General information for g3578.t1
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.t1 | TSS | g3578.t1 | 26525057 | 26525057 |
| chr_3 | g3578 | g3578.t1 | isoform | g3578.t1 | 26525096 | 26528478 |
| chr_3 | g3578 | g3578.t1 | exon | g3578.t1.exon1 | 26525096 | 26525260 |
| chr_3 | g3578 | g3578.t1 | cds | g3578.t1.CDS1 | 26525096 | 26525260 |
| chr_3 | g3578 | g3578.t1 | exon | g3578.t1.exon2 | 26525336 | 26525503 |
| chr_3 | g3578 | g3578.t1 | cds | g3578.t1.CDS2 | 26525336 | 26525503 |
| chr_3 | g3578 | g3578.t1 | exon | g3578.t1.exon3 | 26525560 | 26525751 |
| chr_3 | g3578 | g3578.t1 | cds | g3578.t1.CDS3 | 26525560 | 26525751 |
| chr_3 | g3578 | g3578.t1 | exon | g3578.t1.exon4 | 26525810 | 26527564 |
| chr_3 | g3578 | g3578.t1 | cds | g3578.t1.CDS4 | 26525810 | 26527564 |
| chr_3 | g3578 | g3578.t1 | exon | g3578.t1.exon5 | 26527624 | 26528478 |
| chr_3 | g3578 | g3578.t1 | cds | g3578.t1.CDS5 | 26527624 | 26528478 |
| chr_3 | g3578 | g3578.t1 | TTS | g3578.t1 | 26528550 | 26528550 |
Sequences
>g3578.t1 Gene=g3578 Length=3135
ATGACTAATGTAAAAACTGATGAAGCTGCAAACGAGGAAGTTGTTGAAAAAAGTGCAAAA
CAACTCGAGAAAGAAGCTAAAAAAGCTGCTAAATTAGCTAAGCTTCAAGAAAAACAAGCA
AAACAGGCTACTCAACAAGCAAATACAGCACCTAAGGAAAAAGAGAAAAAAGCTAAATCT
GTAGTGAAAGACATTATTTATGAAGGAAATTCAAAGGATGGTGAAAAGAAGGATTTATCT
GGACCTATGCCAGAAGCTTACTCGCCTCAATACGTTGAAGCAGCGTGGTATTCTTGGTGG
GAGAAACAAGGATTTTTCAAGCCGGAATATTCTATGAAAAATGGAAAAATATCTTCGAAA
GGTCAATTTGTAATGGTTATTCCACCACCGAATGTTACTGGCTCTTTGCATTTAGGTCAT
GCTTTGACAAATTCTATTGAAGATGCAATTGCAAGATGGCATAGAATGCATGGACGAACA
ACTCTTTGGGTTCCAGGTTGTGACCATGCTGGCATTGCAACTCAAGTAGTCGTAGAGAAA
AAATTGTGGAGAGAAGAGAAACTCAGTCGTCATGATCTTGGTCGAGAAAAGTTTATTGAA
AAAATTTGGGAATGGAAAGAGAACAAGGGAGGTAGAATTTATCATCAATTGAGAAAAATT
GGTTCATCTATGGATTGGGATCGTGTTTCCTTCACAATGGATCCAAAACTTTGTCGTGCT
GTTACTGAAGCTTTCAATCAAATGCATGAAAAGGGTTTGATTTATCGTGATAAACGATTA
GTTAATTGGTCATGTACTCTTAAATCTGCTATTTCTGATATTGAAGTTGACAAAGTAGAA
ATTCCTGGTCGTACTTTTTTAGCGATTCCTGGCTATCAAGATAAGATTGAATTTGGAGTT
TTGGTATCGTTTGCATATCAAATTGAAGGCACAAATGAAGAAATTGTTGTTGCTACTACT
CGTATTGAAACAATGCTTGGTGATACTGCTGTTGCTATTCACCCAAAAGACACACGCTAC
ACTCATTTACATGGAAAATTTGTAAAACATCCATTTGTTGATCGTCGCTTACCGATTGTA
TTGGATGATTTCGTCGATATGGAGTTCGGTACTGGTGCTGTCAAAATCACTCCAGCACAT
GATCCTAATGATTATGAAGTTGGAAAGCGACATGATTTACCATTCATTACAATTTTTAGT
GATGATGGTATTATTGTCGGTGATTATGGCAAATTTACGGGAATGAAACGTTTTGATGCA
CGTAAAGCTGTTTTAGCATCACTCAAGGAGCTTGGACTTTATAAAGAAACCATCAATAAT
CCAATGATTGTTCCCATTTGCAGTCGCTCTAAAGATGTTGTTGAGCCTTTAATTAAACCA
CAATGGTATGTTAAATGTGAAGATATGGCTAAGAAAGCAACAGACTCAGTAAAAACAGGT
GAGCTGAAAATCATTCCCGAATCGTTCACGAAAACTTGGTTTCATTGGATGGATGGCATT
AGAGATTGGTGCATTTCACGTCAACTTTGGTGGGGACATAGAATTCCTGCTTATTTCATT
AAATTCAAAGATTCATCAAAAGCTCAAGCAATTACTGAAGAACAAGATTTTTGGATTGTT
GCAAGAAGTATCGATGATGCACATACGAAAGCGAAAAAGAAGTTTAATATTACAAGAGAA
GATTATGAATTGCAACAAGATGAAGATGTGCTCGATACGTGGTTCAGCTCTGGATTGTTT
CCATTTTCTGTATTTGGCTGGCCTGATCAAACAGAAGATTTGAAACTTTTTTATCCAACG
ACTCTTCTCGAAACAGGTCATGATATTTTATTTTTTTGGGTAGCTCGTATGGTTTTCTTT
GGTCAAACTTTATTAGGTAAACTTCCATTTAAGTATGTTTTTCTTCATCCTATGGTTCGC
GATGCGCATGGAAGAAAAATGTCAAAATCGCTTGGAAATGTTATTGATCCTATGGACGTT
ATAAACGGAATCTCGCTCGATGGATTGCATCAACAATTAATAGATTCAAATTTAGATCCT
CGTGAAATTGAAAAAGCAAAAGCAGGTCAAAAACAAGATTTTCCAAACGGTATTCCTGAA
TGTGGAACAGATGCTATGCGATTTACACTTTGTAATTACATGACTCAAGCAAGAGATATT
AATTTAGATATCATGCGTGTACAAGGCTATAGATTTTTCTGCAATAAGCTGTGGAATGCT
ACGAAATTTGCATTAAGATATTTTGAAGATGGTGAAACATATGAAATTCATGATAAAATG
ACATCAAAAGAAAGTAAAGTTGATTTATGGATTCTATCAAAACTTTCCAATACTATTGAA
ATTGTTAATAAATCATTTGAAAATTACGAATTTGCTACTGCAACACAAGTATGTTATACC
TTCTGGTTATATGAGTTATGTGATAACTATTTGGAATGTTTGAAACCGGTATTTGCATCT
GATGACAATGAAAAGAAAGCAATAGCAAGACGTATTCTTTATACATGCTTAGATTATGGC
TTAAGACTTCTATCACCTTTTATGCCGTTCATCACTGAAGAGTTGTTTCAACGTTTACCA
AGAAAAAATATTGAAATTCCGAGCATTTGCGTTGCTCCTTATCCAGATATAGAACAATTT
AACTTTAAGAATGAAGATATCGAGAAAGATTTTGACTTTGTTCAAAAAGTTGTAAAAGAA
ATACGATCTGCACGAAGTGATTATAACATACCAGCAAAGACAAAAACCGAAGCGTTTGCA
ATTTGTTCTGATAGCAAATTAAGTGAAATATTAAATGATTTTAAAGAGGAGTTACAGGCA
TTATCATACTGTTCAAATATAGAGCTAACAACTACAGGCCCTAATGGATGCGCGATTTTA
TCTATCAACGCTCATTGTGAGATTCATTTGCTACTTAAAGGAATTATTGAAGCTGATAAA
GAAATCGCAAAATTAGAAAAGAAGCGAGAAACCATGCAACAAACTATTAATAAACTGAAG
CAGAAAATGAGTATCGAAGATTATGAGAAAAAAGTTCCGGAGAACATTCAACAAGAAAAT
ATTGAAAATTTAAAGCAAACAGAGATAGAAATTGAAAGAATTGGAAATGCAATTGAAGCT
TTGAAATTAATGTAA
>g3578.t1 Gene=g3578 Length=1044
MTNVKTDEAANEEVVEKSAKQLEKEAKKAAKLAKLQEKQAKQATQQANTAPKEKEKKAKS
VVKDIIYEGNSKDGEKKDLSGPMPEAYSPQYVEAAWYSWWEKQGFFKPEYSMKNGKISSK
GQFVMVIPPPNVTGSLHLGHALTNSIEDAIARWHRMHGRTTLWVPGCDHAGIATQVVVEK
KLWREEKLSRHDLGREKFIEKIWEWKENKGGRIYHQLRKIGSSMDWDRVSFTMDPKLCRA
VTEAFNQMHEKGLIYRDKRLVNWSCTLKSAISDIEVDKVEIPGRTFLAIPGYQDKIEFGV
LVSFAYQIEGTNEEIVVATTRIETMLGDTAVAIHPKDTRYTHLHGKFVKHPFVDRRLPIV
LDDFVDMEFGTGAVKITPAHDPNDYEVGKRHDLPFITIFSDDGIIVGDYGKFTGMKRFDA
RKAVLASLKELGLYKETINNPMIVPICSRSKDVVEPLIKPQWYVKCEDMAKKATDSVKTG
ELKIIPESFTKTWFHWMDGIRDWCISRQLWWGHRIPAYFIKFKDSSKAQAITEEQDFWIV
ARSIDDAHTKAKKKFNITREDYELQQDEDVLDTWFSSGLFPFSVFGWPDQTEDLKLFYPT
TLLETGHDILFFWVARMVFFGQTLLGKLPFKYVFLHPMVRDAHGRKMSKSLGNVIDPMDV
INGISLDGLHQQLIDSNLDPREIEKAKAGQKQDFPNGIPECGTDAMRFTLCNYMTQARDI
NLDIMRVQGYRFFCNKLWNATKFALRYFEDGETYEIHDKMTSKESKVDLWILSKLSNTIE
IVNKSFENYEFATATQVCYTFWLYELCDNYLECLKPVFASDDNEKKAIARRILYTCLDYG
LRLLSPFMPFITEELFQRLPRKNIEIPSICVAPYPDIEQFNFKNEDIEKDFDFVQKVVKE
IRSARSDYNIPAKTKTEAFAICSDSKLSEILNDFKEELQALSYCSNIELTTTGPNGCAIL
SINAHCEIHLLLKGIIEADKEIAKLEKKRETMQQTINKLKQKMSIEDYEKKVPENIQQEN
IENLKQTEIEIERIGNAIEALKLM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 22 | g3578.t1 | CDD | cd00817 | ValRS_core | 121 | 722 | 0.0 |
| 21 | g3578.t1 | CDD | cd07962 | Anticodon_Ia_Val | 722 | 859 | 8.79918E-59 |
| 20 | g3578.t1 | Coils | Coil | Coil | 12 | 46 | - |
| 19 | g3578.t1 | Coils | Coil | Coil | 975 | 1002 | - |
| 18 | g3578.t1 | Coils | Coil | Coil | 1024 | 1044 | - |
| 15 | g3578.t1 | Gene3D | G3DSA:3.40.50.620 | HUPs | 85 | 285 | 6.4E-63 |
| 17 | g3578.t1 | Gene3D | G3DSA:3.90.740.10 | - | 297 | 436 | 1.7E-51 |
| 14 | g3578.t1 | Gene3D | G3DSA:3.40.50.620 | HUPs | 437 | 680 | 1.7E-66 |
| 16 | g3578.t1 | Gene3D | G3DSA:1.10.730.10 | - | 727 | 910 | 2.0E-53 |
| 5 | g3578.t1 | Hamap | MF_02004 | Valine–tRNA ligase [valS]. | 83 | 1042 | 14.08032 |
| 25 | g3578.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 61 | - |
| 24 | g3578.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 9 | 35 | - |
| 3 | g3578.t1 | PANTHER | PTHR11946:SF110 | VALINE–TRNA LIGASE | 11 | 1044 | 0.0 |
| 4 | g3578.t1 | PANTHER | PTHR11946 | VALYL-TRNA SYNTHETASES | 11 | 1044 | 0.0 |
| 8 | g3578.t1 | PRINTS | PR00986 | Valyl-tRNA synthetase signature | 123 | 134 | 1.8E-36 |
| 10 | g3578.t1 | PRINTS | PR00986 | Valyl-tRNA synthetase signature | 334 | 351 | 1.8E-36 |
| 6 | g3578.t1 | PRINTS | PR00986 | Valyl-tRNA synthetase signature | 449 | 462 | 1.8E-36 |
| 9 | g3578.t1 | PRINTS | PR00986 | Valyl-tRNA synthetase signature | 567 | 588 | 1.8E-36 |
| 7 | g3578.t1 | PRINTS | PR00986 | Valyl-tRNA synthetase signature | 598 | 616 | 1.8E-36 |
| 1 | g3578.t1 | Pfam | PF00133 | tRNA synthetases class I (I, L, M and V) | 96 | 723 | 1.7E-204 |
| 2 | g3578.t1 | Pfam | PF08264 | Anticodon-binding domain of tRNA ligase | 768 | 917 | 1.1E-42 |
| 23 | g3578.t1 | ProSitePatterns | PS00178 | Aminoacyl-transfer RNA synthetases class-I signature. | 130 | 141 | - |
| 11 | g3578.t1 | SUPERFAMILY | SSF52374 | Nucleotidylyl transferase | 82 | 730 | 4.8E-131 |
| 13 | g3578.t1 | SUPERFAMILY | SSF50677 | ValRS/IleRS/LeuRS editing domain | 295 | 444 | 1.18E-57 |
| 12 | g3578.t1 | SUPERFAMILY | SSF47323 | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 734 | 990 | 1.55E-61 |
| 26 | g3578.t1 | TIGRFAM | TIGR00422 | valS: valine–tRNA ligase | 83 | 1024 | 0.0 |
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 transcript has been annotated with K01873 (valyl-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.
