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.t2 TTS g5489.t2 9844474 9844474
chr_2 g5489 g5489.t2 isoform g5489.t2 9844628 9847795
chr_2 g5489 g5489.t2 exon g5489.t2.exon1 9844628 9845566
chr_2 g5489 g5489.t2 cds g5489.t2.CDS1 9844628 9845566
chr_2 g5489 g5489.t2 exon g5489.t2.exon2 9845626 9846716
chr_2 g5489 g5489.t2 cds g5489.t2.CDS2 9845626 9846716
chr_2 g5489 g5489.t2 exon g5489.t2.exon3 9846810 9846867
chr_2 g5489 g5489.t2 cds g5489.t2.CDS3 9846810 9846867
chr_2 g5489 g5489.t2 exon g5489.t2.exon4 9847451 9847795
chr_2 g5489 g5489.t2 cds g5489.t2.CDS4 9847451 9847795
chr_2 g5489 g5489.t2 TSS g5489.t2 NA NA

Sequences

>g5489.t2 Gene=g5489 Length=2433
ATGGGTAATAATAAAAAGAGACGTCCTCATCATAAGAAAAAAGGTAACTCTCAGAGTGCT
CAAACTGACACAAATAAGCATACAGCTGCAGGACTTGCCGAAAATAATGAGCAAGCTCAA
GAGAAGGAGGACAAGATTGAAGAAGTTTCAAAAGCATTGAAAAGTGAAAATGTATTATTA
GAATCGGAAAAAGTAGCCAAAGTTGAAAAAGAGGCTGAAGAAGGAAATAAAAATGAGAAA
GAAAATAATATTGAAATAGAAAAGAATGAGATCAAGTCTGAAAAGCAGCAAACTAAGAAG
GATGAAAATCCTACAGTCAAGAAAGATGACAAAGCGCCACTTGAGGCCGCAAAACAAAAG
GCTGCGAAAAAGAAGAAACAGGAAGAAATGGGTGTTGAAACAGGAATTAAAGAATTGTCT
CCACCACCATCATACATTGATGAGCGTATCAAACTATATGATCGTTTAAAAGCAGAATAT
CTTGAAGAATTGAAAGCTAAACCGAGAGAAAAAATTCAAATTACATTGCCTGATGGAAAG
ATTGTTGAAGGATTATCATGGGAAACAACACCTTTTCAAATTGCTGCAGGTATCAGTCAA
GGATTAGCAGATAATACTGTTGTTGCAAAAGTAGATGATGAAGTATGGGATTTAGATCGT
GTACTTGAGAAAAGTTGCGCATTGAAACTTTTAAAATTTGATGATCCTGAAGCACAAGCT
GTTTTTTGGCATAGCTCAGCTCATATTCTTGGTGAAGCAATGGAAAGATGTTATGGTGGT
TGTTTATGTTATGGACCTCCAATTGAAAATGGCTTTTATTATGACATGTTTTTGGATGGA
GAAAATGTTTCTCCAACTCATTACAAAACACTCGAGGATCTCATTAAAAAAATTGTCAAA
GAAAAGCAGCCATTTGAACGTTTGGAAATGAAAAAGTCGGATTTATTAAAAATGTTTGAA
TACAATGAGTTTAAAAAGAGAATTCTCAATGAGAAAGTTGACACTGAAACTACTACTGTT
TACCGTTGCGGACCATTAATTGATTTGTGTCGAGGACCTCATGTACGTCACACAGGCAAA
ATTAAGGCAATGAAAGTAACAAAAAGCTCATCAACATATTGGGAAGGAAAAGCTGATGCT
GAAACTTTACAACGCATTTACGGAATTTCATTCCCTGATCCAAAACAATTGAAAGAATGG
GAAAAGATTCAAGAAGAGGCAGCAAAACGTGATCATCGTAAAATTGGACGAGAACAAGAA
CTCTTTTTCTTTCACGAATTATCACCAGGTTCATGCTTTTTCCAACCTCGTGGTGCTCAC
ATTTATAATACATTGATGAGCATGATTAGAGAGGAATATCGCAAGCGAGGTTTTCAAGAA
GTTATTTCGCCAAACATGTATAATGCAAAGTTATGGCAAACATCAGGACATTGGCAACAT
TATGCAGAAAATATGTTTTCGTTTGACGTTGAAAAGGAAAAATATGCTCTTAAGCCGATG
AATTGTCCAGGACATTGTCTAATGTTTGACGTTCGCAATCGCTCTTGGCGTGAATTGCCT
TTAAGAATGGCAGATTTTGGTGTTTTGCATCGTAACGAGTTTTCTGGTGCATTGACAGGT
TTAACCAGAGTTCGCCGATTCCAACAAGATGATGCTCATATCTTTTGTGCGCCTGAACAA
ATAAAACAAGAAATTACAGGATGTTTGGATTTTTTGCGATGTGTCTATGAAAAGTTTGGA
TTTAGTTTCGAATTAGTGCTTTCTACTCGTCCAGAGAAATTTTTGGGTGAAATTGAAGTT
TGGAATGAAGCAGAAAAAGCTCTTTCTGATTCTCTCGATGAATTTGGTGTGAAATGGGGA
TTAAATCCTGGTGATGGAGCATTTTATGGTCCTAAAATTGACATCACAATTAAAGATGCT
CTCAAGCGCTCTCATCAATGTGCTACCATTCAACTTGATTTCCAATTGCCAATTAGATTT
AATTTGAGCTTTGTATCTGAAACAGGTGAAAAACGTCGACCTGTCATTATTCATCGCGCC
ATTCTCGGTTCTGTAGAACGAATGATTGCAATTTTAACTGAAAATTGTGCAGGAAAATGG
CCATTTTGGCTTTCACCAAGACAAGTAATGGTTGTTCCAGTAGGACCGGGTTTGAATGAC
TATGCAGCTGAAGTTAGTGATCGTCTCTATAAAGCTGGTTTCATGTCTGAATTTGATACA
GATGATGGTGATACAATGAATAAAAAGATTCGAAATGCACAATTGGCTCAATTCAATTTC
ATTTTGGTTGTTGGTGATAAAGAAAAAGCATCAGGAACTGTAAACGTACGTACACGAGAT
AACAAAGTTCACGGTGAATTATCAATTGATGAATTGATACAAAAGTTTGAGAAACTACGT
CGTGATTTTGTCAAAGATGAAGAAACATTTTAA

>g5489.t2 Gene=g5489 Length=810
MGNNKKRRPHHKKKGNSQSAQTDTNKHTAAGLAENNEQAQEKEDKIEEVSKALKSENVLL
ESEKVAKVEKEAEEGNKNEKENNIEIEKNEIKSEKQQTKKDENPTVKKDDKAPLEAAKQK
AAKKKKQEEMGVETGIKELSPPPSYIDERIKLYDRLKAEYLEELKAKPREKIQITLPDGK
IVEGLSWETTPFQIAAGISQGLADNTVVAKVDDEVWDLDRVLEKSCALKLLKFDDPEAQA
VFWHSSAHILGEAMERCYGGCLCYGPPIENGFYYDMFLDGENVSPTHYKTLEDLIKKIVK
EKQPFERLEMKKSDLLKMFEYNEFKKRILNEKVDTETTTVYRCGPLIDLCRGPHVRHTGK
IKAMKVTKSSSTYWEGKADAETLQRIYGISFPDPKQLKEWEKIQEEAAKRDHRKIGREQE
LFFFHELSPGSCFFQPRGAHIYNTLMSMIREEYRKRGFQEVISPNMYNAKLWQTSGHWQH
YAENMFSFDVEKEKYALKPMNCPGHCLMFDVRNRSWRELPLRMADFGVLHRNEFSGALTG
LTRVRRFQQDDAHIFCAPEQIKQEITGCLDFLRCVYEKFGFSFELVLSTRPEKFLGEIEV
WNEAEKALSDSLDEFGVKWGLNPGDGAFYGPKIDITIKDALKRSHQCATIQLDFQLPIRF
NLSFVSETGEKRRPVIIHRAILGSVERMIAILTENCAGKWPFWLSPRQVMVVPVGPGLND
YAAEVSDRLYKAGFMSEFDTDDGDTMNKKIRNAQLAQFNFILVVGDKEKASGTVNVRTRD
NKVHGELSIDELIQKFEKLRRDFVKDEETF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
25 g5489.t2 CDD cd01667 TGS_ThrRS 172 237 8.61042E-24
24 g5489.t2 CDD cd00771 ThrRS_core 410 706 0.0
26 g5489.t2 CDD cd00860 ThrRS_anticodon 706 797 2.56699E-33
23 g5489.t2 Coils Coil Coil 29 59 -
21 g5489.t2 Coils Coil Coil 69 101 -
22 g5489.t2 Coils Coil Coil 789 809 -
20 g5489.t2 Gene3D G3DSA:3.10.20.30 - 170 231 1.4E-27
18 g5489.t2 Gene3D G3DSA:3.30.980.10 - 236 391 9.2E-55
19 g5489.t2 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 393 699 7.7E-142
17 g5489.t2 Gene3D G3DSA:3.40.50.800 - 700 809 1.2E-39
7 g5489.t2 Hamap MF_00184 Threonine–tRNA ligase [thrS]. 237 798 29.499563
28 g5489.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 129 -
30 g5489.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 15 -
31 g5489.t2 MobiDBLite mobidb-lite consensus disorder prediction 18 35 -
29 g5489.t2 MobiDBLite mobidb-lite consensus disorder prediction 37 129 -
5 g5489.t2 PANTHER PTHR11451 THREONINE-TRNA LIGASE 118 801 0.0
6 g5489.t2 PANTHER PTHR11451:SF54 THREONYL-TRNA SYNTHETASE 118 801 0.0
9 g5489.t2 PRINTS PR01047 Threonyl-tRNA synthetase signature 497 525 2.5E-54
12 g5489.t2 PRINTS PR01047 Threonyl-tRNA synthetase signature 530 553 2.5E-54
8 g5489.t2 PRINTS PR01047 Threonyl-tRNA synthetase signature 631 659 2.5E-54
11 g5489.t2 PRINTS PR01047 Threonyl-tRNA synthetase signature 674 687 2.5E-54
10 g5489.t2 PRINTS PR01047 Threonyl-tRNA synthetase signature 701 713 2.5E-54
2 g5489.t2 Pfam PF02824 TGS domain 172 232 1.2E-12
1 g5489.t2 Pfam PF07973 Threonyl and Alanyl tRNA synthetase second additional domain 339 387 2.5E-13
3 g5489.t2 Pfam PF00587 tRNA synthetase class II core domain (G, H, P, S and T) 490 695 7.0E-39
4 g5489.t2 Pfam PF03129 Anticodon binding domain 708 798 2.9E-22
34 g5489.t2 ProSiteProfiles PS51880 TGS domain profile. 170 232 19.468
33 g5489.t2 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 438 701 25.127
27 g5489.t2 SMART SM00863 tRNA_SAD_4 338 387 1.0E-18
15 g5489.t2 SUPERFAMILY SSF81271 TGS-like 172 232 7.85E-14
14 g5489.t2 SUPERFAMILY SSF55186 ThrRS/AlaRS common domain 234 410 6.28E-54
13 g5489.t2 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 411 692 3.06E-93
16 g5489.t2 SUPERFAMILY SSF52954 Class II aaRS ABD-related 694 800 2.11E-29
32 g5489.t2 TIGRFAM TIGR00418 thrS: threonine–tRNA ligase 243 798 1.2E-202

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5489/g5489.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5489.t2.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