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.t29 TTS g5489.t29 9844474 9844474
chr_2 g5489 g5489.t29 isoform g5489.t29 9844628 9847310
chr_2 g5489 g5489.t29 exon g5489.t29.exon1 9844628 9845566
chr_2 g5489 g5489.t29 cds g5489.t29.CDS1 9844628 9845566
chr_2 g5489 g5489.t29 exon g5489.t29.exon2 9845626 9846716
chr_2 g5489 g5489.t29 cds g5489.t29.CDS2 9845626 9846716
chr_2 g5489 g5489.t29 exon g5489.t29.exon3 9846810 9846867
chr_2 g5489 g5489.t29 cds g5489.t29.CDS3 9846810 9846867
chr_2 g5489 g5489.t29 exon g5489.t29.exon4 9847129 9847310
chr_2 g5489 g5489.t29 cds g5489.t29.CDS4 9847129 9847230
chr_2 g5489 g5489.t29 TSS g5489.t29 9847335 9847335

Sequences

>g5489.t29 Gene=g5489 Length=2270
ATGAGCAGTGAAATTTCGGAAAAATTAGAAAATTTGGATATAGAATCGAATCAGGCATGA
GATAATAGTTAATTTTAATAATGTTATTCTCAACATTTCAAAAAATAATTAATTTAAATA
AGTTTATTGTGGTAAATCAACTGAAAAGTGGAAATTGGAATCGGCAATGTTTTGCAACTT
TGGCCGCAAAACAAAAGGCTGCGAAAAAGAAGAAACAGGAAGAAATGGGTGTTGAAACAG
GAATTAAAGAATTGTCTCCACCACCATCATACATTGATGAGCGTATCAAACTATATGATC
GTTTAAAAGCAGAATATCTTGAAGAATTGAAAGCTAAACCGAGAGAAAAAATTCAAATTA
CATTGCCTGATGGAAAGATTGTTGAAGGATTATCATGGGAAACAACACCTTTTCAAATTG
CTGCAGGTATCAGTCAAGGATTAGCAGATAATACTGTTGTTGCAAAAGTAGATGATGAAG
TATGGGATTTAGATCGTGTACTTGAGAAAAGTTGCGCATTGAAACTTTTAAAATTTGATG
ATCCTGAAGCACAAGCTGTTTTTTGGCATAGCTCAGCTCATATTCTTGGTGAAGCAATGG
AAAGATGTTATGGTGGTTGTTTATGTTATGGACCTCCAATTGAAAATGGCTTTTATTATG
ACATGTTTTTGGATGGAGAAAATGTTTCTCCAACTCATTACAAAACACTCGAGGATCTCA
TTAAAAAAATTGTCAAAGAAAAGCAGCCATTTGAACGTTTGGAAATGAAAAAGTCGGATT
TATTAAAAATGTTTGAATACAATGAGTTTAAAAAGAGAATTCTCAATGAGAAAGTTGACA
CTGAAACTACTACTGTTTACCGTTGCGGACCATTAATTGATTTGTGTCGAGGACCTCATG
TACGTCACACAGGCAAAATTAAGGCAATGAAAGTAACAAAAAGCTCATCAACATATTGGG
AAGGAAAAGCTGATGCTGAAACTTTACAACGCATTTACGGAATTTCATTCCCTGATCCAA
AACAATTGAAAGAATGGGAAAAGATTCAAGAAGAGGCAGCAAAACGTGATCATCGTAAAA
TTGGACGAGAACAAGAACTCTTTTTCTTTCACGAATTATCACCAGGTTCATGCTTTTTCC
AACCTCGTGGTGCTCACATTTATAATACATTGATGAGCATGATTAGAGAGGAATATCGCA
AGCGAGGTTTTCAAGAAGTTATTTCGCCAAACATGTATAATGCAAAGTTATGGCAAACAT
CAGGACATTGGCAACATTATGCAGAAAATATGTTTTCGTTTGACGTTGAAAAGGAAAAAT
ATGCTCTTAAGCCGATGAATTGTCCAGGACATTGTCTAATGTTTGACGTTCGCAATCGCT
CTTGGCGTGAATTGCCTTTAAGAATGGCAGATTTTGGTGTTTTGCATCGTAACGAGTTTT
CTGGTGCATTGACAGGTTTAACCAGAGTTCGCCGATTCCAACAAGATGATGCTCATATCT
TTTGTGCGCCTGAACAAATAAAACAAGAAATTACAGGATGTTTGGATTTTTTGCGATGTG
TCTATGAAAAGTTTGGATTTAGTTTCGAATTAGTGCTTTCTACTCGTCCAGAGAAATTTT
TGGGTGAAATTGAAGTTTGGAATGAAGCAGAAAAAGCTCTTTCTGATTCTCTCGATGAAT
TTGGTGTGAAATGGGGATTAAATCCTGGTGATGGAGCATTTTATGGTCCTAAAATTGACA
TCACAATTAAAGATGCTCTCAAGCGCTCTCATCAATGTGCTACCATTCAACTTGATTTCC
AATTGCCAATTAGATTTAATTTGAGCTTTGTATCTGAAACAGGTGAAAAACGTCGACCTG
TCATTATTCATCGCGCCATTCTCGGTTCTGTAGAACGAATGATTGCAATTTTAACTGAAA
ATTGTGCAGGAAAATGGCCATTTTGGCTTTCACCAAGACAAGTAATGGTTGTTCCAGTAG
GACCGGGTTTGAATGACTATGCAGCTGAAGTTAGTGATCGTCTCTATAAAGCTGGTTTCA
TGTCTGAATTTGATACAGATGATGGTGATACAATGAATAAAAAGATTCGAAATGCACAAT
TGGCTCAATTCAATTTCATTTTGGTTGTTGGTGATAAAGAAAAAGCATCAGGAACTGTAA
ACGTACGTACACGAGATAACAAAGTTCACGGTGAATTATCAATTGATGAATTGATACAAA
AGTTTGAGAAACTACGTCGTGATTTTGTCAAAGATGAAGAAACATTTTAA

>g5489.t29 Gene=g5489 Length=729
MLFSTFQKIINLNKFIVVNQLKSGNWNRQCFATLAAKQKAAKKKKQEEMGVETGIKELSP
PPSYIDERIKLYDRLKAEYLEELKAKPREKIQITLPDGKIVEGLSWETTPFQIAAGISQG
LADNTVVAKVDDEVWDLDRVLEKSCALKLLKFDDPEAQAVFWHSSAHILGEAMERCYGGC
LCYGPPIENGFYYDMFLDGENVSPTHYKTLEDLIKKIVKEKQPFERLEMKKSDLLKMFEY
NEFKKRILNEKVDTETTTVYRCGPLIDLCRGPHVRHTGKIKAMKVTKSSSTYWEGKADAE
TLQRIYGISFPDPKQLKEWEKIQEEAAKRDHRKIGREQELFFFHELSPGSCFFQPRGAHI
YNTLMSMIREEYRKRGFQEVISPNMYNAKLWQTSGHWQHYAENMFSFDVEKEKYALKPMN
CPGHCLMFDVRNRSWRELPLRMADFGVLHRNEFSGALTGLTRVRRFQQDDAHIFCAPEQI
KQEITGCLDFLRCVYEKFGFSFELVLSTRPEKFLGEIEVWNEAEKALSDSLDEFGVKWGL
NPGDGAFYGPKIDITIKDALKRSHQCATIQLDFQLPIRFNLSFVSETGEKRRPVIIHRAI
LGSVERMIAILTENCAGKWPFWLSPRQVMVVPVGPGLNDYAAEVSDRLYKAGFMSEFDTD
DGDTMNKKIRNAQLAQFNFILVVGDKEKASGTVNVRTRDNKVHGELSIDELIQKFEKLRR
DFVKDEETF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g5489.t29 CDD cd01667 TGS_ThrRS 91 156 2.33636E-24
22 g5489.t29 CDD cd00771 ThrRS_core 329 625 0.0
24 g5489.t29 CDD cd00860 ThrRS_anticodon 625 716 2.80456E-34
21 g5489.t29 Coils Coil Coil 708 728 -
20 g5489.t29 Gene3D G3DSA:3.10.20.30 - 89 150 1.2E-27
18 g5489.t29 Gene3D G3DSA:3.30.980.10 - 155 310 7.7E-55
19 g5489.t29 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 312 618 6.1E-142
17 g5489.t29 Gene3D G3DSA:3.40.50.800 - 619 728 1.1E-39
7 g5489.t29 Hamap MF_00184 Threonine–tRNA ligase [thrS]. 156 717 29.499563
5 g5489.t29 PANTHER PTHR11451 THREONINE-TRNA LIGASE 38 720 0.0
6 g5489.t29 PANTHER PTHR11451:SF54 THREONYL-TRNA SYNTHETASE 38 720 0.0
9 g5489.t29 PRINTS PR01047 Threonyl-tRNA synthetase signature 416 444 1.9E-54
12 g5489.t29 PRINTS PR01047 Threonyl-tRNA synthetase signature 449 472 1.9E-54
8 g5489.t29 PRINTS PR01047 Threonyl-tRNA synthetase signature 550 578 1.9E-54
10 g5489.t29 PRINTS PR01047 Threonyl-tRNA synthetase signature 593 606 1.9E-54
11 g5489.t29 PRINTS PR01047 Threonyl-tRNA synthetase signature 620 632 1.9E-54
2 g5489.t29 Pfam PF02824 TGS domain 91 151 1.0E-12
1 g5489.t29 Pfam PF07973 Threonyl and Alanyl tRNA synthetase second additional domain 258 306 2.2E-13
3 g5489.t29 Pfam PF00587 tRNA synthetase class II core domain (G, H, P, S and T) 409 614 5.8E-39
4 g5489.t29 Pfam PF03129 Anticodon binding domain 627 717 2.5E-22
28 g5489.t29 ProSiteProfiles PS51880 TGS domain profile. 89 151 19.468
27 g5489.t29 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 357 620 25.127
25 g5489.t29 SMART SM00863 tRNA_SAD_4 257 306 1.0E-18
15 g5489.t29 SUPERFAMILY SSF81271 TGS-like 91 151 6.87E-14
14 g5489.t29 SUPERFAMILY SSF55186 ThrRS/AlaRS common domain 153 329 5.23E-54
13 g5489.t29 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 330 611 2.49E-93
16 g5489.t29 SUPERFAMILY SSF52954 Class II aaRS ABD-related 613 719 1.81E-29
26 g5489.t29 TIGRFAM TIGR00418 thrS: threonine–tRNA ligase 162 717 8.5E-203

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5489/g5489.t29; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5489.t29.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