRHSKAVTSFWSTLVNNKAIYKADYSGWYCV
PDETFLTESQLITDNSGKKFSLESGHPVEWTSEENYMFKLSKYQDEIIYWARQDNRVIPT
KFNKILLDMLYQEILPDLSVSRPSTRMSWGISVPNDDSQNIYVWLDALVNYLTVAGYPDQ
LRLWPPNVQVIGKDILKFHGIYWPAFLIAANINSLPEQLLVHSHWTVEGQKMSKSKMNVI
DPNERASLYTMEGIRYFLLREGTFHNDGNYSDTKITRILNSELADTMGNLLSRACAKSLN
PKQQFPQVHQDQLSELIKLDSCKMLFEKLSEMPDKCRQHYTEYNFHFVVDTIMSTLHAAN
GFFETTKPWLLKNSVDKSQQKRLETIIAITFECLRICGIALQPIVPSYSKNLLDRLNVSN
ELRFWKDTKLSLSKVSKPLVDLGSNVLFKRILTSEKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g1890.t4 | CDD | cd00814 | MetRS_core | 7 | 330 | 0e+00 |
| 12 | g1890.t4 | Gene3D | G3DSA:3.40.50.620 | HUPs | 3 | 327 | 0e+00 |
| 11 | g1890.t4 | Gene3D | G3DSA:2.170.220.10 | - | 108 | 223 | 0e+00 |
| 13 | g1890.t4 | Gene3D | G3DSA:1.10.730.10 | - | 331 | 517 | 0e+00 |
| 3 | g1890.t4 | PANTHER | PTHR43326 | METHIONYL-TRNA SYNTHETASE | 3 | 514 | 0e+00 |
| 5 | g1890.t4 | PRINTS | PR01041 | Methionyl-tRNA synthetase signature | 31 | 45 | 0e+00 |
| 7 | g1890.t4 | PRINTS | PR01041 | Methionyl-tRNA synthetase signature | 79 | 90 | 0e+00 |
| 6 | g1890.t4 | PRINTS | PR01041 | Methionyl-tRNA synthetase signature | 221 | 232 | 0e+00 |
| 8 | g1890.t4 | PRINTS | PR01041 | Methionyl-tRNA synthetase signature | 249 | 264 | 0e+00 |
| 4 | g1890.t4 | PRINTS | PR01041 | Methionyl-tRNA synthetase signature | 342 | 353 | 0e+00 |
| 2 | g1890.t4 | Pfam | PF09334 | tRNA synthetases class I (M) | 3 | 354 | 0e+00 |
| 1 | g1890.t4 | Pfam | PF08264 | Anticodon-binding domain of tRNA ligase | 386 | 476 | 2e-07 |
| 9 | g1890.t4 | SUPERFAMILY | SSF52374 | Nucleotidylyl transferase | 8 | 341 | 0e+00 |
| 10 | g1890.t4 | SUPERFAMILY | SSF47323 | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 343 | 511 | 0e+00 |
| 14 | g1890.t4 | TIGRFAM | TIGR00398 | metG: methionine–tRNA ligase | 3 | 487 | 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
- This transcript has been annotated with K01874 (methionyl-tRNA synthetase)
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.
