Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t10 TTS g11187.t10 14480735 14480735
chr_1 g11187 g11187.t10 isoform g11187.t10 14481402 14482016
chr_1 g11187 g11187.t10 exon g11187.t10.exon1 14481402 14481887
chr_1 g11187 g11187.t10 cds g11187.t10.CDS1 14481402 14481887
chr_1 g11187 g11187.t10 exon g11187.t10.exon2 14481951 14482016
chr_1 g11187 g11187.t10 cds g11187.t10.CDS2 14481951 14482016
chr_1 g11187 g11187.t10 TSS g11187.t10 14482053 14482053

Sequences

>g11187.t10 Gene=g11187 Length=552
ATGTTAAGCACGAGATTTTTAAAAGATCCATTTAAGGAAATTGTGAGAAAGTTCAGTAAT
TCAACTAATAAACAAGTGAAAAAAGTATTTTCGGGAATACAGCCAACTGGAAATTTACAT
TTAGGCAATTATTTCGGTGCTGTCAAGCGATGGATTGATTTACAAAATAGCAATTATGAT
GTTACTTATTGTATTGTTGATTTACATTCAATAACTCTTCCACAAAAACCCTTAGAATTA
AAAGAAAATATTCTTAGAATTTGTGCAACTCTCTTAGCTTGTGGTATTGATCCACAAAAA
TCTACTCTATTTCTTCAATCGTCTGTTAGAGAGCACTCAGAATTATGCTGGATTTTGAGT
TGCAATACTACAATGGCTCGCTTAACACATCTTCCACAATATAAAGAAAAATCAGAAAAA
ATGAAAGAAATTCCACTTGGTCTCTATCTCTATCCTGTTTTACAAGCAGCTGATATTATG
CTGCATAAAGCTAATTTGGTTCCTGTTGGTGAAGATCAAATACAGCATATCCAACTCGCT
CAGAGTTTGACA

>g11187.t10 Gene=g11187 Length=184
MLSTRFLKDPFKEIVRKFSNSTNKQVKKVFSGIQPTGNLHLGNYFGAVKRWIDLQNSNYD
VTYCIVDLHSITLPQKPLELKENILRICATLLACGIDPQKSTLFLQSSVREHSELCWILS
CNTTMARLTHLPQYKEKSEKMKEIPLGLYLYPVLQAADIMLHKANLVPVGEDQIQHIQLA
QSLT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g11187.t10 Gene3D G3DSA:3.40.50.620 HUPs 26 184 1.1E-74
2 g11187.t10 PANTHER PTHR43766:SF1 TRYPTOPHAN–TRNA LIGASE, MITOCHONDRIAL 21 183 2.3E-71
3 g11187.t10 PANTHER PTHR43766 TRYPTOPHAN–TRNA LIGASE, MITOCHONDRIAL 21 183 2.3E-71
6 g11187.t10 PRINTS PR01039 Tryptophanyl-tRNA synthetase signature 39 55 6.7E-22
5 g11187.t10 PRINTS PR01039 Tryptophanyl-tRNA synthetase signature 90 109 6.7E-22
4 g11187.t10 PRINTS PR01039 Tryptophanyl-tRNA synthetase signature 165 184 6.7E-22
1 g11187.t10 Pfam PF00579 tRNA synthetases class I (W and Y) 26 183 1.7E-49
8 g11187.t10 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature. 35 44 -
7 g11187.t10 SUPERFAMILY SSF52374 Nucleotidylyl transferase 27 181 1.66E-50
10 g11187.t10 TIGRFAM TIGR00233 trpS: tryptophan–tRNA ligase 27 183 7.3E-56

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. There were no conditions that were differentially expressed