General information for g6570.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Phenylalanine–tRNA ligase beta subunit.
Parent gene
- The parent gene g6570 is located on chr_2: 17671180..17673020 (+ 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 | g6570 | g6570.t3 | TSS | g6570.t3 | 17671026 | 17671026 |
| chr_2 | g6570 | g6570.t3 | isoform | g6570.t3 | 17671129 | 17673020 |
| chr_2 | g6570 | g6570.t3 | exon | g6570.t3.exon1 | 17671129 | 17671186 |
| chr_2 | g6570 | g6570.t3 | cds | g6570.t3.CDS1 | 17671129 | 17671186 |
| chr_2 | g6570 | g6570.t3 | exon | g6570.t3.exon2 | 17671256 | 17672810 |
| chr_2 | g6570 | g6570.t3 | cds | g6570.t3.CDS2 | 17671256 | 17672226 |
| chr_2 | g6570 | g6570.t3 | exon | g6570.t3.exon3 | 17672869 | 17673020 |
| chr_2 | g6570 | g6570.t3 | TTS | g6570.t3 | 17673081 | 17673081 |
Sequences
>g6570.t3 Gene=g6570 Length=1765
ATGCCGACAATTGGAATCAAGCGTGATTTATTATTTGAAACCTTGGGCAAAACTTACACC
GATGATGAATTTCAAGAATTATGCTTTGAATTTGGATTAGAACTTGATGAAGTGACAACT
GAAAAGCAAATGCTTACGAAAGAGCAAGGTGAAGGAGCACAAGCACAAGATGCATCTGAG
GAAATTATTTACAGAATAGAGATTCCAGCAAATCGATACGACCTTTTATGTTTGGAAGGC
TTGAGCAATGGATTGCTAGTCTTTCAGAAAAAACGTGAATCGCCGATATATGAAAAAGTC
ATACCTGAAAAAATTGAAAAATTATTTGTTACAAAGACAACAGCGCAAATAAGACCATAT
GTAGTTGCTGCTATTTTGAGAGATGTAAAACTAAATAAGGATCGTTATGCGAATTTCATT
GATTTACAAGATAAATTACATCAGAATATTTGTCGAAAAAGAACCCTAGTTGCTATCGGA
ACACACGATTTAGACACAATCAAAGGTCCATTTACATATGACGCAAAGAAGCCTCAAGAT
ATTCGTTTTATTCCATTGAATCAAACAAAAGAGATGAATGGGGAGGAGCTAATGAACTTC
TACTCAAATCATGCTCAACTTAAATCTTATCTTCCAATCATAAAAGATTCTCCTGTCTAT
CCAGTTATTTATGATTCAAGAAATACAATTCTTTCACTGCCGCCTATTATCAATGGGGAT
CATTCAAAAATTTCTGTTGACAGTAAAAATATCTTTATAGAATGTACTGCAACTGATTTG
ACAAAGGCAAAAATTGTTCTTGATACAATGGTAACATTATTTTCTCAATACTGTTCAGAG
CCATTTAAAATTGAAGCCGTGGAAGTTCATAATGCTGATGACACAATCATCACTTATCCT
GAATTAAGTGTCCGAAATGAAAAAGTTTTAGTCGATAAATTAAACAAATACATTGGAATC
AATGTTGATGCAGAAAATGTAGCCGACATGTTAAGTCGAATAGCTTTTAAGGGCTACTGT
TTTAAATGATAATGAAGTTTCTGTAGAAATTCCACCTACACGTCACGACGTTATACACAC
TACTGACATTATAGAAGATGTTGCTATCGCTTATGGCTATAATAAAATTGAGCATACAAT
TCCAAATATCAATACGGTTGGTGGAATGTTTCCTCTGAATAAACTTACAGAGTTACTACG
TGTAGAGCTTGCTCAATCAGGTTTTACTGAAGGTCTCACTTTTACATTATGCTCTCGTGA
TGATGTAGCGAAAAAAATGAACAAAAATATTGATGAAATTCCGGCAGTTCATATTTCAAA
TCCAAAAACTGCCGAATTTCAGATTGCAAGAACAACATTAATTCCAGGCTTGCTTAAAAC
TATTTCTGCAAACAAAAAAATGCCACTACCATTGAAGCTTTTTGAAATTTCTGACGTTAT
TTTAAAAGATGATGAGGCAGAAGTCGGTGCACGAAATGAAAGGAGATTATGTGCTGTAAA
CTACAATAAACATGCCGGATTTGAGGTCGTACATGGTATCCTTGATCGAATTATGCAAGT
TTTAGAAGTTCCATGGAATAAATCAAATGGCTATTCGTTAAAAGCAGTAGACGATCCTGC
TTATTTTCCAAGAAGATGTGCATCTGTCCTTTATAAAGGCATTAGTATAGGAAAAATTGG
AATTTTACATCCAACAGTTTTAGAAGCTTTTGAGCTTGTAAATCCTGTTTCGGTAGTAGA
ATTAACAATTGAACCTTTTGTTTAA
>g6570.t3 Gene=g6570 Length=342
MPTIGIKRDLLFETLGKTYTDDEFQELCFEFGLELDEVTTEKQMLTKEQGEGAQAQDASE
EIIYRIEIPANRYDLLCLEGLSNGLLVFQKKRESPIYEKVIPEKIEKLFVTKTTAQIRPY
VVAAILRDVKLNKDRYANFIDLQDKLHQNICRKRTLVAIGTHDLDTIKGPFTYDAKKPQD
IRFIPLNQTKEMNGEELMNFYSNHAQLKSYLPIIKDSPVYPVIYDSRNTILSLPPIINGD
HSKISVDSKNIFIECTATDLTKAKIVLDTMVTLFSQYCSEPFKIEAVEVHNADDTIITYP
ELSVRNEKVLVDKLNKYIGINVDAENVADMLSRIAFKGYCFK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g6570.t3 | Gene3D | G3DSA:3.30.56.10 | - | 1 | 90 | 0.00e+00 |
| 8 | g6570.t3 | Gene3D | G3DSA:3.50.40.10 | - | 99 | 303 | 0.00e+00 |
| 3 | g6570.t3 | PANTHER | PTHR10947 | PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN AND LEUCINE-RICH REPEAT-CONTAINING PROTEIN 47 | 1 | 337 | 0.00e+00 |
| 4 | g6570.t3 | PANTHER | PTHR10947:SF0 | PHENYLALANINE–TRNA LIGASE BETA SUBUNIT | 1 | 337 | 0.00e+00 |
| 1 | g6570.t3 | Pfam | PF18262 | Phe-tRNA synthetase beta subunit B1 domain | 1 | 91 | 0.00e+00 |
| 2 | g6570.t3 | Pfam | PF03483 | B3/4 domain | 118 | 278 | 0.00e+00 |
| 7 | g6570.t3 | SMART | SM00873 | B3_4_2 | 117 | 279 | 0.00e+00 |
| 5 | g6570.t3 | SUPERFAMILY | SSF46955 | Putative DNA-binding domain | 6 | 85 | 0.00e+00 |
| 6 | g6570.t3 | SUPERFAMILY | SSF56037 | PheT/TilS domain | 220 | 279 | 1.05e-05 |
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:0004826 | phenylalanine-tRNA ligase activity | MF |
| GO:0003723 | RNA binding | 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.
