General information for g3578.t22
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.t22 | TSS | g3578.t22 | 26525057 | 26525057 |
| chr_3 | g3578 | g3578.t22 | isoform | g3578.t22 | 26526053 | 26528478 |
| chr_3 | g3578 | g3578.t22 | exon | g3578.t22.exon1 | 26526053 | 26527564 |
| chr_3 | g3578 | g3578.t22 | cds | g3578.t22.CDS1 | 26526257 | 26527564 |
| chr_3 | g3578 | g3578.t22 | exon | g3578.t22.exon2 | 26527624 | 26528478 |
| chr_3 | g3578 | g3578.t22 | cds | g3578.t22.CDS2 | 26527624 | 26528478 |
| chr_3 | g3578 | g3578.t22 | TTS | g3578.t22 | 26528550 | 26528550 |
Sequences
>g3578.t22 Gene=g3578 Length=2367
GATAAACGATTAGTTAATTGGTCATGTACTCTTAAATCTGCTATTTCTGATATTGAAGTT
GACAAAGTAGAAATTCCTGGTCGTACTTTTTTAGCGATTCCTGGCTATCAAGATAAGATT
GAATTTGGAGTTTTGGTATCGTTTGCATATCAAATTGAAGGCACAAATGAAGAAATTGTT
GTTGCTACTACTCGTATTGAAACAATGCTTGGTGATACTGCTGTTGCTATTCACCCAAAA
GACACACGCTACACTCATTTACATGGAAAATTTGTAAAACATCCATTTGTTGATCGTCGC
TTACCGATTGTATTGGATGATTTCGTCGATATGGAGTTCGGTACTGGTGCTGTCAAAATC
ACTCCAGCACATGATCCTAATGATTATGAAGTTGGAAAGCGACATGATTTACCATTCATT
ACAATTTTTAGTGATGATGGTATTATTGTCGGTGATTATGGCAAATTTACGGGAATGAAA
CGTTTTGATGCACGTAAAGCTGTTTTAGCATCACTCAAGGAGCTTGGACTTTATAAAGAA
ACCATCAATAATCCAATGATTGTTCCCATTTGCAGTCGCTCTAAAGATGTTGTTGAGCCT
TTAATTAAACCACAATGGTATGTTAAATGTGAAGATATGGCTAAGAAAGCAACAGACTCA
GTAAAAACAGGTGAGCTGAAAATCATTCCCGAATCGTTCACGAAAACTTGGTTTCATTGG
ATGGATGGCATTAGAGATTGGTGCATTTCACGTCAACTTTGGTGGGGACATAGAATTCCT
GCTTATTTCATTAAATTCAAAGATTCATCAAAAGCTCAAGCAATTACTGAAGAACAAGAT
TTTTGGATTGTTGCAAGAAGTATCGATGATGCACATACGAAAGCGAAAAAGAAGTTTAAT
ATTACAAGAGAAGATTATGAATTGCAACAAGATGAAGATGTGCTCGATACGTGGTTCAGC
TCTGGATTGTTTCCATTTTCTGTATTTGGCTGGCCTGATCAAACAGAAGATTTGAAACTT
TTTTATCCAACGACTCTTCTCGAAACAGGTCATGATATTTTATTTTTTTGGGTAGCTCGT
ATGGTTTTCTTTGGTCAAACTTTATTAGGTAAACTTCCATTTAAGTATGTTTTTCTTCAT
CCTATGGTTCGCGATGCGCATGGAAGAAAAATGTCAAAATCGCTTGGAAATGTTATTGAT
CCTATGGACGTTATAAACGGAATCTCGCTCGATGGATTGCATCAACAATTAATAGATTCA
AATTTAGATCCTCGTGAAATTGAAAAAGCAAAAGCAGGTCAAAAACAAGATTTTCCAAAC
GGTATTCCTGAATGTGGAACAGATGCTATGCGATTTACACTTTGTAATTACATGACTCAA
GCAAGAGATATTAATTTAGATATCATGCGTGTACAAGGCTATAGATTTTTCTGCAATAAG
CTGTGGAATGCTACGAAATTTGCATTAAGATATTTTGAAGATGGTGAAACATATGAAATT
CATGATAAAATGACATCAAAAGAAAGTAAAGTTGATTTATGGATTCTATCAAAACTTTCC
AATACTATTGAAATTGTTAATAAATCATTTGAAAATTACGAATTTGCTACTGCAACACAA
GTATGTTATACCTTCTGGTTATATGAGTTATGTGATAACTATTTGGAATGTTTGAAACCG
GTATTTGCATCTGATGACAATGAAAAGAAAGCAATAGCAAGACGTATTCTTTATACATGC
TTAGATTATGGCTTAAGACTTCTATCACCTTTTATGCCGTTCATCACTGAAGAGTTGTTT
CAACGTTTACCAAGAAAAAATATTGAAATTCCGAGCATTTGCGTTGCTCCTTATCCAGAT
ATAGAACAATTTAACTTTAAGAATGAAGATATCGAGAAAGATTTTGACTTTGTTCAAAAA
GTTGTAAAAGAAATACGATCTGCACGAAGTGATTATAACATACCAGCAAAGACAAAAACC
GAAGCGTTTGCAATTTGTTCTGATAGCAAATTAAGTGAAATATTAAATGATTTTAAAGAG
GAGTTACAGGCATTATCATACTGTTCAAATATAGAGCTAACAACTACAGGCCCTAATGGA
TGCGCGATTTTATCTATCAACGCTCATTGTGAGATTCATTTGCTACTTAAAGGAATTATT
GAAGCTGATAAAGAAATCGCAAAATTAGAAAAGAAGCGAGAAACCATGCAACAAACTATT
AATAAACTGAAGCAGAAAATGAGTATCGAAGATTATGAGAAAAAAGTTCCGGAGAACATT
CAACAAGAAAATATTGAAAATTTAAAGCAAACAGAGATAGAAATTGAAAGAATTGGAAAT
GCAATTGAAGCTTTGAAATTAATGTAA
>g3578.t22 Gene=g3578 Length=720
MLGDTAVAIHPKDTRYTHLHGKFVKHPFVDRRLPIVLDDFVDMEFGTGAVKITPAHDPND
YEVGKRHDLPFITIFSDDGIIVGDYGKFTGMKRFDARKAVLASLKELGLYKETINNPMIV
PICSRSKDVVEPLIKPQWYVKCEDMAKKATDSVKTGELKIIPESFTKTWFHWMDGIRDWC
ISRQLWWGHRIPAYFIKFKDSSKAQAITEEQDFWIVARSIDDAHTKAKKKFNITREDYEL
QQDEDVLDTWFSSGLFPFSVFGWPDQTEDLKLFYPTTLLETGHDILFFWVARMVFFGQTL
LGKLPFKYVFLHPMVRDAHGRKMSKSLGNVIDPMDVINGISLDGLHQQLIDSNLDPREIE
KAKAGQKQDFPNGIPECGTDAMRFTLCNYMTQARDINLDIMRVQGYRFFCNKLWNATKFA
LRYFEDGETYEIHDKMTSKESKVDLWILSKLSNTIEIVNKSFENYEFATATQVCYTFWLY
ELCDNYLECLKPVFASDDNEKKAIARRILYTCLDYGLRLLSPFMPFITEELFQRLPRKNI
EIPSICVAPYPDIEQFNFKNEDIEKDFDFVQKVVKEIRSARSDYNIPAKTKTEAFAICSD
SKLSEILNDFKEELQALSYCSNIELTTTGPNGCAILSINAHCEIHLLLKGIIEADKEIAK
LEKKRETMQQTINKLKQKMSIEDYEKKVPENIQQENIENLKQTEIEIERIGNAIEALKLM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g3578.t22 | CDD | cd07962 | Anticodon_Ia_Val | 398 | 535 | 3.98342E-59 |
| 16 | g3578.t22 | Coils | Coil | Coil | 651 | 678 | - |
| 17 | g3578.t22 | Coils | Coil | Coil | 700 | 720 | - |
| 15 | g3578.t22 | Gene3D | G3DSA:3.90.740.10 | - | 1 | 112 | 2.3E-41 |
| 13 | g3578.t22 | Gene3D | G3DSA:3.40.50.620 | HUPs | 113 | 356 | 8.8E-67 |
| 14 | g3578.t22 | Gene3D | G3DSA:1.10.730.10 | - | 403 | 586 | 1.1E-53 |
| 3 | g3578.t22 | PANTHER | PTHR11946:SF110 | VALINE–TRNA LIGASE | 1 | 720 | 0.0 |
| 4 | g3578.t22 | PANTHER | PTHR11946 | VALYL-TRNA SYNTHETASES | 1 | 720 | 0.0 |
| 6 | g3578.t22 | PRINTS | PR00986 | Valyl-tRNA synthetase signature | 10 | 27 | 4.4E-30 |
| 7 | g3578.t22 | PRINTS | PR00986 | Valyl-tRNA synthetase signature | 125 | 138 | 4.4E-30 |
| 5 | g3578.t22 | PRINTS | PR00986 | Valyl-tRNA synthetase signature | 243 | 264 | 4.4E-30 |
| 8 | g3578.t22 | PRINTS | PR00986 | Valyl-tRNA synthetase signature | 274 | 292 | 4.4E-30 |
| 1 | g3578.t22 | Pfam | PF00133 | tRNA synthetases class I (I, L, M and V) | 12 | 399 | 2.2E-124 |
| 2 | g3578.t22 | Pfam | PF08264 | Anticodon-binding domain of tRNA ligase | 444 | 593 | 6.0E-43 |
| 11 | g3578.t22 | SUPERFAMILY | SSF50677 | ValRS/IleRS/LeuRS editing domain | 1 | 120 | 1.01E-46 |
| 9 | g3578.t22 | SUPERFAMILY | SSF52374 | Nucleotidylyl transferase | 120 | 406 | 7.17E-69 |
| 10 | g3578.t22 | SUPERFAMILY | SSF47323 | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 410 | 666 | 7.48E-62 |
| 12 | g3578.t22 | SUPERFAMILY | SSF46589 | tRNA-binding arm | 655 | 717 | 8.89E-5 |
| 19 | g3578.t22 | TIGRFAM | TIGR00422 | valS: valine–tRNA ligase | 1 | 700 | 6.3E-220 |
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:0004832 | valine-tRNA ligase activity | MF |
| GO:0002161 | aminoacyl-tRNA editing activity | MF |
| GO:0006418 | tRNA aminoacylation for protein translation | BP |
| GO:0000166 | nucleotide binding | MF |
| GO:0006438 | valyl-tRNA aminoacylation | BP |
| 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.
