General information for g11187.t8
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Tryptophan–tRNA ligase, mitochondrial.
Parent gene
- The parent gene g11187 is located on chr_1: 14481402..14482827 (- 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_1 | g11187 | g11187.t8 | isoform | g11187.t8 | 14480705 | 14482016 |
| chr_1 | g11187 | g11187.t8 | exon | g11187.t8.exon1 | 14480705 | 14481011 |
| chr_1 | g11187 | g11187.t8 | TTS | g11187.t8 | 14480735 | 14480735 |
| chr_1 | g11187 | g11187.t8 | cds | g11187.t8.CDS1 | 14480783 | 14481011 |
| chr_1 | g11187 | g11187.t8 | exon | g11187.t8.exon2 | 14481073 | 14481877 |
| chr_1 | g11187 | g11187.t8 | cds | g11187.t8.CDS2 | 14481073 | 14481877 |
| chr_1 | g11187 | g11187.t8 | exon | g11187.t8.exon3 | 14481947 | 14482016 |
| chr_1 | g11187 | g11187.t8 | cds | g11187.t8.CDS3 | 14481947 | 14482016 |
| chr_1 | g11187 | g11187.t8 | TSS | g11187.t8 | 14482053 | 14482053 |
Sequences
>g11187.t8 Gene=g11187 Length=1182
ATGTTAAGCACGAGATTTTTAAAAGATCCATTTAAGGAAATTGTGAGAAAGTTCAGTAAT
TCAACTGTGATGAAAAAAGTATTTTCGGGAATACAGCCAACTGGAAATTTACATTTAGGC
AATTATTTCGGTGCTGTCAAGCGATGGATTGATTTACAAAATAGCAATTATGATGTTACT
TATTGTATTGTTGATTTACATTCAATAACTCTTCCACAAAAACCCTTAGAATTAAAAGAA
AATATTCTTAGAATTTGTGCAACTCTCTTAGCTTGTGGTATTGATCCACAAAAATCTACT
CTATTTCTTCAATCGTCTGTTAGAGAGCACTCAGAATTATGCTGGATTTTGAGTTGCAAT
ACTACAATGGCTCGCTTAACACATCTTCCACAATATAAAGAAAAATCAGAAAAAATGAAA
GAAATTCCACTTGGTCTCTATCTCTATCCTGTTTTACAAGCAGCTGATATTATGCTGCAT
AAAGCTAATTTGGTTCCTGTTGGTGAAGATCAAATACAGCATATCCAACTCGCTCAGAGT
TTGACAAAAAATTTCAATCATAGATTTGGTCCAACTTTTCCAACATGTGAACCAATGATC
TCTGAAGATTTAAGTAGTCGAATAAAATCACTGCGTGATCCTACTAAGAAAATGTCAAAA
TCAGATCCTGATCCAAAGAGTTGTGTTATGCTAACAGATTCGCCCGATCAGATAACATCA
AAAATTAAGAAGGCTGTCACAGACTTTACTTCCGCAGTCACATTTGACCCACAAAATCGT
CAAGGTGTTGCAAATTTGCTAACAATTCATTCACTTGCTAGCAATAAGAGTATAGAGCAA
ATTTGTGATGAATCACAAAGATTAGATACTGGACAATATAAATTTAAAGTAGCTGAGGCA
ATAATTGAACATTTTAATCCAATTAGACTAAAGATTGATGATTATCTTAAAAATCCTGAT
TATTTATGGAGTATTCTTGACATAGGAAATGAAAAAGCACAAGAAGTTGCTGAGAAAACA
ATGAATGAAGTAAAAGCACGAGTGGGATTGGGAAATTATGATATGTCGCAATACATCAAA
AATAAAGTGCAAACGAGAATATAATAGAGAAAATATTGACTTAATAAAGAGAAAAGAGAT
AACGAAACCTTTCAAAAATTAGTAAAGTTAAAAAATGAGAAA
>g11187.t8 Gene=g11187 Length=367
MLSTRFLKDPFKEIVRKFSNSTVMKKVFSGIQPTGNLHLGNYFGAVKRWIDLQNSNYDVT
YCIVDLHSITLPQKPLELKENILRICATLLACGIDPQKSTLFLQSSVREHSELCWILSCN
TTMARLTHLPQYKEKSEKMKEIPLGLYLYPVLQAADIMLHKANLVPVGEDQIQHIQLAQS
LTKNFNHRFGPTFPTCEPMISEDLSSRIKSLRDPTKKMSKSDPDPKSCVMLTDSPDQITS
KIKKAVTDFTSAVTFDPQNRQGVANLLTIHSLASNKSIEQICDESQRLDTGQYKFKVAEA
IIEHFNPIRLKIDDYLKNPDYLWSILDIGNEKAQEVAEKTMNEVKARVGLGNYDMSQYIK
NKVQTRI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g11187.t8 | CDD | cd00806 | TrpRS_core | 27 | 304 | 1.01686E-122 |
| 11 | g11187.t8 | Gene3D | G3DSA:3.40.50.620 | HUPs | 27 | 349 | 4.9E-131 |
| 10 | g11187.t8 | Gene3D | G3DSA:1.10.240.10 | - | 208 | 318 | 4.9E-131 |
| 4 | g11187.t8 | Hamap | MF_00140_B | Tryptophan–tRNA ligase [trpS]. | 24 | 351 | 36.859161 |
| 2 | g11187.t8 | PANTHER | PTHR43766:SF1 | TRYPTOPHAN–TRNA LIGASE, MITOCHONDRIAL | 21 | 350 | 1.5E-135 |
| 3 | g11187.t8 | PANTHER | PTHR43766 | TRYPTOPHAN–TRNA LIGASE, MITOCHONDRIAL | 21 | 350 | 1.5E-135 |
| 8 | g11187.t8 | PRINTS | PR01039 | Tryptophanyl-tRNA synthetase signature | 37 | 53 | 7.0E-26 |
| 5 | g11187.t8 | PRINTS | PR01039 | Tryptophanyl-tRNA synthetase signature | 88 | 107 | 7.0E-26 |
| 7 | g11187.t8 | PRINTS | PR01039 | Tryptophanyl-tRNA synthetase signature | 163 | 184 | 7.0E-26 |
| 6 | g11187.t8 | PRINTS | PR01039 | Tryptophanyl-tRNA synthetase signature | 217 | 227 | 7.0E-26 |
| 1 | g11187.t8 | Pfam | PF00579 | tRNA synthetases class I (W and Y) | 26 | 305 | 3.0E-70 |
| 13 | g11187.t8 | ProSitePatterns | PS00178 | Aminoacyl-transfer RNA synthetases class-I signature. | 33 | 42 | - |
| 9 | g11187.t8 | SUPERFAMILY | SSF52374 | Nucleotidylyl transferase | 25 | 350 | 1.17E-90 |
| 14 | g11187.t8 | TIGRFAM | TIGR00233 | trpS: tryptophan–tRNA ligase | 25 | 350 | 1.3E-92 |
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:0004830 | tryptophan-tRNA ligase activity | MF |
| GO:0005524 | ATP binding | MF |
| GO:0006436 | tryptophanyl-tRNA aminoacylation | BP |
| GO:0006418 | tRNA aminoacylation for protein translation | BP |
| GO:0000166 | nucleotide binding | MF |
| GO:0004812 | aminoacyl-tRNA ligase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K01867 (tryptophanyl-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.
