General information for g1890.t2
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.t2 | isoform | g1890.t2 | 13710020 | 13711125 |
| chr_3 | g1890 | g1890.t2 | exon | g1890.t2.exon1 | 13710020 | 13710101 |
| chr_3 | g1890 | g1890.t2 | cds | g1890.t2.CDS1 | 13710020 | 13710101 |
| chr_3 | g1890 | g1890.t2 | exon | g1890.t2.exon2 | 13710160 | 13711125 |
| chr_3 | g1890 | g1890.t2 | cds | g1890.t2.CDS2 | 13710160 | 13711124 |
| chr_3 | g1890 | g1890.t2 | TTS | g1890.t2 | 13712015 | 13712015 |
| chr_3 | g1890 | g1890.t2 | TSS | g1890.t2 | NA | NA |
Sequences
>g1890.t2 Gene=g1890 Length=1048
ATGAATAAGATAATATTTAGAAAATTTTCAAATTTATCAAATGGATTCTTTATAACAACT
CCAATCTATTATGTTAACGCATCGCCTCATTTGGGACATTTATATACTTCTTTGATTGCC
GACACTATAAATCGGTTTGAAAAATTAACTGCAACACATAGTGATTATATATTTAGCACT
GGAACTGATGAACATGGTGAAAAGGTTTTACGAGCTGCAAAGCAAAATAATTCATCAGTT
ACTGAATATTGCAAAAATATTTCAGAGAAATACAAAAGTTTATTTAGAAAATGCGATATT
GAATTTACTGATTATGTGAGAACCACAGAAGACCGTCATTCAAAAGCAGTTACTTCATTT
TGGAGTACTTTAGTGAATAATAAAGCAATTTATAAAGCAGATTATTCTGGTTGGTATTGT
GTTCCTGATGAAACATTTTTGACTGAATCACAGCTGATTACTGACAATTCAGGCAAGAAA
TTTTCACTCGAAAGTGGTCATCCGGTTGAGTGGACAAGTGAAGAAAATTATATGTTCAAA
TTAAGCAAATATCAAGATGAAATAATTTATTGGGCGAGACAAGACAATCGTGTTATTCCA
ACAAAATTTAATAAAATCCTTCTTGATATGCTTTATCAAGAAATACTGCCAGACCTCTCA
GTTTCAAGACCATCAACCAGAATGTCTTGGGGTATATCGGTGCCTAATGATGATTCACAA
AACATATATGTTTGGCTCGACGCACTCGTCAACTATTTGACAGTTGCTGGTTATCCTGAT
CAATTGCGTTTGTGGCCTCCAAATGTGCAAGTTATAGGAAAAGATATTTTAAAATTTCAT
GGGATATATTGGCCTGCATTTCTTATAGCTGCAAATATCAATTCATTACCTGAACAGCTC
TTAGTACATTCGCATTGGACTGTTGAAGGGCAAAAGATGTCAAAGAGTAAAATGAATGTA
ATTGATCCAAATGAAAGAGCAAGTTTATATACAATGGAGGGTATTCGATACTTTTTACTT
CGCGAAGGAACTTTTCATAACGATGGAA
>g1890.t2 Gene=g1890 Length=349
MNKIIFRKFSNLSNGFFITTPIYYVNASPHLGHLYTSLIADTINRFEKLTATHSDYIFST
GTDEHGEKVLRAAKQNNSSVTEYCKNISEKYKSLFRKCDIEFTDYVRTTEDRHSKAVTSF
WSTLVNNKAIYKADYSGWYCVPDETFLTESQLITDNSGKKFSLESGHPVEWTSEENYMFK
LSKYQDEIIYWARQDNRVIPTKFNKILLDMLYQEILPDLSVSRPSTRMSWGISVPNDDSQ
NIYVWLDALVNYLTVAGYPDQLRLWPPNVQVIGKDILKFHGIYWPAFLIAANINSLPEQL
LVHSHWTVEGQKMSKSKMNVIDPNERASLYTMEGIRYFLLREGTFHNDG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g1890.t2 | CDD | cd00814 | MetRS_core | 16 | 349 | 0 |
| 10 | g1890.t2 | Gene3D | G3DSA:3.40.50.620 | HUPs | 16 | 348 | 0 |
| 9 | g1890.t2 | Gene3D | G3DSA:2.170.220.10 | - | 129 | 244 | 0 |
| 2 | g1890.t2 | PANTHER | PTHR43326 | METHIONYL-TRNA SYNTHETASE | 13 | 349 | 0 |
| 5 | g1890.t2 | PRINTS | PR01041 | Methionyl-tRNA synthetase signature | 18 | 31 | 0 |
| 4 | g1890.t2 | PRINTS | PR01041 | Methionyl-tRNA synthetase signature | 52 | 66 | 0 |
| 7 | g1890.t2 | PRINTS | PR01041 | Methionyl-tRNA synthetase signature | 100 | 111 | 0 |
| 6 | g1890.t2 | PRINTS | PR01041 | Methionyl-tRNA synthetase signature | 242 | 253 | 0 |
| 3 | g1890.t2 | PRINTS | PR01041 | Methionyl-tRNA synthetase signature | 270 | 285 | 0 |
| 1 | g1890.t2 | Pfam | PF09334 | tRNA synthetases class I (M) | 17 | 348 | 0 |
| 8 | g1890.t2 | SUPERFAMILY | SSF52374 | Nucleotidylyl transferase | 15 | 348 | 0 |
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. There were no conditions that were differentially expressed