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.t26 TTS g5489.t26 9844474 9844474
chr_2 g5489 g5489.t26 isoform g5489.t26 9844628 9845566
chr_2 g5489 g5489.t26 exon g5489.t26.exon1 9844628 9845566
chr_2 g5489 g5489.t26 cds g5489.t26.CDS1 9844628 9845563
chr_2 g5489 g5489.t26 TSS g5489.t26 NA NA

Sequences

>g5489.t26 Gene=g5489 Length=939
CCGATGAATTGTCCAGGACATTGTCTAATGTTTGACGTTCGCAATCGCTCTTGGCGTGAA
TTGCCTTTAAGAATGGCAGATTTTGGTGTTTTGCATCGTAACGAGTTTTCTGGTGCATTG
ACAGGTTTAACCAGAGTTCGCCGATTCCAACAAGATGATGCTCATATCTTTTGTGCGCCT
GAACAAATAAAACAAGAAATTACAGGATGTTTGGATTTTTTGCGATGTGTCTATGAAAAG
TTTGGATTTAGTTTCGAATTAGTGCTTTCTACTCGTCCAGAGAAATTTTTGGGTGAAATT
GAAGTTTGGAATGAAGCAGAAAAAGCTCTTTCTGATTCTCTCGATGAATTTGGTGTGAAA
TGGGGATTAAATCCTGGTGATGGAGCATTTTATGGTCCTAAAATTGACATCACAATTAAA
GATGCTCTCAAGCGCTCTCATCAATGTGCTACCATTCAACTTGATTTCCAATTGCCAATT
AGATTTAATTTGAGCTTTGTATCTGAAACAGGTGAAAAACGTCGACCTGTCATTATTCAT
CGCGCCATTCTCGGTTCTGTAGAACGAATGATTGCAATTTTAACTGAAAATTGTGCAGGA
AAATGGCCATTTTGGCTTTCACCAAGACAAGTAATGGTTGTTCCAGTAGGACCGGGTTTG
AATGACTATGCAGCTGAAGTTAGTGATCGTCTCTATAAAGCTGGTTTCATGTCTGAATTT
GATACAGATGATGGTGATACAATGAATAAAAAGATTCGAAATGCACAATTGGCTCAATTC
AATTTCATTTTGGTTGTTGGTGATAAAGAAAAAGCATCAGGAACTGTAAACGTACGTACA
CGAGATAACAAAGTTCACGGTGAATTATCAATTGATGAATTGATACAAAAGTTTGAGAAA
CTACGTCGTGATTTTGTCAAAGATGAAGAAACATTTTAA

>g5489.t26 Gene=g5489 Length=311
MNCPGHCLMFDVRNRSWRELPLRMADFGVLHRNEFSGALTGLTRVRRFQQDDAHIFCAPE
QIKQEITGCLDFLRCVYEKFGFSFELVLSTRPEKFLGEIEVWNEAEKALSDSLDEFGVKW
GLNPGDGAFYGPKIDITIKDALKRSHQCATIQLDFQLPIRFNLSFVSETGEKRRPVIIHR
AILGSVERMIAILTENCAGKWPFWLSPRQVMVVPVGPGLNDYAAEVSDRLYKAGFMSEFD
TDDGDTMNKKIRNAQLAQFNFILVVGDKEKASGTVNVRTRDNKVHGELSIDELIQKFEKL
RRDFVKDEETF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g5489.t26 CDD cd00771 ThrRS_core 1 207 8.63701E-134
15 g5489.t26 CDD cd00860 ThrRS_anticodon 207 298 1.95961E-36
13 g5489.t26 Coils Coil Coil 290 310 -
12 g5489.t26 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 1 199 3.0E-94
11 g5489.t26 Gene3D G3DSA:3.40.50.800 - 200 310 2.4E-40
3 g5489.t26 PANTHER PTHR11451:SF51 THREONYL-TRNA SYNTHETASE-LIKE 2 1 305 4.2E-177
4 g5489.t26 PANTHER PTHR11451 THREONINE-TRNA LIGASE 1 305 4.2E-177
6 g5489.t26 PRINTS PR01047 Threonyl-tRNA synthetase signature 31 54 1.3E-39
7 g5489.t26 PRINTS PR01047 Threonyl-tRNA synthetase signature 132 160 1.3E-39
8 g5489.t26 PRINTS PR01047 Threonyl-tRNA synthetase signature 175 188 1.3E-39
5 g5489.t26 PRINTS PR01047 Threonyl-tRNA synthetase signature 202 214 1.3E-39
1 g5489.t26 Pfam PF00587 tRNA synthetase class II core domain (G, H, P, S and T) 1 196 7.8E-35
2 g5489.t26 Pfam PF03129 Anticodon binding domain 209 299 6.2E-23
17 g5489.t26 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 18 202 15.9
9 g5489.t26 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 1 193 9.67E-60
10 g5489.t26 SUPERFAMILY SSF52954 Class II aaRS ABD-related 195 301 3.93E-30
16 g5489.t26 TIGRFAM TIGR00418 thrS: threonine–tRNA ligase 1 299 4.3E-123

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5489/g5489.t26; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5489.t26.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:0006418 tRNA aminoacylation for protein translation BP
GO:0000166 nucleotide binding MF
GO:0004812 aminoacyl-tRNA ligase activity MF
GO:0006435 threonyl-tRNA aminoacylation BP
GO:0005737 cytoplasm CC

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