General information for g5489.t31
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Threonine–tRNA ligase 1, cytoplasmic.
Parent gene
- The parent gene g5489 is located on chr_2: 9846707..9847795 (- strand)
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.t31 | TTS | g5489.t31 | 9844474 | 9844474 |
| chr_2 | g5489 | g5489.t31 | isoform | g5489.t31 | 9844941 | 9847310 |
| chr_2 | g5489 | g5489.t31 | exon | g5489.t31.exon1 | 9844941 | 9845566 |
| chr_2 | g5489 | g5489.t31 | cds | g5489.t31.CDS1 | 9844943 | 9845566 |
| chr_2 | g5489 | g5489.t31 | exon | g5489.t31.exon2 | 9845626 | 9846716 |
| chr_2 | g5489 | g5489.t31 | cds | g5489.t31.CDS2 | 9845626 | 9846716 |
| chr_2 | g5489 | g5489.t31 | exon | g5489.t31.exon3 | 9846810 | 9846867 |
| chr_2 | g5489 | g5489.t31 | cds | g5489.t31.CDS3 | 9846810 | 9846867 |
| chr_2 | g5489 | g5489.t31 | exon | g5489.t31.exon4 | 9847254 | 9847310 |
| chr_2 | g5489 | g5489.t31 | cds | g5489.t31.CDS4 | 9847254 | 9847310 |
| chr_2 | g5489 | g5489.t31 | TSS | g5489.t31 | 9847335 | 9847335 |
Sequences
>g5489.t31 Gene=g5489 Length=1832
ATGAGCAGTGAAATTTCGGAAAAATTAGAAAATTTGGATATAGAATCGAATCAGGCAGCC
GCAAAACAAAAGGCTGCGAAAAAGAAGAAACAGGAAGAAATGGGTGTTGAAACAGGAATT
AAAGAATTGTCTCCACCACCATCATACATTGATGAGCGTATCAAACTATATGATCGTTTA
AAAGCAGAATATCTTGAAGAATTGAAAGCTAAACCGAGAGAAAAAATTCAAATTACATTG
CCTGATGGAAAGATTGTTGAAGGATTATCATGGGAAACAACACCTTTTCAAATTGCTGCA
GGTATCAGTCAAGGATTAGCAGATAATACTGTTGTTGCAAAAGTAGATGATGAAGTATGG
GATTTAGATCGTGTACTTGAGAAAAGTTGCGCATTGAAACTTTTAAAATTTGATGATCCT
GAAGCACAAGCTGTTTTTTGGCATAGCTCAGCTCATATTCTTGGTGAAGCAATGGAAAGA
TGTTATGGTGGTTGTTTATGTTATGGACCTCCAATTGAAAATGGCTTTTATTATGACATG
TTTTTGGATGGAGAAAATGTTTCTCCAACTCATTACAAAACACTCGAGGATCTCATTAAA
AAAATTGTCAAAGAAAAGCAGCCATTTGAACGTTTGGAAATGAAAAAGTCGGATTTATTA
AAAATGTTTGAATACAATGAGTTTAAAAAGAGAATTCTCAATGAGAAAGTTGACACTGAA
ACTACTACTGTTTACCGTTGCGGACCATTAATTGATTTGTGTCGAGGACCTCATGTACGT
CACACAGGCAAAATTAAGGCAATGAAAGTAACAAAAAGCTCATCAACATATTGGGAAGGA
AAAGCTGATGCTGAAACTTTACAACGCATTTACGGAATTTCATTCCCTGATCCAAAACAA
TTGAAAGAATGGGAAAAGATTCAAGAAGAGGCAGCAAAACGTGATCATCGTAAAATTGGA
CGAGAACAAGAACTCTTTTTCTTTCACGAATTATCACCAGGTTCATGCTTTTTCCAACCT
CGTGGTGCTCACATTTATAATACATTGATGAGCATGATTAGAGAGGAATATCGCAAGCGA
GGTTTTCAAGAAGTTATTTCGCCAAACATGTATAATGCAAAGTTATGGCAAACATCAGGA
CATTGGCAACATTATGCAGAAAATATGTTTTCGTTTGACGTTGAAAAGGAAAAATATGCT
CTTAAGCCGATGAATTGTCCAGGACATTGTCTAATGTTTGACGTTCGCAATCGCTCTTGG
CGTGAATTGCCTTTAAGAATGGCAGATTTTGGTGTTTTGCATCGTAACGAGTTTTCTGGT
GCATTGACAGGTTTAACCAGAGTTCGCCGATTCCAACAAGATGATGCTCATATCTTTTGT
GCGCCTGAACAAATAAAACAAGAAATTACAGGATGTTTGGATTTTTTGCGATGTGTCTAT
GAAAAGTTTGGATTTAGTTTCGAATTAGTGCTTTCTACTCGTCCAGAGAAATTTTTGGGT
GAAATTGAAGTTTGGAATGAAGCAGAAAAAGCTCTTTCTGATTCTCTCGATGAATTTGGT
GTGAAATGGGGATTAAATCCTGGTGATGGAGCATTTTATGGTCCTAAAATTGACATCACA
ATTAAAGATGCTCTCAAGCGCTCTCATCAATGTGCTACCATTCAACTTGATTTCCAATTG
CCAATTAGATTTAATTTGAGCTTTGTATCTGAAACAGGTGAAAAACGTCGACCTGTCATT
ATTCATCGCGCCATTCTCGGTTCTGTAGAACGAATGATTGCAATTTTAACTGAAAATTGT
GCAGGAAAATGGCCATTTTGGCTTTCACCAAG
>g5489.t31 Gene=g5489 Length=610
MSSEISEKLENLDIESNQAAAKQKAAKKKKQEEMGVETGIKELSPPPSYIDERIKLYDRL
KAEYLEELKAKPREKIQITLPDGKIVEGLSWETTPFQIAAGISQGLADNTVVAKVDDEVW
DLDRVLEKSCALKLLKFDDPEAQAVFWHSSAHILGEAMERCYGGCLCYGPPIENGFYYDM
FLDGENVSPTHYKTLEDLIKKIVKEKQPFERLEMKKSDLLKMFEYNEFKKRILNEKVDTE
TTTVYRCGPLIDLCRGPHVRHTGKIKAMKVTKSSSTYWEGKADAETLQRIYGISFPDPKQ
LKEWEKIQEEAAKRDHRKIGREQELFFFHELSPGSCFFQPRGAHIYNTLMSMIREEYRKR
GFQEVISPNMYNAKLWQTSGHWQHYAENMFSFDVEKEKYALKPMNCPGHCLMFDVRNRSW
RELPLRMADFGVLHRNEFSGALTGLTRVRRFQQDDAHIFCAPEQIKQEITGCLDFLRCVY
EKFGFSFELVLSTRPEKFLGEIEVWNEAEKALSDSLDEFGVKWGLNPGDGAFYGPKIDIT
IKDALKRSHQCATIQLDFQLPIRFNLSFVSETGEKRRPVIIHRAILGSVERMIAILTENC
AGKWPFWLSP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g5489.t31 | CDD | cd01667 | TGS_ThrRS | 76 | 141 | 1.72334E-24 |
| 18 | g5489.t31 | CDD | cd00771 | ThrRS_core | 314 | 610 | 0.0 |
| 17 | g5489.t31 | Coils | Coil | Coil | 9 | 29 | - |
| 16 | g5489.t31 | Gene3D | G3DSA:3.10.20.30 | - | 74 | 135 | 9.5E-28 |
| 14 | g5489.t31 | Gene3D | G3DSA:3.30.980.10 | - | 140 | 295 | 5.7E-55 |
| 15 | g5489.t31 | Gene3D | G3DSA:3.30.930.10 | Bira Bifunctional Protein; Domain 2 | 297 | 604 | 4.0E-142 |
| 21 | g5489.t31 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 42 | - |
| 22 | g5489.t31 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 18 | - |
| 4 | g5489.t31 | PANTHER | PTHR11451 | THREONINE-TRNA LIGASE | 26 | 610 | 0.0 |
| 5 | g5489.t31 | PANTHER | PTHR11451:SF54 | THREONYL-TRNA SYNTHETASE | 26 | 610 | 0.0 |
| 6 | g5489.t31 | PRINTS | PR01047 | Threonyl-tRNA synthetase signature | 401 | 429 | 3.3E-52 |
| 10 | g5489.t31 | PRINTS | PR01047 | Threonyl-tRNA synthetase signature | 434 | 457 | 3.3E-52 |
| 9 | g5489.t31 | PRINTS | PR01047 | Threonyl-tRNA synthetase signature | 535 | 563 | 3.3E-52 |
| 8 | g5489.t31 | PRINTS | PR01047 | Threonyl-tRNA synthetase signature | 578 | 591 | 3.3E-52 |
| 7 | g5489.t31 | PRINTS | PR01047 | Threonyl-tRNA synthetase signature | 605 | 610 | 3.3E-52 |
| 2 | g5489.t31 | Pfam | PF02824 | TGS domain | 76 | 136 | 8.1E-13 |
| 1 | g5489.t31 | Pfam | PF07973 | Threonyl and Alanyl tRNA synthetase second additional domain | 243 | 291 | 1.8E-13 |
| 3 | g5489.t31 | Pfam | PF00587 | tRNA synthetase class II core domain (G, H, P, S and T) | 394 | 599 | 4.1E-39 |
| 25 | g5489.t31 | ProSiteProfiles | PS51880 | TGS domain profile. | 74 | 136 | 19.468 |
| 24 | g5489.t31 | ProSiteProfiles | PS50862 | Aminoacyl-transfer RNA synthetases class-II family profile. | 342 | 605 | 25.127 |
| 20 | g5489.t31 | SMART | SM00863 | tRNA_SAD_4 | 242 | 291 | 1.0E-18 |
| 13 | g5489.t31 | SUPERFAMILY | SSF81271 | TGS-like | 76 | 136 | 5.56E-14 |
| 12 | g5489.t31 | SUPERFAMILY | SSF55186 | ThrRS/AlaRS common domain | 138 | 314 | 3.79E-54 |
| 11 | g5489.t31 | SUPERFAMILY | SSF55681 | Class II aaRS and biotin synthetases | 315 | 596 | 1.67E-93 |
| 23 | g5489.t31 | TIGRFAM | TIGR00418 | thrS: threonine–tRNA ligase | 147 | 610 | 6.1E-174 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5489/g5489.t31; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5489.t31.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
- This transcript has been annotated with K01868 (threonyl-tRNA synthetase)
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. There were no conditions that were differentially expressed