General information for g5489.t33
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.t33 | isoform | g5489.t33 | 9845634 | 9847310 |
| chr_2 | g5489 | g5489.t33 | exon | g5489.t33.exon1 | 9845634 | 9846716 |
| chr_2 | g5489 | g5489.t33 | cds | g5489.t33.CDS1 | 9845635 | 9846716 |
| chr_2 | g5489 | g5489.t33 | exon | g5489.t33.exon2 | 9846810 | 9846867 |
| chr_2 | g5489 | g5489.t33 | cds | g5489.t33.CDS2 | 9846810 | 9846867 |
| chr_2 | g5489 | g5489.t33 | exon | g5489.t33.exon3 | 9847257 | 9847310 |
| chr_2 | g5489 | g5489.t33 | cds | g5489.t33.CDS3 | 9847257 | 9847310 |
| chr_2 | g5489 | g5489.t33 | TSS | g5489.t33 | 9847335 | 9847335 |
| chr_2 | g5489 | g5489.t33 | TTS | g5489.t33 | NA | NA |
Sequences
>g5489.t33 Gene=g5489 Length=1195
ATGAGCAGTGAAATTTCGGAAAAATTAGAAAATTTGGATATAGAATCGAATCAGGCCGCA
AAACAAAAGGCTGCGAAAAAGAAGAAACAGGAAGAAATGGGTGTTGAAACAGGAATTAAA
GAATTGTCTCCACCACCATCATACATTGATGAGCGTATCAAACTATATGATCGTTTAAAA
GCAGAATATCTTGAAGAATTGAAAGCTAAACCGAGAGAAAAAATTCAAATTACATTGCCT
GATGGAAAGATTGTTGAAGGATTATCATGGGAAACAACACCTTTTCAAATTGCTGCAGGT
ATCAGTCAAGGATTAGCAGATAATACTGTTGTTGCAAAAGTAGATGATGAAGTATGGGAT
TTAGATCGTGTACTTGAGAAAAGTTGCGCATTGAAACTTTTAAAATTTGATGATCCTGAA
GCACAAGCTGTTTTTTGGCATAGCTCAGCTCATATTCTTGGTGAAGCAATGGAAAGATGT
TATGGTGGTTGTTTATGTTATGGACCTCCAATTGAAAATGGCTTTTATTATGACATGTTT
TTGGATGGAGAAAATGTTTCTCCAACTCATTACAAAACACTCGAGGATCTCATTAAAAAA
ATTGTCAAAGAAAAGCAGCCATTTGAACGTTTGGAAATGAAAAAGTCGGATTTATTAAAA
ATGTTTGAATACAATGAGTTTAAAAAGAGAATTCTCAATGAGAAAGTTGACACTGAAACT
ACTACTGTTTACCGTTGCGGACCATTAATTGATTTGTGTCGAGGACCTCATGTACGTCAC
ACAGGCAAAATTAAGGCAATGAAAGTAACAAAAAGCTCATCAACATATTGGGAAGGAAAA
GCTGATGCTGAAACTTTACAACGCATTTACGGAATTTCATTCCCTGATCCAAAACAATTG
AAAGAATGGGAAAAGATTCAAGAAGAGGCAGCAAAACGTGATCATCGTAAAATTGGACGA
GAACAAGAACTCTTTTTCTTTCACGAATTATCACCAGGTTCATGCTTTTTCCAACCTCGT
GGTGCTCACATTTATAATACATTGATGAGCATGATTAGAGAGGAATATCGCAAGCGAGGT
TTTCAAGAAGTTATTTCGCCAAACATGTATAATGCAAAGTTATGGCAAACATCAGGACAT
TGGCAACATTATGCAGAAAATATGTTTTCGTTTGACGTTGAAAAGGAAAAATATG
>g5489.t33 Gene=g5489 Length=398
MSSEISEKLENLDIESNQAAKQKAAKKKKQEEMGVETGIKELSPPPSYIDERIKLYDRLK
AEYLEELKAKPREKIQITLPDGKIVEGLSWETTPFQIAAGISQGLADNTVVAKVDDEVWD
LDRVLEKSCALKLLKFDDPEAQAVFWHSSAHILGEAMERCYGGCLCYGPPIENGFYYDMF
LDGENVSPTHYKTLEDLIKKIVKEKQPFERLEMKKSDLLKMFEYNEFKKRILNEKVDTET
TTVYRCGPLIDLCRGPHVRHTGKIKAMKVTKSSSTYWEGKADAETLQRIYGISFPDPKQL
KEWEKIQEEAAKRDHRKIGREQELFFFHELSPGSCFFQPRGAHIYNTLMSMIREEYRKRG
FQEVISPNMYNAKLWQTSGHWQHYAENMFSFDVEKEKY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g5489.t33 | CDD | cd01667 | TGS_ThrRS | 75 | 140 | 1.15957E-24 |
| 11 | g5489.t33 | Coils | Coil | Coil | 9 | 32 | - |
| 10 | g5489.t33 | Gene3D | G3DSA:3.10.20.30 | - | 73 | 134 | 5.1E-28 |
| 8 | g5489.t33 | Gene3D | G3DSA:3.30.980.10 | - | 139 | 294 | 2.4E-55 |
| 9 | g5489.t33 | Gene3D | G3DSA:3.30.930.10 | Bira Bifunctional Protein; Domain 2 | 296 | 398 | 1.1E-37 |
| 15 | g5489.t33 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 18 | - |
| 16 | g5489.t33 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 41 | - |
| 14 | g5489.t33 | MobiDBLite | mobidb-lite | consensus disorder prediction | 20 | 36 | - |
| 3 | g5489.t33 | PANTHER | PTHR11451 | THREONINE-TRNA LIGASE | 25 | 397 | 2.0E-202 |
| 4 | g5489.t33 | PANTHER | PTHR11451:SF54 | THREONYL-TRNA SYNTHETASE | 25 | 397 | 2.0E-202 |
| 2 | g5489.t33 | Pfam | PF02824 | TGS domain | 75 | 135 | 4.4E-13 |
| 1 | g5489.t33 | Pfam | PF07973 | Threonyl and Alanyl tRNA synthetase second additional domain | 242 | 290 | 1.0E-13 |
| 18 | g5489.t33 | ProSiteProfiles | PS51880 | TGS domain profile. | 73 | 135 | 19.468 |
| 17 | g5489.t33 | ProSiteProfiles | PS50862 | Aminoacyl-transfer RNA synthetases class-II family profile. | 341 | 398 | 9.658 |
| 13 | g5489.t33 | SMART | SM00863 | tRNA_SAD_4 | 241 | 290 | 1.0E-18 |
| 7 | g5489.t33 | SUPERFAMILY | SSF81271 | TGS-like | 75 | 135 | 2.91E-14 |
| 6 | g5489.t33 | SUPERFAMILY | SSF55186 | ThrRS/AlaRS common domain | 137 | 313 | 1.57E-54 |
| 5 | g5489.t33 | SUPERFAMILY | SSF55681 | Class II aaRS and biotin synthetases | 290 | 392 | 7.36E-25 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5489/g5489.t33; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5489.t33.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:0000166 | nucleotide binding | MF |
| GO:0043039 | tRNA aminoacylation | BP |
| GO:0004812 | aminoacyl-tRNA ligase activity | MF |
| GO:0006435 | threonyl-tRNA aminoacylation | BP |
| GO:0005737 | cytoplasm | CC |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
