General information for g10589.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable phenylalanine–tRNA ligase, mitochondrial.
Parent gene
- The parent gene g10589 is located on chr_1: 10567566..10568909 (+ 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_1 | g10589 | g10589.t3 | TSS | g10589.t3 | 10566652 | 10566652 |
| chr_1 | g10589 | g10589.t3 | isoform | g10589.t3 | 10566681 | 10568909 |
| chr_1 | g10589 | g10589.t3 | exon | g10589.t3.exon1 | 10566681 | 10567380 |
| chr_1 | g10589 | g10589.t3 | cds | g10589.t3.CDS1 | 10567213 | 10567380 |
| chr_1 | g10589 | g10589.t3 | exon | g10589.t3.exon2 | 10567559 | 10567909 |
| chr_1 | g10589 | g10589.t3 | cds | g10589.t3.CDS2 | 10567559 | 10567909 |
| chr_1 | g10589 | g10589.t3 | exon | g10589.t3.exon3 | 10567974 | 10568127 |
| chr_1 | g10589 | g10589.t3 | cds | g10589.t3.CDS3 | 10567974 | 10568127 |
| chr_1 | g10589 | g10589.t3 | exon | g10589.t3.exon4 | 10568183 | 10568274 |
| chr_1 | g10589 | g10589.t3 | cds | g10589.t3.CDS4 | 10568183 | 10568274 |
| chr_1 | g10589 | g10589.t3 | exon | g10589.t3.exon5 | 10568334 | 10568909 |
| chr_1 | g10589 | g10589.t3 | cds | g10589.t3.CDS5 | 10568334 | 10568909 |
| chr_1 | g10589 | g10589.t3 | TTS | g10589.t3 | 10569008 | 10569008 |
Sequences
>g10589.t3 Gene=g10589 Length=1873
ATGGCTCAACGTATTGACGCAAACGAAATAAAAATTATTTATTGTAGTTGTGGAAAACGT
CTGTTAGTTTTTTGGAATTATAATATCAATTTTTCAGCAATAAAGTGTTCACAATGCCTC
GCCAAAGAACTTTCTCGAAGGTATAAATTTTATAATTTTGAATATTAACAATCTTATGAT
TTTTTTATTACAGTTATCAAACATGTCGTTTTCATTTTCCTATAGGTTAATTAATTATTT
CTAATTATAAAGGTCTTAATTAAATATGACTTGTAAAAGAAATATTAAAAATTTAACACT
CTGAAAATCATCATTATGATATATTAGGTATATTAAAATAAATGTCATTAAATATTTTAA
ATAGAACAGTAATTTTTTCAATTAACAGAAAACTTAAAGTTCAGTTATGAGTCATGGTGA
AATAACGTCCTTGCAATTCTTAATGTGTAACGGTCTTAAAATATTTAAATTTAAATTATT
AATATGAGGTGAAAAATCTGATAAAAACAAAAACATTTCATAAATAGCAGACATGATTTT
CAAAATATCGCGGTTTAGTGGAATTAAATGTGCTTCTCAGACACTTTATCGTCTTTTGAG
TACTCAACCAATACAAAGTGTCATTGAATTACATAACAACAAGTACGAGTCAGACGATTA
TTTTAATCTAACACCAAAAATTTTGACTTATCTTGATCAGAACTTACATCTTAAAAAGAA
TCATCCACTTTCATTAATAAGGCAGAGAATTGTCAATTTCTTCTACAATGAATATGCTAA
TCCCAAAGGAACCCCATTGTTTAGTGTTTTTGATAGAATGAGTCCAATTGTTACTGTCAA
ACAAAATTTTGATTCACTTCTAATTCCTGAGAATCATCCAAGTCGTGCTAAAAGTGATTG
CTATTATATTAATAGAGAATATATGTTGAGGGCTCATTGCACAGCACATCAAGTGGAATT
GTTAAGATCTGGACTCGACAACTTTTTAATTGTAGGTGATGTTTATCGAAGAGATGAAAT
TGATGCCACTCATTTTCCAGTTTTTCATCAAGTTGATGCTGTAAGAGTAATTCATAATGA
CAAACTATTCAAAAATAATCCAGATTTGGAAATATTTGAGAAAAATTATAGTGAAAATCA
TAATTCAACTTCAATTGGTTCATCAGAAAAATGTATTGATCAAGTGAAACAACCATGTCA
TACAGTTGAGTCAGTTAAATTGGTTGAATATGAAATGAAAAATGCTTTAGAACGACTCGT
AATAACACTTTTTGGAAAAAAACTCAAATTCAGATGGGTTGATGCCTATTTTCCCTTTAC
TCAACCGTCGTGGGAGTTAGAGATTTATCACAATGACAAATGGTTTGAAATCCTTGGTTG
TGGAATAATGCGAAATGAAATTCTTAGCAAAGCAGGAATTCATAATTCGATAGGTTATGC
TTTCGGTTTAGGTTTAGAAAGATTAGCAATGATTATTTATGATATTCCAGATATAAGACT
TTTCTGGAGCCAAGATTCGGGTTTTCTTAATCAGTTTAATGAGAAAGATCTTAATAAAAC
TATAAAATATAAACCTATTTCGCAATTTCCACAATGCTCCAATGATATCTCGTTTTGGTT
GCCATCTGAATTGTCATTTGAAACATTCTCTTTAAATGATGTGTATGATGTAGTAAGGAA
TATTGGTGGTGATATTGTTGAACAAGTAACATTACTCGATAAATTCACTCATCCAAAAAC
TGGTAAAAATAGTCTTACATTTCGCATAATATATCGTCATATGGAGCGGACTTTGACACA
GAAAGAAGTTAATGAAGTCCATGAAGCTATTTCAAATGAACTGATTAAAAAATATAATAT
TAAAATTCGTTAA
>g10589.t3 Gene=g10589 Length=446
MIFKISRFSGIKCASQTLYRLLSTQPIQSVIELHNNKYESDDYFNLTPKILTYLDQNLHL
KKNHPLSLIRQRIVNFFYNEYANPKGTPLFSVFDRMSPIVTVKQNFDSLLIPENHPSRAK
SDCYYINREYMLRAHCTAHQVELLRSGLDNFLIVGDVYRRDEIDATHFPVFHQVDAVRVI
HNDKLFKNNPDLEIFEKNYSENHNSTSIGSSEKCIDQVKQPCHTVESVKLVEYEMKNALE
RLVITLFGKKLKFRWVDAYFPFTQPSWELEIYHNDKWFEILGCGIMRNEILSKAGIHNSI
GYAFGLGLERLAMIIYDIPDIRLFWSQDSGFLNQFNEKDLNKTIKYKPISQFPQCSNDIS
FWLPSELSFETFSLNDVYDVVRNIGGDIVEQVTLLDKFTHPKTGKNSLTFRIIYRHMERT
LTQKEVNEVHEAISNELIKKYNIKIR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g10589.t3 | CDD | cd00496 | PheRS_alpha_core | 64 | 328 | 0.000 |
| 8 | g10589.t3 | Gene3D | G3DSA:3.30.930.10 | Bira Bifunctional Protein; Domain 2 | 19 | 345 | 0.000 |
| 9 | g10589.t3 | Gene3D | G3DSA:3.30.70.380 | - | 346 | 446 | 0.000 |
| 4 | g10589.t3 | PANTHER | PTHR11538 | PHENYLALANYL-TRNA SYNTHETASE | 25 | 439 | 0.000 |
| 5 | g10589.t3 | PANTHER | PTHR11538:SF41 | PHENYLALANINE–TRNA LIGASE, MITOCHONDRIAL | 25 | 439 | 0.000 |
| 2 | g10589.t3 | Pfam | PF01409 | tRNA synthetases class II core domain (F) | 62 | 182 | 0.000 |
| 3 | g10589.t3 | Pfam | PF01409 | tRNA synthetases class II core domain (F) | 234 | 335 | 0.000 |
| 1 | g10589.t3 | Pfam | PF03147 | Ferredoxin-fold anticodon binding domain | 350 | 446 | 0.000 |
| 12 | g10589.t3 | ProSiteProfiles | PS50862 | Aminoacyl-transfer RNA synthetases class-II family profile. | 69 | 348 | 12.747 |
| 13 | g10589.t3 | ProSiteProfiles | PS51447 | Ferredoxin-fold anticodon binding (FDX-ACB) domain profile. | 350 | 446 | 27.479 |
| 11 | g10589.t3 | SMART | SM00896 | FDX_ACB_2 | 350 | 446 | 0.000 |
| 6 | g10589.t3 | SUPERFAMILY | SSF55681 | Class II aaRS and biotin synthetases | 57 | 336 | 0.000 |
| 7 | g10589.t3 | SUPERFAMILY | SSF54991 | Anticodon-binding domain of PheRS | 345 | 446 | 0.000 |
| 14 | g10589.t3 | TIGRFAM | TIGR00469 | pheS_mito: phenylalanine–tRNA ligase | 31 | 445 | 0.000 |
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:0006432 | phenylalanyl-tRNA aminoacylation | BP |
| GO:0005524 | ATP binding | MF |
| GO:0000049 | tRNA binding | MF |
| GO:0005737 | cytoplasm | CC |
| GO:0004826 | phenylalanine-tRNA ligase activity | MF |
| GO:0000166 | nucleotide binding | MF |
| GO:0043039 | tRNA aminoacylation | BP |
| GO:0004812 | aminoacyl-tRNA ligase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K01889 (phenylalanyl-tRNA synthetase alpha chain)
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.
