Gene loci information

Transcript annotation

  • This transcript has been annotated as Threonine–tRNA ligase 1, cytoplasmic.

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_2 g5489 g5489.t36 isoform g5489.t36 9845935 9846865
chr_2 g5489 g5489.t36 exon g5489.t36.exon1 9845935 9846716
chr_2 g5489 g5489.t36 cds g5489.t36.CDS1 9845935 9846716
chr_2 g5489 g5489.t36 exon g5489.t36.exon2 9846810 9846865
chr_2 g5489 g5489.t36 cds g5489.t36.CDS2 9846810 9846825
chr_2 g5489 g5489.t36 TSS g5489.t36 9847335 9847335
chr_2 g5489 g5489.t36 TTS g5489.t36 NA NA

Sequences

>g5489.t36 Gene=g5489 Length=838
CGCAAAACAAAAGGCTGCGAAAAAGAAGAAACAGGAAGAAATGGGTGTTGAAACAGGAAT
TAAAGAATTGTCTCCACCACCATCATACATTGATGAGCGTATCAAACTATATGATCGTTT
AAAAGCAGAATATCTTGAAGAATTGAAAGCTAAACCGAGAGAAAAAATTCAAATTACATT
GCCTGATGGAAAGATTGTTGAAGGATTATCATGGGAAACAACACCTTTTCAAATTGCTGC
AGGTATCAGTCAAGGATTAGCAGATAATACTGTTGTTGCAAAAGTAGATGATGAAGTATG
GGATTTAGATCGTGTACTTGAGAAAAGTTGCGCATTGAAACTTTTAAAATTTGATGATCC
TGAAGCACAAGCTGTTTTTTGGCATAGCTCAGCTCATATTCTTGGTGAAGCAATGGAAAG
ATGTTATGGTGGTTGTTTATGTTATGGACCTCCAATTGAAAATGGCTTTTATTATGACAT
GTTTTTGGATGGAGAAAATGTTTCTCCAACTCATTACAAAACACTCGAGGATCTCATTAA
AAAAATTGTCAAAGAAAAGCAGCCATTTGAACGTTTGGAAATGAAAAAGTCGGATTTATT
AAAAATGTTTGAATACAATGAGTTTAAAAAGAGAATTCTCAATGAGAAAGTTGACACTGA
AACTACTACTGTTTACCGTTGCGGACCATTAATTGATTTGTGTCGAGGACCTCATGTACG
TCACACAGGCAAAATTAAGGCAATGAAAGTAACAAAAAGCTCATCAACATATTGGGAAGG
AAAAGCTGATGCTGAAACTTTACAACGCATTTACGGAATTTCATTCCCTGATCCAAAA

>g5489.t36 Gene=g5489 Length=266
MGVETGIKELSPPPSYIDERIKLYDRLKAEYLEELKAKPREKIQITLPDGKIVEGLSWET
TPFQIAAGISQGLADNTVVAKVDDEVWDLDRVLEKSCALKLLKFDDPEAQAVFWHSSAHI
LGEAMERCYGGCLCYGPPIENGFYYDMFLDGENVSPTHYKTLEDLIKKIVKEKQPFERLE
MKKSDLLKMFEYNEFKKRILNEKVDTETTTVYRCGPLIDLCRGPHVRHTGKIKAMKVTKS
SSTYWEGKADAETLQRIYGISFPDPK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g5489.t36 CDD cd01667 TGS_ThrRS 43 108 0.000
9 g5489.t36 Gene3D G3DSA:3.10.20.30 - 41 102 0.000
8 g5489.t36 Gene3D G3DSA:3.30.980.10 - 107 262 0.000
3 g5489.t36 PANTHER PTHR11451 THREONINE-TRNA LIGASE 5 266 0.000
4 g5489.t36 PANTHER PTHR11451:SF54 THREONYL-TRNA SYNTHETASE 5 266 0.000
2 g5489.t36 Pfam PF02824 TGS domain 43 103 0.000
1 g5489.t36 Pfam PF07973 Threonyl and Alanyl tRNA synthetase second additional domain 210 258 0.000
10 g5489.t36 ProSiteProfiles PS51880 TGS domain profile. 41 103 19.468
7 g5489.t36 SMART SM00863 tRNA_SAD_4 209 258 0.000
6 g5489.t36 SUPERFAMILY SSF81271 TGS-like 43 103 0.000
5 g5489.t36 SUPERFAMILY SSF55186 ThrRS/AlaRS common domain 105 265 0.000

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5489/g5489.t36; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5489.t36.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005524 ATP binding MF
GO:0004829 threonine-tRNA ligase activity MF
GO:0000166 nucleotide binding MF
GO:0043039 tRNA aminoacylation BP
GO:0004812 aminoacyl-tRNA ligase activity MF
GO:0006435 threonyl-tRNA aminoacylation BP
GO:0005737 cytoplasm CC

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