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.t27 TTS g5489.t27 9844474 9844474
chr_2 g5489 g5489.t27 isoform g5489.t27 9844628 9846345
chr_2 g5489 g5489.t27 exon g5489.t27.exon1 9844628 9845566
chr_2 g5489 g5489.t27 cds g5489.t27.CDS1 9844628 9845566
chr_2 g5489 g5489.t27 exon g5489.t27.exon2 9845626 9846345
chr_2 g5489 g5489.t27 cds g5489.t27.CDS2 9845626 9846294
chr_2 g5489 g5489.t27 TSS g5489.t27 9847335 9847335

Sequences

>g5489.t27 Gene=g5489 Length=1659
GGTGGTTGTTTATGTTATGGACCTCCAATTGAAAATGGCTTTTATTATGACATGTTTTTG
GATGGAGAAAATGTTTCTCCAACTCATTACAAAACACTCGAGGATCTCATTAAAAAAATT
GTCAAAGAAAAGCAGCCATTTGAACGTTTGGAAATGAAAAAGTCGGATTTATTAAAAATG
TTTGAATACAATGAGTTTAAAAAGAGAATTCTCAATGAGAAAGTTGACACTGAAACTACT
ACTGTTTACCGTTGCGGACCATTAATTGATTTGTGTCGAGGACCTCATGTACGTCACACA
GGCAAAATTAAGGCAATGAAAGTAACAAAAAGCTCATCAACATATTGGGAAGGAAAAGCT
GATGCTGAAACTTTACAACGCATTTACGGAATTTCATTCCCTGATCCAAAACAATTGAAA
GAATGGGAAAAGATTCAAGAAGAGGCAGCAAAACGTGATCATCGTAAAATTGGACGAGAA
CAAGAACTCTTTTTCTTTCACGAATTATCACCAGGTTCATGCTTTTTCCAACCTCGTGGT
GCTCACATTTATAATACATTGATGAGCATGATTAGAGAGGAATATCGCAAGCGAGGTTTT
CAAGAAGTTATTTCGCCAAACATGTATAATGCAAAGTTATGGCAAACATCAGGACATTGG
CAACATTATGCAGAAAATATGTTTTCGTTTGACGTTGAAAAGGAAAAATATGCTCTTAAG
CCGATGAATTGTCCAGGACATTGTCTAATGTTTGACGTTCGCAATCGCTCTTGGCGTGAA
TTGCCTTTAAGAATGGCAGATTTTGGTGTTTTGCATCGTAACGAGTTTTCTGGTGCATTG
ACAGGTTTAACCAGAGTTCGCCGATTCCAACAAGATGATGCTCATATCTTTTGTGCGCCT
GAACAAATAAAACAAGAAATTACAGGATGTTTGGATTTTTTGCGATGTGTCTATGAAAAG
TTTGGATTTAGTTTCGAATTAGTGCTTTCTACTCGTCCAGAGAAATTTTTGGGTGAAATT
GAAGTTTGGAATGAAGCAGAAAAAGCTCTTTCTGATTCTCTCGATGAATTTGGTGTGAAA
TGGGGATTAAATCCTGGTGATGGAGCATTTTATGGTCCTAAAATTGACATCACAATTAAA
GATGCTCTCAAGCGCTCTCATCAATGTGCTACCATTCAACTTGATTTCCAATTGCCAATT
AGATTTAATTTGAGCTTTGTATCTGAAACAGGTGAAAAACGTCGACCTGTCATTATTCAT
CGCGCCATTCTCGGTTCTGTAGAACGAATGATTGCAATTTTAACTGAAAATTGTGCAGGA
AAATGGCCATTTTGGCTTTCACCAAGACAAGTAATGGTTGTTCCAGTAGGACCGGGTTTG
AATGACTATGCAGCTGAAGTTAGTGATCGTCTCTATAAAGCTGGTTTCATGTCTGAATTT
GATACAGATGATGGTGATACAATGAATAAAAAGATTCGAAATGCACAATTGGCTCAATTC
AATTTCATTTTGGTTGTTGGTGATAAAGAAAAAGCATCAGGAACTGTAAACGTACGTACA
CGAGATAACAAAGTTCACGGTGAATTATCAATTGATGAATTGATACAAAAGTTTGAGAAA
CTACGTCGTGATTTTGTCAAAGATGAAGAAACATTTTAA

>g5489.t27 Gene=g5489 Length=535
MFLDGENVSPTHYKTLEDLIKKIVKEKQPFERLEMKKSDLLKMFEYNEFKKRILNEKVDT
ETTTVYRCGPLIDLCRGPHVRHTGKIKAMKVTKSSSTYWEGKADAETLQRIYGISFPDPK
QLKEWEKIQEEAAKRDHRKIGREQELFFFHELSPGSCFFQPRGAHIYNTLMSMIREEYRK
RGFQEVISPNMYNAKLWQTSGHWQHYAENMFSFDVEKEKYALKPMNCPGHCLMFDVRNRS
WRELPLRMADFGVLHRNEFSGALTGLTRVRRFQQDDAHIFCAPEQIKQEITGCLDFLRCV
YEKFGFSFELVLSTRPEKFLGEIEVWNEAEKALSDSLDEFGVKWGLNPGDGAFYGPKIDI
TIKDALKRSHQCATIQLDFQLPIRFNLSFVSETGEKRRPVIIHRAILGSVERMIAILTEN
CAGKWPFWLSPRQVMVVPVGPGLNDYAAEVSDRLYKAGFMSEFDTDDGDTMNKKIRNAQL
AQFNFILVVGDKEKASGTVNVRTRDNKVHGELSIDELIQKFEKLRRDFVKDEETF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g5489.t27 CDD cd00771 ThrRS_core 135 431 0.0
20 g5489.t27 CDD cd00860 ThrRS_anticodon 431 522 1.39723E-34
18 g5489.t27 Coils Coil Coil 514 534 -
16 g5489.t27 Gene3D G3DSA:3.30.980.10 - 1 116 1.7E-37
17 g5489.t27 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 118 424 2.8E-142
15 g5489.t27 Gene3D G3DSA:3.40.50.800 - 425 534 6.6E-40
6 g5489.t27 Hamap MF_00184 Threonine–tRNA ligase [thrS]. 3 523 26.883047
4 g5489.t27 PANTHER PTHR11451 THREONINE-TRNA LIGASE 1 533 0.0
5 g5489.t27 PANTHER PTHR11451:SF36 THREONINE–TRNA LIGASE, CYTOPLASMIC 1 533 0.0
10 g5489.t27 PRINTS PR01047 Threonyl-tRNA synthetase signature 222 250 4.1E-55
11 g5489.t27 PRINTS PR01047 Threonyl-tRNA synthetase signature 255 278 4.1E-55
8 g5489.t27 PRINTS PR01047 Threonyl-tRNA synthetase signature 356 384 4.1E-55
9 g5489.t27 PRINTS PR01047 Threonyl-tRNA synthetase signature 399 412 4.1E-55
7 g5489.t27 PRINTS PR01047 Threonyl-tRNA synthetase signature 426 438 4.1E-55
1 g5489.t27 Pfam PF07973 Threonyl and Alanyl tRNA synthetase second additional domain 64 112 1.5E-13
2 g5489.t27 Pfam PF00587 tRNA synthetase class II core domain (G, H, P, S and T) 215 420 3.1E-39
3 g5489.t27 Pfam PF03129 Anticodon binding domain 433 523 1.6E-22
23 g5489.t27 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 163 426 25.127
21 g5489.t27 SMART SM00863 tRNA_SAD_4 63 112 1.0E-18
13 g5489.t27 SUPERFAMILY SSF55186 ThrRS/AlaRS common domain 5 135 4.71E-38
12 g5489.t27 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 136 417 1.19E-93
14 g5489.t27 SUPERFAMILY SSF52954 Class II aaRS ABD-related 419 525 1.1E-29
22 g5489.t27 TIGRFAM TIGR00418 thrS: threonine–tRNA ligase 7 523 1.2E-194

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5489/g5489.t27; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5489.t27.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:0005737 cytoplasm CC
GO:0000166 nucleotide binding MF
GO:0006418 tRNA aminoacylation for protein translation BP
GO:0043039 tRNA aminoacylation BP
GO:0004812 aminoacyl-tRNA ligase activity MF
GO:0006435 threonyl-tRNA aminoacylation BP

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