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.t1 TTS g5489.t1 9844474 9844474
chr_2 g5489 g5489.t1 isoform g5489.t1 9844628 9847310
chr_2 g5489 g5489.t1 exon g5489.t1.exon1 9844628 9845566
chr_2 g5489 g5489.t1 cds g5489.t1.CDS1 9844628 9845566
chr_2 g5489 g5489.t1 exon g5489.t1.exon2 9845626 9846716
chr_2 g5489 g5489.t1 cds g5489.t1.CDS2 9845626 9846716
chr_2 g5489 g5489.t1 exon g5489.t1.exon3 9846810 9846867
chr_2 g5489 g5489.t1 cds g5489.t1.CDS3 9846810 9846867
chr_2 g5489 g5489.t1 exon g5489.t1.exon4 9847257 9847310
chr_2 g5489 g5489.t1 cds g5489.t1.CDS4 9847257 9847310
chr_2 g5489 g5489.t1 TSS g5489.t1 9847335 9847335

Sequences

>g5489.t1 Gene=g5489 Length=2142
ATGAGCAGTGAAATTTCGGAAAAATTAGAAAATTTGGATATAGAATCGAATCAGGCCGCA
AAACAAAAGGCTGCGAAAAAGAAGAAACAGGAAGAAATGGGTGTTGAAACAGGAATTAAA
GAATTGTCTCCACCACCATCATACATTGATGAGCGTATCAAACTATATGATCGTTTAAAA
GCAGAATATCTTGAAGAATTGAAAGCTAAACCGAGAGAAAAAATTCAAATTACATTGCCT
GATGGAAAGATTGTTGAAGGATTATCATGGGAAACAACACCTTTTCAAATTGCTGCAGGT
ATCAGTCAAGGATTAGCAGATAATACTGTTGTTGCAAAAGTAGATGATGAAGTATGGGAT
TTAGATCGTGTACTTGAGAAAAGTTGCGCATTGAAACTTTTAAAATTTGATGATCCTGAA
GCACAAGCTGTTTTTTGGCATAGCTCAGCTCATATTCTTGGTGAAGCAATGGAAAGATGT
TATGGTGGTTGTTTATGTTATGGACCTCCAATTGAAAATGGCTTTTATTATGACATGTTT
TTGGATGGAGAAAATGTTTCTCCAACTCATTACAAAACACTCGAGGATCTCATTAAAAAA
ATTGTCAAAGAAAAGCAGCCATTTGAACGTTTGGAAATGAAAAAGTCGGATTTATTAAAA
ATGTTTGAATACAATGAGTTTAAAAAGAGAATTCTCAATGAGAAAGTTGACACTGAAACT
ACTACTGTTTACCGTTGCGGACCATTAATTGATTTGTGTCGAGGACCTCATGTACGTCAC
ACAGGCAAAATTAAGGCAATGAAAGTAACAAAAAGCTCATCAACATATTGGGAAGGAAAA
GCTGATGCTGAAACTTTACAACGCATTTACGGAATTTCATTCCCTGATCCAAAACAATTG
AAAGAATGGGAAAAGATTCAAGAAGAGGCAGCAAAACGTGATCATCGTAAAATTGGACGA
GAACAAGAACTCTTTTTCTTTCACGAATTATCACCAGGTTCATGCTTTTTCCAACCTCGT
GGTGCTCACATTTATAATACATTGATGAGCATGATTAGAGAGGAATATCGCAAGCGAGGT
TTTCAAGAAGTTATTTCGCCAAACATGTATAATGCAAAGTTATGGCAAACATCAGGACAT
TGGCAACATTATGCAGAAAATATGTTTTCGTTTGACGTTGAAAAGGAAAAATATGCTCTT
AAGCCGATGAATTGTCCAGGACATTGTCTAATGTTTGACGTTCGCAATCGCTCTTGGCGT
GAATTGCCTTTAAGAATGGCAGATTTTGGTGTTTTGCATCGTAACGAGTTTTCTGGTGCA
TTGACAGGTTTAACCAGAGTTCGCCGATTCCAACAAGATGATGCTCATATCTTTTGTGCG
CCTGAACAAATAAAACAAGAAATTACAGGATGTTTGGATTTTTTGCGATGTGTCTATGAA
AAGTTTGGATTTAGTTTCGAATTAGTGCTTTCTACTCGTCCAGAGAAATTTTTGGGTGAA
ATTGAAGTTTGGAATGAAGCAGAAAAAGCTCTTTCTGATTCTCTCGATGAATTTGGTGTG
AAATGGGGATTAAATCCTGGTGATGGAGCATTTTATGGTCCTAAAATTGACATCACAATT
AAAGATGCTCTCAAGCGCTCTCATCAATGTGCTACCATTCAACTTGATTTCCAATTGCCA
ATTAGATTTAATTTGAGCTTTGTATCTGAAACAGGTGAAAAACGTCGACCTGTCATTATT
CATCGCGCCATTCTCGGTTCTGTAGAACGAATGATTGCAATTTTAACTGAAAATTGTGCA
GGAAAATGGCCATTTTGGCTTTCACCAAGACAAGTAATGGTTGTTCCAGTAGGACCGGGT
TTGAATGACTATGCAGCTGAAGTTAGTGATCGTCTCTATAAAGCTGGTTTCATGTCTGAA
TTTGATACAGATGATGGTGATACAATGAATAAAAAGATTCGAAATGCACAATTGGCTCAA
TTCAATTTCATTTTGGTTGTTGGTGATAAAGAAAAAGCATCAGGAACTGTAAACGTACGT
ACACGAGATAACAAAGTTCACGGTGAATTATCAATTGATGAATTGATACAAAAGTTTGAG
AAACTACGTCGTGATTTTGTCAAAGATGAAGAAACATTTTAA

>g5489.t1 Gene=g5489 Length=713
MSSEISEKLENLDIESNQAAKQKAAKKKKQEEMGVETGIKELSPPPSYIDERIKLYDRLK
AEYLEELKAKPREKIQITLPDGKIVEGLSWETTPFQIAAGISQGLADNTVVAKVDDEVWD
LDRVLEKSCALKLLKFDDPEAQAVFWHSSAHILGEAMERCYGGCLCYGPPIENGFYYDMF
LDGENVSPTHYKTLEDLIKKIVKEKQPFERLEMKKSDLLKMFEYNEFKKRILNEKVDTET
TTVYRCGPLIDLCRGPHVRHTGKIKAMKVTKSSSTYWEGKADAETLQRIYGISFPDPKQL
KEWEKIQEEAAKRDHRKIGREQELFFFHELSPGSCFFQPRGAHIYNTLMSMIREEYRKRG
FQEVISPNMYNAKLWQTSGHWQHYAENMFSFDVEKEKYALKPMNCPGHCLMFDVRNRSWR
ELPLRMADFGVLHRNEFSGALTGLTRVRRFQQDDAHIFCAPEQIKQEITGCLDFLRCVYE
KFGFSFELVLSTRPEKFLGEIEVWNEAEKALSDSLDEFGVKWGLNPGDGAFYGPKIDITI
KDALKRSHQCATIQLDFQLPIRFNLSFVSETGEKRRPVIIHRAILGSVERMIAILTENCA
GKWPFWLSPRQVMVVPVGPGLNDYAAEVSDRLYKAGFMSEFDTDDGDTMNKKIRNAQLAQ
FNFILVVGDKEKASGTVNVRTRDNKVHGELSIDELIQKFEKLRRDFVKDEETF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
24 g5489.t1 CDD cd01667 TGS_ThrRS 75 140 3.71505E-24
23 g5489.t1 CDD cd00771 ThrRS_core 313 609 0.0
25 g5489.t1 CDD cd00860 ThrRS_anticodon 609 700 3.98421E-34
22 g5489.t1 Coils Coil Coil 9 32 -
21 g5489.t1 Coils Coil Coil 692 712 -
20 g5489.t1 Gene3D G3DSA:3.10.20.30 - 73 134 1.2E-27
18 g5489.t1 Gene3D G3DSA:3.30.980.10 - 139 294 7.4E-55
19 g5489.t1 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 296 602 5.8E-142
17 g5489.t1 Gene3D G3DSA:3.40.50.800 - 603 712 1.0E-39
7 g5489.t1 Hamap MF_00184 Threonine–tRNA ligase [thrS]. 140 701 29.499563
28 g5489.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 18 -
29 g5489.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 41 -
27 g5489.t1 MobiDBLite mobidb-lite consensus disorder prediction 20 36 -
5 g5489.t1 PANTHER PTHR11451 THREONINE-TRNA LIGASE 25 704 0.0
6 g5489.t1 PANTHER PTHR11451:SF54 THREONYL-TRNA SYNTHETASE 25 704 0.0
9 g5489.t1 PRINTS PR01047 Threonyl-tRNA synthetase signature 400 428 1.8E-54
12 g5489.t1 PRINTS PR01047 Threonyl-tRNA synthetase signature 433 456 1.8E-54
10 g5489.t1 PRINTS PR01047 Threonyl-tRNA synthetase signature 534 562 1.8E-54
8 g5489.t1 PRINTS PR01047 Threonyl-tRNA synthetase signature 577 590 1.8E-54
11 g5489.t1 PRINTS PR01047 Threonyl-tRNA synthetase signature 604 616 1.8E-54
2 g5489.t1 Pfam PF02824 TGS domain 75 135 9.9E-13
1 g5489.t1 Pfam PF07973 Threonyl and Alanyl tRNA synthetase second additional domain 242 290 2.2E-13
3 g5489.t1 Pfam PF00587 tRNA synthetase class II core domain (G, H, P, S and T) 393 598 5.6E-39
4 g5489.t1 Pfam PF03129 Anticodon binding domain 611 701 2.4E-22
32 g5489.t1 ProSiteProfiles PS51880 TGS domain profile. 73 135 19.468
31 g5489.t1 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 341 604 25.127
26 g5489.t1 SMART SM00863 tRNA_SAD_4 241 290 1.0E-18
15 g5489.t1 SUPERFAMILY SSF81271 TGS-like 75 135 6.87E-14
14 g5489.t1 SUPERFAMILY SSF55186 ThrRS/AlaRS common domain 137 313 4.97E-54
13 g5489.t1 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 314 595 2.3E-93
16 g5489.t1 SUPERFAMILY SSF52954 Class II aaRS ABD-related 597 703 1.66E-29
30 g5489.t1 TIGRFAM TIGR00418 thrS: threonine–tRNA ligase 146 701 7.9E-203

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5489/g5489.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5489.t1.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