General information for g3578.t20
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Valine–tRNA ligase.
Parent gene
- The parent gene g3578 is located on chr_3: 26527032..26528478 (+ 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_3 | g3578 | g3578.t20 | TSS | g3578.t20 | 26525057 | 26525057 |
| chr_3 | g3578 | g3578.t20 | isoform | g3578.t20 | 26525096 | 26526647 |
| chr_3 | g3578 | g3578.t20 | exon | g3578.t20.exon1 | 26525096 | 26525751 |
| chr_3 | g3578 | g3578.t20 | cds | g3578.t20.CDS1 | 26525599 | 26525751 |
| chr_3 | g3578 | g3578.t20 | exon | g3578.t20.exon2 | 26525810 | 26526647 |
| chr_3 | g3578 | g3578.t20 | cds | g3578.t20.CDS2 | 26525810 | 26526646 |
| chr_3 | g3578 | g3578.t20 | TTS | g3578.t20 | NA | NA |
Sequences
>g3578.t20 Gene=g3578 Length=1494
ATGACTAATGTAAAAACTGATGAAGCTGCAAACGAGGAAGTTGTTGAAAAAAGTGCAAAA
CAACTCGAGAAAGAAGCTAAAAAAGCTGCTAAATTAGCTAAGCTTCAAGAAAAACAAGCA
AAACAGGCTACTCAACAAGCAAATACAGCACCTAAGGAAAAAGAGGTAAATTGAAATAAA
AATTTGGTTATTTACACATGTCCACGAATCATTTACTTACTTTCACAATTGCATACGTAG
AAAAAAGCTAAATCTGTAGTGAAAGACATTATTTATGAAGGAAATTCAAAGGATGGTGAA
AAGAAGGATTTATCTGGACCTATGCCAGAAGCTTACTCGCCTCAATACGTTGAAGCAGCG
TGGTATTCTTGGTGGGAGAAACAAGGATTTTTCAAGCCGGAATATTCTGTAAGAATTTTA
AATATTGCGAAAATAAATCATTACGTTTAAAGCTTATTTTATAGATGAAAAATGGAAAAA
TATCTTCGAAAGGTCAATTTGTAATGGTTATTCCACCACCGAATGTTACTGGCTCTTTGC
ATTTAGGTCATGCTTTGACAAATTCTATTGAAGATGCAATTGCAAGATGGCATAGAATGC
ATGGACGAACAACTCTTTGGGTTCCAGGTTGTGACCATGCTGGCATTGCAACTCAAGTAG
TCGTAGAGAAAAAATTGTGGAGAGAAGAGAAACTCAGTCGTCATGATCTTGGTCGAGAAA
AGTTTATTGAAAAAATTTGGGAATGGAAAGAGAACAAGGGAGGTAGAATTTATCATCAAT
TGAGAAAAATTGGTTCATCTATGGATTGGGATCGTGTTTCCTTCACAATGGATCCAAAAC
TTTGTCGTGCTGTTACTGAAGCTTTCAATCAAATGCATGAAAAGGGTTTGATTTATCGTG
ATAAACGATTAGTTAATTGGTCATGTACTCTTAAATCTGCTATTTCTGATATTGAAGTTG
ACAAAGTAGAAATTCCTGGTCGTACTTTTTTAGCGATTCCTGGCTATCAAGATAAGATTG
AATTTGGAGTTTTGGTATCGTTTGCATATCAAATTGAAGGCACAAATGAAGAAATTGTTG
TTGCTACTACTCGTATTGAAACAATGCTTGGTGATACTGCTGTTGCTATTCACCCAAAAG
ACACACGCTACACTCATTTACATGGAAAATTTGTAAAACATCCATTTGTTGATCGTCGCT
TACCGATTGTATTGGATGATTTCGTCGATATGGAGTTCGGTACTGGTGCTGTCAAAATCA
CTCCAGCACATGATCCTAATGATTATGAAGTTGGAAAGCGACATGATTTACCATTCATTA
CAATTTTTAGTGATGATGGTATTATTGTCGGTGATTATGGCAAATTTACGGGAATGAAAC
GTTTTGATGCACGTAAAGCTGTTTTAGCATCACTCAAGGAGCTTGGACTTTATAAAGAAA
CCATCAATAATCCAATGATTGTTCCCATTTGCAGTCGCTCTAAAGATGTTGTTG
>g3578.t20 Gene=g3578 Length=330
MVIPPPNVTGSLHLGHALTNSIEDAIARWHRMHGRTTLWVPGCDHAGIATQVVVEKKLWR
EEKLSRHDLGREKFIEKIWEWKENKGGRIYHQLRKIGSSMDWDRVSFTMDPKLCRAVTEA
FNQMHEKGLIYRDKRLVNWSCTLKSAISDIEVDKVEIPGRTFLAIPGYQDKIEFGVLVSF
AYQIEGTNEEIVVATTRIETMLGDTAVAIHPKDTRYTHLHGKFVKHPFVDRRLPIVLDDF
VDMEFGTGAVKITPAHDPNDYEVGKRHDLPFITIFSDDGIIVGDYGKFTGMKRFDARKAV
LASLKELGLYKETINNPMIVPICSRSKDVV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g3578.t20 | Gene3D | G3DSA:3.40.50.620 | HUPs | 1 | 161 | 1.5E-53 |
| 8 | g3578.t20 | Gene3D | G3DSA:3.90.740.10 | - | 173 | 315 | 2.2E-52 |
| 2 | g3578.t20 | PANTHER | PTHR11946:SF110 | VALINE–TRNA LIGASE | 1 | 330 | 2.1E-189 |
| 3 | g3578.t20 | PANTHER | PTHR11946 | VALYL-TRNA SYNTHETASES | 1 | 330 | 2.1E-189 |
| 1 | g3578.t20 | Pfam | PF00133 | tRNA synthetases class I (I, L, M and V) | 2 | 330 | 7.1E-114 |
| 6 | g3578.t20 | ProSitePatterns | PS00178 | Aminoacyl-transfer RNA synthetases class-I signature. | 6 | 17 | - |
| 4 | g3578.t20 | SUPERFAMILY | SSF52374 | Nucleotidylyl transferase | 3 | 329 | 7.82E-53 |
| 5 | g3578.t20 | SUPERFAMILY | SSF50677 | ValRS/IleRS/LeuRS editing domain | 171 | 320 | 1.44E-58 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005524 | ATP binding | MF |
| GO:0002161 | aminoacyl-tRNA editing activity | MF |
| GO:0006418 | tRNA aminoacylation for protein translation | BP |
| GO:0000166 | nucleotide binding | MF |
| GO:0004812 | aminoacyl-tRNA ligase activity | MF |
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.
