General information for g11187.t1
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.t1 | isoform | g11187.t1 | 14479718 | 14482016 |
| chr_1 | g11187 | g11187.t1 | exon | g11187.t1.exon1 | 14479718 | 14479961 |
| chr_1 | g11187 | g11187.t1 | cds | g11187.t1.CDS1 | 14479718 | 14479961 |
| chr_1 | g11187 | g11187.t1 | exon | g11187.t1.exon2 | 14480016 | 14480572 |
| chr_1 | g11187 | g11187.t1 | cds | g11187.t1.CDS2 | 14480016 | 14480572 |
| chr_1 | g11187 | g11187.t1 | exon | g11187.t1.exon3 | 14480858 | 14481011 |
| chr_1 | g11187 | g11187.t1 | cds | g11187.t1.CDS3 | 14480858 | 14481011 |
| chr_1 | g11187 | g11187.t1 | exon | g11187.t1.exon4 | 14481073 | 14481887 |
| chr_1 | g11187 | g11187.t1 | cds | g11187.t1.CDS4 | 14481073 | 14481887 |
| chr_1 | g11187 | g11187.t1 | exon | g11187.t1.exon5 | 14481951 | 14482016 |
| chr_1 | g11187 | g11187.t1 | cds | g11187.t1.CDS5 | 14481951 | 14482016 |
| chr_1 | g11187 | g11187.t1 | TSS | g11187.t1 | 14482053 | 14482053 |
| chr_1 | g11187 | g11187.t1 | TTS | g11187.t1 | NA | NA |
Sequences
>g11187.t1 Gene=g11187 Length=1836
ATGTTAAGCACGAGATTTTTAAAAGATCCATTTAAGGAAATTGTGAGAAAGTTCAGTAAT
TCAACTAATAAACAAGTGAAAAAAGTATTTTCGGGAATACAGCCAACTGGAAATTTACAT
TTAGGCAATTATTTCGGTGCTGTCAAGCGATGGATTGATTTACAAAATAGCAATTATGAT
GTTACTTATTGTATTGTTGATTTACATTCAATAACTCTTCCACAAAAACCCTTAGAATTA
AAAGAAAATATTCTTAGAATTTGTGCAACTCTCTTAGCTTGTGGTATTGATCCACAAAAA
TCTACTCTATTTCTTCAATCGTCTGTTAGAGAGCACTCAGAATTATGCTGGATTTTGAGT
TGCAATACTACAATGGCTCGCTTAACACATCTTCCACAATATAAAGAAAAATCAGAAAAA
ATGAAAGAAATTCCACTTGGTCTCTATCTCTATCCTGTTTTACAAGCAGCTGATATTATG
CTGCATAAAGCTAATTTGGTTCCTGTTGGTGAAGATCAAATACAGCATATCCAACTCGCT
CAGAGTTTGACAAAAAATTTCAATCATAGATTTGGTCCAACTTTTCCAACATGTGAACCA
ATGATCTCTGAAGATTTAAGTAGTCGAATAAAATCACTGCGTGATCCTACTAAGAAAATG
TCAAAATCAGATCCTGATCCAAAGAGTTGTGTTATGCTAACAGATTCGCCCGATCAGATA
ACATCAAAAATTAAGAAGGCTGTCACAGACTTTACTTCCGCAGTCACATTTGACCCACAA
AATCGTCAAGGTGTTGCAAATTTGCTAACAATTCATTCACTTGCTAGCAATAAGAGTATA
GAGCAAATTTGTGATGAATCACAAAGATTAGATACTGGACAATATAAATTTAAAGTAGCT
GAGGCAATAATTGAACATTTTAATCCAATTAGACTAAAGATTGATGATTATCTTAAAAAT
CCTGATTATTTATGGAGTATTCTTGACATAGGAAATGAAAAAGCACAAGAAGTTGCTGAG
AAAACAATGAATGAAATTATTTTGCTGTTCCTTTTCTTGGGAGGTGGAATTTTTTATGGT
CTAAAAGTATGGCAAGGAACTGCACTTGGATGTCCTGAACCAATTATTCAAGAAGTGAAA
CATCATGATGGAATTATTCCCTATCATTCACACTTTTCTGATATTTCGTATTCTGCACCA
CCACCAGATGCATTTGGCGGTTATAATGGTTTTAGTGGATATAGTGGTGCTGATATAGGC
GGAATTTATTCAAATACACCTGCCTCACCGTCTTTTAATGGTCCAACAGGTTTTAGTAAT
GGAGCAGCAGCAACAGGAAGTGGAGCATCTGTGGGAACAATTGACGCAGGATCAGTTGTA
GGTCCATCAAATACTTATTTACCACCAAGTAGCCGAAGAAGAAGAGTAAGCGGAAATGCT
AGAAGTGATAGCTCAAGCGAATCTATTTCATCCATGTTCACTGATCTCATGTTTCGTTTT
CTTGGAGTGAACACTGATTCATGCAAGAGACGATTCGTTTGTGAGTTAGAATTTAGAAAT
CCATTCGTTGGCTATGCTATGAATTACATTGGAAATGATTTATTTAGTGAATTTAGAATG
GAAAAAAATAGTCCAGAATCACCTAAGAAATTTTCTGATTGCGCTAAATTATATGCCGAT
TGTGAAGTTCCAAAAGAACATACATTCGCCACAAAGAAACGTAGACGTTATTATTTGAAG
AAGAGATTGAATCAAACAACGGTTGAAGAAAAAGAAGAAACTACAATCAACCCAAACAAT
GATTTAGTTACAAAATACGTTAAGAATCAAGAGTAA
>g11187.t1 Gene=g11187 Length=611
MLSTRFLKDPFKEIVRKFSNSTNKQVKKVFSGIQPTGNLHLGNYFGAVKRWIDLQNSNYD
VTYCIVDLHSITLPQKPLELKENILRICATLLACGIDPQKSTLFLQSSVREHSELCWILS
CNTTMARLTHLPQYKEKSEKMKEIPLGLYLYPVLQAADIMLHKANLVPVGEDQIQHIQLA
QSLTKNFNHRFGPTFPTCEPMISEDLSSRIKSLRDPTKKMSKSDPDPKSCVMLTDSPDQI
TSKIKKAVTDFTSAVTFDPQNRQGVANLLTIHSLASNKSIEQICDESQRLDTGQYKFKVA
EAIIEHFNPIRLKIDDYLKNPDYLWSILDIGNEKAQEVAEKTMNEIILLFLFLGGGIFYG
LKVWQGTALGCPEPIIQEVKHHDGIIPYHSHFSDISYSAPPPDAFGGYNGFSGYSGADIG
GIYSNTPASPSFNGPTGFSNGAAATGSGASVGTIDAGSVVGPSNTYLPPSSRRRRVSGNA
RSDSSSESISSMFTDLMFRFLGVNTDSCKRRFVCELEFRNPFVGYAMNYIGNDLFSEFRM
EKNSPESPKKFSDCAKLYADCEVPKEHTFATKKRRRYYLKKRLNQTTVEEKEETTINPNN
DLVTKYVKNQE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g11187.t1 | CDD | cd00806 | TrpRS_core | 29 | 306 | 1.24266E-120 |
| 11 | g11187.t1 | Gene3D | G3DSA:3.40.50.620 | HUPs | 29 | 346 | 2.1E-128 |
| 10 | g11187.t1 | Gene3D | G3DSA:1.10.240.10 | - | 210 | 320 | 2.1E-128 |
| 4 | g11187.t1 | Hamap | MF_00140_B | Tryptophan–tRNA ligase [trpS]. | 26 | 353 | 35.999969 |
| 17 | g11187.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 462 | 484 | - |
| 2 | g11187.t1 | PANTHER | PTHR43766:SF1 | TRYPTOPHAN–TRNA LIGASE, MITOCHONDRIAL | 21 | 346 | 4.2E-133 |
| 3 | g11187.t1 | PANTHER | PTHR43766 | TRYPTOPHAN–TRNA LIGASE, MITOCHONDRIAL | 21 | 346 | 4.2E-133 |
| 6 | g11187.t1 | PRINTS | PR01039 | Tryptophanyl-tRNA synthetase signature | 39 | 55 | 4.1E-25 |
| 5 | g11187.t1 | PRINTS | PR01039 | Tryptophanyl-tRNA synthetase signature | 90 | 109 | 4.1E-25 |
| 8 | g11187.t1 | PRINTS | PR01039 | Tryptophanyl-tRNA synthetase signature | 165 | 186 | 4.1E-25 |
| 7 | g11187.t1 | PRINTS | PR01039 | Tryptophanyl-tRNA synthetase signature | 219 | 229 | 4.1E-25 |
| 1 | g11187.t1 | Pfam | PF00579 | tRNA synthetases class I (W and Y) | 27 | 307 | 8.5E-70 |
| 12 | g11187.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 345 | - |
| 14 | g11187.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 346 | 364 | - |
| 13 | g11187.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 365 | 611 | - |
| 16 | g11187.t1 | ProSitePatterns | PS00178 | Aminoacyl-transfer RNA synthetases class-I signature. | 35 | 44 | - |
| 9 | g11187.t1 | SUPERFAMILY | SSF52374 | Nucleotidylyl transferase | 27 | 346 | 2.21E-88 |
| 18 | g11187.t1 | TIGRFAM | TIGR00233 | trpS: tryptophan–tRNA ligase | 27 | 346 | 2.9E-90 |
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.
