Gene loci information

Transcript annotation

  • This transcript has been annotated as Tryptophan–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_1 g11187 g11187.t9 isoform g11187.t9 14480705 14482016
chr_1 g11187 g11187.t9 exon g11187.t9.exon1 14480705 14480901
chr_1 g11187 g11187.t9 TTS g11187.t9 14480735 14480735
chr_1 g11187 g11187.t9 exon g11187.t9.exon2 14480999 14481887
chr_1 g11187 g11187.t9 cds g11187.t9.CDS1 14481069 14481887
chr_1 g11187 g11187.t9 exon g11187.t9.exon3 14481951 14482016
chr_1 g11187 g11187.t9 cds g11187.t9.CDS2 14481951 14482016
chr_1 g11187 g11187.t9 TSS g11187.t9 14482053 14482053

Sequences

>g11187.t9 Gene=g11187 Length=1152
ATGTTAAGCACGAGATTTTTAAAAGATCCATTTAAGGAAATTGTGAGAAAGTTCAGTAAT
TCAACTAATAAACAAGTGAAAAAAGTATTTTCGGGAATACAGCCAACTGGAAATTTACAT
TTAGGCAATTATTTCGGTGCTGTCAAGCGATGGATTGATTTACAAAATAGCAATTATGAT
GTTACTTATTGTATTGTTGATTTACATTCAATAACTCTTCCACAAAAACCCTTAGAATTA
AAAGAAAATATTCTTAGAATTTGTGCAACTCTCTTAGCTTGTGGTATTGATCCACAAAAA
TCTACTCTATTTCTTCAATCGTCTGTTAGAGAGCACTCAGAATTATGCTGGATTTTGAGT
TGCAATACTACAATGGCTCGCTTAACACATCTTCCACAATATAAAGAAAAATCAGAAAAA
ATGAAAGAAATTCCACTTGGTCTCTATCTCTATCCTGTTTTACAAGCAGCTGATATTATG
CTGCATAAAGCTAATTTGGTTCCTGTTGGTGAAGATCAAATACAGCATATCCAACTCGCT
CAGAGTTTGACAAAAAATTTCAATCATAGATTTGGTCCAACTTTTCCAACATGTGAACCA
ATGATCTCTGAAGATTTAAGTAGTCGAATAAAATCACTGCGTGATCCTACTAAGAAAATG
TCAAAATCAGATCCTGATCCAAAGAGTTGTGTTATGCTAACAGATTCGCCCGATCAGATA
ACATCAAAAATTAAGAAGGCTGTCACAGACTTTACTTCCGCAGTCACATTTGACCCACAA
AATCGTCAAGGTGTTGCAAATTTGCTAACAATTCATTCACTTGCTAGCAATAAGAGTATA
GAGCAAATTTGTGATGAATCACAAAGATTAGATACTGGACAGTAAGAACTTTTGTTTAAA
AGACGATTTATTTTTGAAATTAAATGTTAATTTATGTTATAGATATAAATTTAAAGAAAT
GAAAAAGCACAAGAAGTTGCTGAGAAAACAATGAATGAAGTAAAAGCACGAGTGGGATTG
GGAAATTATGATATGTCGCAATACATCAAAAATAAAGTGCAAACGAGAATATAATAGAGA
AAATATTGACTTAATAAAGAGAAAAGAGATAACGAAACCTTTCAAAAATTAGTAAAGTTA
AAAAATGAGAAA

>g11187.t9 Gene=g11187 Length=294
MLSTRFLKDPFKEIVRKFSNSTNKQVKKVFSGIQPTGNLHLGNYFGAVKRWIDLQNSNYD
VTYCIVDLHSITLPQKPLELKENILRICATLLACGIDPQKSTLFLQSSVREHSELCWILS
CNTTMARLTHLPQYKEKSEKMKEIPLGLYLYPVLQAADIMLHKANLVPVGEDQIQHIQLA
QSLTKNFNHRFGPTFPTCEPMISEDLSSRIKSLRDPTKKMSKSDPDPKSCVMLTDSPDQI
TSKIKKAVTDFTSAVTFDPQNRQGVANLLTIHSLASNKSIEQICDESQRLDTGQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g11187.t9 CDD cd00806 TrpRS_core 29 283 2.52636E-120
10 g11187.t9 Gene3D G3DSA:3.40.50.620 HUPs 29 209 3.3E-113
9 g11187.t9 Gene3D G3DSA:1.10.240.10 - 210 291 3.3E-113
2 g11187.t9 PANTHER PTHR43766:SF1 TRYPTOPHAN–TRNA LIGASE, MITOCHONDRIAL 21 293 1.7E-115
3 g11187.t9 PANTHER PTHR43766 TRYPTOPHAN–TRNA LIGASE, MITOCHONDRIAL 21 293 1.7E-115
5 g11187.t9 PRINTS PR01039 Tryptophanyl-tRNA synthetase signature 39 55 3.4E-26
4 g11187.t9 PRINTS PR01039 Tryptophanyl-tRNA synthetase signature 90 109 3.4E-26
7 g11187.t9 PRINTS PR01039 Tryptophanyl-tRNA synthetase signature 165 186 3.4E-26
6 g11187.t9 PRINTS PR01039 Tryptophanyl-tRNA synthetase signature 219 229 3.4E-26
1 g11187.t9 Pfam PF00579 tRNA synthetases class I (W and Y) 26 281 8.0E-69
12 g11187.t9 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature. 35 44 -
8 g11187.t9 SUPERFAMILY SSF52374 Nucleotidylyl transferase 27 288 8.0E-78
13 g11187.t9 TIGRFAM TIGR00233 trpS: tryptophan–tRNA ligase 27 286 1.4E-82

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

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