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.t6 isoform g11187.t6 14480702 14481887
chr_1 g11187 g11187.t6 exon g11187.t6.exon1 14480702 14481011
chr_1 g11187 g11187.t6 TTS g11187.t6 14480735 14480735
chr_1 g11187 g11187.t6 cds g11187.t6.CDS1 14480783 14481011
chr_1 g11187 g11187.t6 exon g11187.t6.exon2 14481073 14481887
chr_1 g11187 g11187.t6 cds g11187.t6.CDS2 14481073 14481581
chr_1 g11187 g11187.t6 TSS g11187.t6 14482053 14482053

Sequences

>g11187.t6 Gene=g11187 Length=1125
AATAAACAAGTGAAAAAAGTATTTTCGGGAATACAGCCAACTGGAAATTTACATTTAGGC
AATTATTTCGGTGCTGTCAAGCGATGGATTGATTTACAAAATAGCAATTATGATGTTACT
TATTGTATTGTTGATTTACATTCAATAACTCTTCCACAAAAACCCTTAGAATTAAAAGAA
AATATTCTTAGAATTTGTGCAACTCTCTTAGCTTGTGGTATTGATCCACAAAAATCTACT
CTATTTCTTCAATCGTCTGTTAGAGAGCACTCAGAATTATGCTGGATTTTGAGTTGCAAT
ACTACAATGGCTCGCTTAACACATCTTCCACAATATAAAGAAAAATCAGAAAAAATGAAA
GAAATTCCACTTGGTCTCTATCTCTATCCTGTTTTACAAGCAGCTGATATTATGCTGCAT
AAAGCTAATTTGGTTCCTGTTGGTGAAGATCAAATACAGCATATCCAACTCGCTCAGAGT
TTGACAAAAAATTTCAATCATAGATTTGGTCCAACTTTTCCAACATGTGAACCAATGATC
TCTGAAGATTTAAGTAGTCGAATAAAATCACTGCGTGATCCTACTAAGAAAATGTCAAAA
TCAGATCCTGATCCAAAGAGTTGTGTTATGCTAACAGATTCGCCCGATCAGATAACATCA
AAAATTAAGAAGGCTGTCACAGACTTTACTTCCGCAGTCACATTTGACCCACAAAATCGT
CAAGGTGTTGCAAATTTGCTAACAATTCATTCACTTGCTAGCAATAAGAGTATAGAGCAA
ATTTGTGATGAATCACAAAGATTAGATACTGGACAATATAAATTTAAAGTAGCTGAGGCA
ATAATTGAACATTTTAATCCAATTAGACTAAAGATTGATGATTATCTTAAAAATCCTGAT
TATTTATGGAGTATTCTTGACATAGGAAATGAAAAAGCACAAGAAGTTGCTGAGAAAACA
ATGAATGAAGTAAAAGCACGAGTGGGATTGGGAAATTATGATATGTCGCAATACATCAAA
AATAAAGTGCAAACGAGAATATAATAGAGAAAATATTGACTTAATAAAGAGAAAAGAGAT
AACGAAACCTTTCAAAAATTAGTAAAGTTAAAAAATGAGAAATTA

>g11187.t6 Gene=g11187 Length=245
MARLTHLPQYKEKSEKMKEIPLGLYLYPVLQAADIMLHKANLVPVGEDQIQHIQLAQSLT
KNFNHRFGPTFPTCEPMISEDLSSRIKSLRDPTKKMSKSDPDPKSCVMLTDSPDQITSKI
KKAVTDFTSAVTFDPQNRQGVANLLTIHSLASNKSIEQICDESQRLDTGQYKFKVAEAII
EHFNPIRLKIDDYLKNPDYLWSILDIGNEKAQEVAEKTMNEVKARVGLGNYDMSQYIKNK
VQTRI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g11187.t6 Gene3D G3DSA:3.40.50.620 HUPs 1 80 0e+00
7 g11187.t6 Gene3D G3DSA:1.10.240.10 - 86 196 0e+00
2 g11187.t6 PANTHER PTHR43766:SF1 TRYPTOPHAN–TRNA LIGASE, MITOCHONDRIAL 1 228 0e+00
3 g11187.t6 PANTHER PTHR43766 TRYPTOPHAN–TRNA LIGASE, MITOCHONDRIAL 1 228 0e+00
4 g11187.t6 PRINTS PR01039 Tryptophanyl-tRNA synthetase signature 41 62 2e-07
5 g11187.t6 PRINTS PR01039 Tryptophanyl-tRNA synthetase signature 95 105 2e-07
1 g11187.t6 Pfam PF00579 tRNA synthetases class I (W and Y) 3 183 0e+00
6 g11187.t6 SUPERFAMILY SSF52374 Nucleotidylyl transferase 2 228 0e+00
9 g11187.t6 TIGRFAM TIGR00233 trpS: tryptophan–tRNA ligase 2 228 0e+00

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 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.

Raw TPM values