General information for g5489.t30
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.t30 | TTS | g5489.t30 | 9844474 | 9844474 |
| chr_2 | g5489 | g5489.t30 | isoform | g5489.t30 | 9844941 | 9847310 |
| chr_2 | g5489 | g5489.t30 | exon | g5489.t30.exon1 | 9844941 | 9845566 |
| chr_2 | g5489 | g5489.t30 | cds | g5489.t30.CDS1 | 9844943 | 9845566 |
| chr_2 | g5489 | g5489.t30 | exon | g5489.t30.exon2 | 9845626 | 9846707 |
| chr_2 | g5489 | g5489.t30 | cds | g5489.t30.CDS2 | 9845626 | 9846707 |
| chr_2 | g5489 | g5489.t30 | exon | g5489.t30.exon3 | 9846806 | 9846867 |
| chr_2 | g5489 | g5489.t30 | cds | g5489.t30.CDS3 | 9846806 | 9846867 |
| chr_2 | g5489 | g5489.t30 | exon | g5489.t30.exon4 | 9847260 | 9847310 |
| chr_2 | g5489 | g5489.t30 | cds | g5489.t30.CDS4 | 9847260 | 9847261 |
| chr_2 | g5489 | g5489.t30 | TSS | g5489.t30 | 9847335 | 9847335 |
Sequences
>g5489.t30 Gene=g5489 Length=1821
ATGAGCAGTGAAATTTCGGAAAAATTAGAAAATTTGGATATAGAATCGAATGCCGCAAAA
CAAAAGGCTGCGAAAAAGAAGAAACAGGAAGAAATGGGTGTTGAAACAGGTTAAATTGTC
TCCACCACCATCATACATTGATGAGCGTATCAAACTATATGATCGTTTAAAAGCAGAATA
TCTTGAAGAATTGAAAGCTAAACCGAGAGAAAAAATTCAAATTACATTGCCTGATGGAAA
GATTGTTGAAGGATTATCATGGGAAACAACACCTTTTCAAATTGCTGCAGGTATCAGTCA
AGGATTAGCAGATAATACTGTTGTTGCAAAAGTAGATGATGAAGTATGGGATTTAGATCG
TGTACTTGAGAAAAGTTGCGCATTGAAACTTTTAAAATTTGATGATCCTGAAGCACAAGC
TGTTTTTTGGCATAGCTCAGCTCATATTCTTGGTGAAGCAATGGAAAGATGTTATGGTGG
TTGTTTATGTTATGGACCTCCAATTGAAAATGGCTTTTATTATGACATGTTTTTGGATGG
AGAAAATGTTTCTCCAACTCATTACAAAACACTCGAGGATCTCATTAAAAAAATTGTCAA
AGAAAAGCAGCCATTTGAACGTTTGGAAATGAAAAAGTCGGATTTATTAAAAATGTTTGA
ATACAATGAGTTTAAAAAGAGAATTCTCAATGAGAAAGTTGACACTGAAACTACTACTGT
TTACCGTTGCGGACCATTAATTGATTTGTGTCGAGGACCTCATGTACGTCACACAGGCAA
AATTAAGGCAATGAAAGTAACAAAAAGCTCATCAACATATTGGGAAGGAAAAGCTGATGC
TGAAACTTTACAACGCATTTACGGAATTTCATTCCCTGATCCAAAACAATTGAAAGAATG
GGAAAAGATTCAAGAAGAGGCAGCAAAACGTGATCATCGTAAAATTGGACGAGAACAAGA
ACTCTTTTTCTTTCACGAATTATCACCAGGTTCATGCTTTTTCCAACCTCGTGGTGCTCA
CATTTATAATACATTGATGAGCATGATTAGAGAGGAATATCGCAAGCGAGGTTTTCAAGA
AGTTATTTCGCCAAACATGTATAATGCAAAGTTATGGCAAACATCAGGACATTGGCAACA
TTATGCAGAAAATATGTTTTCGTTTGACGTTGAAAAGGAAAAATATGCTCTTAAGCCGAT
GAATTGTCCAGGACATTGTCTAATGTTTGACGTTCGCAATCGCTCTTGGCGTGAATTGCC
TTTAAGAATGGCAGATTTTGGTGTTTTGCATCGTAACGAGTTTTCTGGTGCATTGACAGG
TTTAACCAGAGTTCGCCGATTCCAACAAGATGATGCTCATATCTTTTGTGCGCCTGAACA
AATAAAACAAGAAATTACAGGATGTTTGGATTTTTTGCGATGTGTCTATGAAAAGTTTGG
ATTTAGTTTCGAATTAGTGCTTTCTACTCGTCCAGAGAAATTTTTGGGTGAAATTGAAGT
TTGGAATGAAGCAGAAAAAGCTCTTTCTGATTCTCTCGATGAATTTGGTGTGAAATGGGG
ATTAAATCCTGGTGATGGAGCATTTTATGGTCCTAAAATTGACATCACAATTAAAGATGC
TCTCAAGCGCTCTCATCAATGTGCTACCATTCAACTTGATTTCCAATTGCCAATTAGATT
TAATTTGAGCTTTGTATCTGAAACAGGTGAAAAACGTCGACCTGTCATTATTCATCGCGC
CATTCTCGGTTCTGTAGAACGAATGATTGCAATTTTAACTGAAAATTGTGCAGGAAAATG
GCCATTTTGGCTTTCACCAAG
>g5489.t30 Gene=g5489 Length=590
MPQNKRLRKRRNRKKWVLKQVKLSPPPSYIDERIKLYDRLKAEYLEELKAKPREKIQITL
PDGKIVEGLSWETTPFQIAAGISQGLADNTVVAKVDDEVWDLDRVLEKSCALKLLKFDDP
EAQAVFWHSSAHILGEAMERCYGGCLCYGPPIENGFYYDMFLDGENVSPTHYKTLEDLIK
KIVKEKQPFERLEMKKSDLLKMFEYNEFKKRILNEKVDTETTTVYRCGPLIDLCRGPHVR
HTGKIKAMKVTKSSSTYWEGKADAETLQRIYGISFPDPKQLKEWEKIQEEAAKRDHRKIG
REQELFFFHELSPGSCFFQPRGAHIYNTLMSMIREEYRKRGFQEVISPNMYNAKLWQTSG
HWQHYAENMFSFDVEKEKYALKPMNCPGHCLMFDVRNRSWRELPLRMADFGVLHRNEFSG
ALTGLTRVRRFQQDDAHIFCAPEQIKQEITGCLDFLRCVYEKFGFSFELVLSTRPEKFLG
EIEVWNEAEKALSDSLDEFGVKWGLNPGDGAFYGPKIDITIKDALKRSHQCATIQLDFQL
PIRFNLSFVSETGEKRRPVIIHRAILGSVERMIAILTENCAGKWPFWLSP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g5489.t30 | CDD | cd01667 | TGS_ThrRS | 56 | 121 | 0.000 |
| 17 | g5489.t30 | CDD | cd00771 | ThrRS_core | 294 | 590 | 0.000 |
| 16 | g5489.t30 | Gene3D | G3DSA:3.10.20.30 | - | 54 | 115 | 0.000 |
| 14 | g5489.t30 | Gene3D | G3DSA:3.30.980.10 | - | 120 | 275 | 0.000 |
| 15 | g5489.t30 | Gene3D | G3DSA:3.30.930.10 | Bira Bifunctional Protein; Domain 2 | 277 | 584 | 0.000 |
| 4 | g5489.t30 | PANTHER | PTHR11451 | THREONINE-TRNA LIGASE | 15 | 590 | 0.000 |
| 5 | g5489.t30 | PANTHER | PTHR11451:SF54 | THREONYL-TRNA SYNTHETASE | 15 | 590 | 0.000 |
| 10 | g5489.t30 | PRINTS | PR01047 | Threonyl-tRNA synthetase signature | 381 | 409 | 0.000 |
| 9 | g5489.t30 | PRINTS | PR01047 | Threonyl-tRNA synthetase signature | 414 | 437 | 0.000 |
| 7 | g5489.t30 | PRINTS | PR01047 | Threonyl-tRNA synthetase signature | 515 | 543 | 0.000 |
| 6 | g5489.t30 | PRINTS | PR01047 | Threonyl-tRNA synthetase signature | 558 | 571 | 0.000 |
| 8 | g5489.t30 | PRINTS | PR01047 | Threonyl-tRNA synthetase signature | 585 | 590 | 0.000 |
| 2 | g5489.t30 | Pfam | PF02824 | TGS domain | 56 | 116 | 0.000 |
| 1 | g5489.t30 | Pfam | PF07973 | Threonyl and Alanyl tRNA synthetase second additional domain | 223 | 271 | 0.000 |
| 3 | g5489.t30 | Pfam | PF00587 | tRNA synthetase class II core domain (G, H, P, S and T) | 374 | 579 | 0.000 |
| 22 | g5489.t30 | ProSiteProfiles | PS51880 | TGS domain profile. | 54 | 116 | 19.468 |
| 21 | g5489.t30 | ProSiteProfiles | PS50862 | Aminoacyl-transfer RNA synthetases class-II family profile. | 322 | 585 | 25.127 |
| 19 | g5489.t30 | SMART | SM00863 | tRNA_SAD_4 | 222 | 271 | 0.000 |
| 13 | g5489.t30 | SUPERFAMILY | SSF81271 | TGS-like | 56 | 116 | 0.000 |
| 12 | g5489.t30 | SUPERFAMILY | SSF55186 | ThrRS/AlaRS common domain | 118 | 294 | 0.000 |
| 11 | g5489.t30 | SUPERFAMILY | SSF55681 | Class II aaRS and biotin synthetases | 295 | 576 | 0.000 |
| 20 | g5489.t30 | TIGRFAM | TIGR00418 | thrS: threonine–tRNA ligase | 127 | 590 | 0.000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5489/g5489.t30; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5489.t30.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.
