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.t28 TTS g5489.t28 9844474 9844474
chr_2 g5489 g5489.t28 isoform g5489.t28 9844628 9847310
chr_2 g5489 g5489.t28 exon g5489.t28.exon1 9844628 9845566
chr_2 g5489 g5489.t28 cds g5489.t28.CDS1 9844628 9845566
chr_2 g5489 g5489.t28 exon g5489.t28.exon2 9845626 9846716
chr_2 g5489 g5489.t28 cds g5489.t28.CDS2 9845626 9846716
chr_2 g5489 g5489.t28 exon g5489.t28.exon3 9846810 9847310
chr_2 g5489 g5489.t28 cds g5489.t28.CDS3 9846810 9846825
chr_2 g5489 g5489.t28 TSS g5489.t28 9847335 9847335

Sequences

>g5489.t28 Gene=g5489 Length=2531
ATGAGCAGTGAAATTTCGGAAAAATTAGAAAATTTGGATATAGAATCGAATCAGGCATGA
GATAATAGTTAATTTTAATAATGTTATTCTCAACATTTCAAAAAATAATTAATTTAAATA
AGTTTATTGTGGTAAATCAACTGAAAAGTGGAAATTGGAATCGGCAATGTTTTGCAACTT
TGGTTCGTGATGATCGCTTTAAAAACTATAATTTGATAGATTTAGTGATACATTAATACA
CTTTGAGTTATGCTTATAACATACAATGTTATTAATCTTTGTTTTATTTTATTTGACCTA
ATTTTCATTTTTCCACGTTGATTTCATTCCATAAATTTTTCTCATTCCTTAAACAAAACA
AATATTACGTCAGACATTTCTGCACGTTTATTAAGTGAAGTGAATCATTTTATAATTTTA
ACTTTATTTCATCATAATTTTAGGCCGCAAAACAAAAGGCTGCGAAAAAGAAGAAACAGG
AAGAAATGGGTGTTGAAACAGGAATTAAAGAATTGTCTCCACCACCATCATACATTGATG
AGCGTATCAAACTATATGATCGTTTAAAAGCAGAATATCTTGAAGAATTGAAAGCTAAAC
CGAGAGAAAAAATTCAAATTACATTGCCTGATGGAAAGATTGTTGAAGGATTATCATGGG
AAACAACACCTTTTCAAATTGCTGCAGGTATCAGTCAAGGATTAGCAGATAATACTGTTG
TTGCAAAAGTAGATGATGAAGTATGGGATTTAGATCGTGTACTTGAGAAAAGTTGCGCAT
TGAAACTTTTAAAATTTGATGATCCTGAAGCACAAGCTGTTTTTTGGCATAGCTCAGCTC
ATATTCTTGGTGAAGCAATGGAAAGATGTTATGGTGGTTGTTTATGTTATGGACCTCCAA
TTGAAAATGGCTTTTATTATGACATGTTTTTGGATGGAGAAAATGTTTCTCCAACTCATT
ACAAAACACTCGAGGATCTCATTAAAAAAATTGTCAAAGAAAAGCAGCCATTTGAACGTT
TGGAAATGAAAAAGTCGGATTTATTAAAAATGTTTGAATACAATGAGTTTAAAAAGAGAA
TTCTCAATGAGAAAGTTGACACTGAAACTACTACTGTTTACCGTTGCGGACCATTAATTG
ATTTGTGTCGAGGACCTCATGTACGTCACACAGGCAAAATTAAGGCAATGAAAGTAACAA
AAAGCTCATCAACATATTGGGAAGGAAAAGCTGATGCTGAAACTTTACAACGCATTTACG
GAATTTCATTCCCTGATCCAAAACAATTGAAAGAATGGGAAAAGATTCAAGAAGAGGCAG
CAAAACGTGATCATCGTAAAATTGGACGAGAACAAGAACTCTTTTTCTTTCACGAATTAT
CACCAGGTTCATGCTTTTTCCAACCTCGTGGTGCTCACATTTATAATACATTGATGAGCA
TGATTAGAGAGGAATATCGCAAGCGAGGTTTTCAAGAAGTTATTTCGCCAAACATGTATA
ATGCAAAGTTATGGCAAACATCAGGACATTGGCAACATTATGCAGAAAATATGTTTTCGT
TTGACGTTGAAAAGGAAAAATATGCTCTTAAGCCGATGAATTGTCCAGGACATTGTCTAA
TGTTTGACGTTCGCAATCGCTCTTGGCGTGAATTGCCTTTAAGAATGGCAGATTTTGGTG
TTTTGCATCGTAACGAGTTTTCTGGTGCATTGACAGGTTTAACCAGAGTTCGCCGATTCC
AACAAGATGATGCTCATATCTTTTGTGCGCCTGAACAAATAAAACAAGAAATTACAGGAT
GTTTGGATTTTTTGCGATGTGTCTATGAAAAGTTTGGATTTAGTTTCGAATTAGTGCTTT
CTACTCGTCCAGAGAAATTTTTGGGTGAAATTGAAGTTTGGAATGAAGCAGAAAAAGCTC
TTTCTGATTCTCTCGATGAATTTGGTGTGAAATGGGGATTAAATCCTGGTGATGGAGCAT
TTTATGGTCCTAAAATTGACATCACAATTAAAGATGCTCTCAAGCGCTCTCATCAATGTG
CTACCATTCAACTTGATTTCCAATTGCCAATTAGATTTAATTTGAGCTTTGTATCTGAAA
CAGGTGAAAAACGTCGACCTGTCATTATTCATCGCGCCATTCTCGGTTCTGTAGAACGAA
TGATTGCAATTTTAACTGAAAATTGTGCAGGAAAATGGCCATTTTGGCTTTCACCAAGAC
AAGTAATGGTTGTTCCAGTAGGACCGGGTTTGAATGACTATGCAGCTGAAGTTAGTGATC
GTCTCTATAAAGCTGGTTTCATGTCTGAATTTGATACAGATGATGGTGATACAATGAATA
AAAAGATTCGAAATGCACAATTGGCTCAATTCAATTTCATTTTGGTTGTTGGTGATAAAG
AAAAAGCATCAGGAACTGTAAACGTACGTACACGAGATAACAAAGTTCACGGTGAATTAT
CAATTGATGAATTGATACAAAAGTTTGAGAAACTACGTCGTGATTTTGTCAAAGATGAAG
AAACATTTTAA

>g5489.t28 Gene=g5489 Length=681
MGVETGIKELSPPPSYIDERIKLYDRLKAEYLEELKAKPREKIQITLPDGKIVEGLSWET
TPFQIAAGISQGLADNTVVAKVDDEVWDLDRVLEKSCALKLLKFDDPEAQAVFWHSSAHI
LGEAMERCYGGCLCYGPPIENGFYYDMFLDGENVSPTHYKTLEDLIKKIVKEKQPFERLE
MKKSDLLKMFEYNEFKKRILNEKVDTETTTVYRCGPLIDLCRGPHVRHTGKIKAMKVTKS
SSTYWEGKADAETLQRIYGISFPDPKQLKEWEKIQEEAAKRDHRKIGREQELFFFHELSP
GSCFFQPRGAHIYNTLMSMIREEYRKRGFQEVISPNMYNAKLWQTSGHWQHYAENMFSFD
VEKEKYALKPMNCPGHCLMFDVRNRSWRELPLRMADFGVLHRNEFSGALTGLTRVRRFQQ
DDAHIFCAPEQIKQEITGCLDFLRCVYEKFGFSFELVLSTRPEKFLGEIEVWNEAEKALS
DSLDEFGVKWGLNPGDGAFYGPKIDITIKDALKRSHQCATIQLDFQLPIRFNLSFVSETG
EKRRPVIIHRAILGSVERMIAILTENCAGKWPFWLSPRQVMVVPVGPGLNDYAAEVSDRL
YKAGFMSEFDTDDGDTMNKKIRNAQLAQFNFILVVGDKEKASGTVNVRTRDNKVHGELSI
DELIQKFEKLRRDFVKDEETF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g5489.t28 CDD cd01667 TGS_ThrRS 43 108 2.54335E-24
22 g5489.t28 CDD cd00771 ThrRS_core 281 577 0.0
24 g5489.t28 CDD cd00860 ThrRS_anticodon 577 668 2.64321E-34
21 g5489.t28 Coils Coil Coil 660 680 -
20 g5489.t28 Gene3D G3DSA:3.10.20.30 - 41 102 1.1E-27
18 g5489.t28 Gene3D G3DSA:3.30.980.10 - 107 262 6.9E-55
19 g5489.t28 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 264 570 5.2E-142
17 g5489.t28 Gene3D G3DSA:3.40.50.800 - 571 680 9.6E-40
7 g5489.t28 Hamap MF_00184 Threonine–tRNA ligase [thrS]. 108 669 29.499563
5 g5489.t28 PANTHER PTHR11451 THREONINE-TRNA LIGASE 5 672 0.0
6 g5489.t28 PANTHER PTHR11451:SF54 THREONYL-TRNA SYNTHETASE 5 672 0.0
10 g5489.t28 PRINTS PR01047 Threonyl-tRNA synthetase signature 368 396 7.9E-55
12 g5489.t28 PRINTS PR01047 Threonyl-tRNA synthetase signature 401 424 7.9E-55
11 g5489.t28 PRINTS PR01047 Threonyl-tRNA synthetase signature 502 530 7.9E-55
9 g5489.t28 PRINTS PR01047 Threonyl-tRNA synthetase signature 545 558 7.9E-55
8 g5489.t28 PRINTS PR01047 Threonyl-tRNA synthetase signature 572 584 7.9E-55
2 g5489.t28 Pfam PF02824 TGS domain 43 103 9.3E-13
1 g5489.t28 Pfam PF07973 Threonyl and Alanyl tRNA synthetase second additional domain 210 258 2.0E-13
3 g5489.t28 Pfam PF00587 tRNA synthetase class II core domain (G, H, P, S and T) 361 566 5.1E-39
4 g5489.t28 Pfam PF03129 Anticodon binding domain 579 669 2.3E-22
28 g5489.t28 ProSiteProfiles PS51880 TGS domain profile. 41 103 19.468
27 g5489.t28 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 309 572 25.127
25 g5489.t28 SMART SM00863 tRNA_SAD_4 209 258 1.0E-18
15 g5489.t28 SUPERFAMILY SSF81271 TGS-like 43 103 6.21E-14
14 g5489.t28 SUPERFAMILY SSF55186 ThrRS/AlaRS common domain 105 281 4.58E-54
13 g5489.t28 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 282 563 2.11E-93
16 g5489.t28 SUPERFAMILY SSF52954 Class II aaRS ABD-related 565 671 1.66E-29
26 g5489.t28 TIGRFAM TIGR00418 thrS: threonine–tRNA ligase 114 669 6.7E-203

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5489/g5489.t28; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5489.t28.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