General information for g3578.t19
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.t19 | TSS | g3578.t19 | 26525057 | 26525057 |
| chr_3 | g3578 | g3578.t19 | isoform | g3578.t19 | 26525096 | 26526053 |
| chr_3 | g3578 | g3578.t19 | exon | g3578.t19.exon1 | 26525096 | 26525503 |
| chr_3 | g3578 | g3578.t19 | cds | g3578.t19.CDS1 | 26525417 | 26525503 |
| chr_3 | g3578 | g3578.t19 | exon | g3578.t19.exon2 | 26525560 | 26525751 |
| chr_3 | g3578 | g3578.t19 | cds | g3578.t19.CDS2 | 26525560 | 26525751 |
| chr_3 | g3578 | g3578.t19 | exon | g3578.t19.exon3 | 26525810 | 26526053 |
| chr_3 | g3578 | g3578.t19 | cds | g3578.t19.CDS3 | 26525810 | 26526052 |
| chr_3 | g3578 | g3578.t19 | TTS | g3578.t19 | NA | NA |
Sequences
>g3578.t19 Gene=g3578 Length=844
ATGACTAATGTAAAAACTGATGAAGCTGCAAACGAGGAAGTTGTTGAAAAAAGTGCAAAA
CAACTCGAGAAAGAAGCTAAAAAAGCTGCTAAATTAGCTAAGCTTCAAGAAAAACAAGCA
AAACAGGCTACTCAACAAGCAAATACAGCACCTAAGGAAAAAGAGGTAAATTGAAATAAA
AATTTGGTTATTTACACATGTCCACGAATCATTTACTTACTTTCACAATTGCATACGTAG
AAAAAAGCTAAATCTGTAGTGAAAGACATTATTTATGAAGGAAATTCAAAGGATGGTGAA
AAGAAGGATTTATCTGGACCTATGCCAGAAGCTTACTCGCCTCAATACGTTGAAGCAGCG
TGGTATTCTTGGTGGGAGAAACAAGGATTTTTCAAGCCGGAATATTCTATGAAAAATGGA
AAAATATCTTCGAAAGGTCAATTTGTAATGGTTATTCCACCACCGAATGTTACTGGCTCT
TTGCATTTAGGTCATGCTTTGACAAATTCTATTGAAGATGCAATTGCAAGATGGCATAGA
ATGCATGGACGAACAACTCTTTGGGTTCCAGGTTGTGACCATGCTGGCATTGCAACTCAA
GTAGTCGTAGAGAAAAAATTGTGGAGAGAAGAGAAACTCAGTCGTCATGATCTTGGTCGA
GAAAAGTTTATTGAAAAAATTTGGGAATGGAAAGAGAACAAGGGAGGTAGAATTTATCAT
CAATTGAGAAAAATTGGTTCATCTATGGATTGGGATCGTGTTTCCTTCACAATGGATCCA
AAACTTTGTCGTGCTGTTACTGAAGCTTTCAATCAAATGCATGAAAAGGGTTTGATTTAT
CGTG
>g3578.t19 Gene=g3578 Length=174
MPEAYSPQYVEAAWYSWWEKQGFFKPEYSMKNGKISSKGQFVMVIPPPNVTGSLHLGHAL
TNSIEDAIARWHRMHGRTTLWVPGCDHAGIATQVVVEKKLWREEKLSRHDLGREKFIEKI
WEWKENKGGRIYHQLRKIGSSMDWDRVSFTMDPKLCRAVTEAFNQMHEKGLIYR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g3578.t19 | Gene3D | G3DSA:3.40.50.620 | HUPs | 3 | 174 | 2.7E-54 |
| 2 | g3578.t19 | PANTHER | PTHR11946:SF110 | VALINE–TRNA LIGASE | 1 | 174 | 5.0E-96 |
| 3 | g3578.t19 | PANTHER | PTHR11946 | VALYL-TRNA SYNTHETASES | 1 | 174 | 5.0E-96 |
| 1 | g3578.t19 | Pfam | PF00133 | tRNA synthetases class I (I, L, M and V) | 14 | 174 | 2.0E-59 |
| 5 | g3578.t19 | ProSitePatterns | PS00178 | Aminoacyl-transfer RNA synthetases class-I signature. | 48 | 59 | - |
| 4 | g3578.t19 | SUPERFAMILY | SSF52374 | Nucleotidylyl transferase | 1 | 174 | 2.82E-52 |
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: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.
