Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable phenylalanine–tRNA ligase, mitochondrial.

Parent gene

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.t1 TSS g10589.t1 10566652 10566652
chr_1 g10589 g10589.t1 isoform g10589.t1 10566681 10568909
chr_1 g10589 g10589.t1 exon g10589.t1.exon1 10566681 10566820
chr_1 g10589 g10589.t1 cds g10589.t1.CDS1 10566681 10566820
chr_1 g10589 g10589.t1 exon g10589.t1.exon2 10566874 10566905
chr_1 g10589 g10589.t1 cds g10589.t1.CDS2 10566874 10566905
chr_1 g10589 g10589.t1 exon g10589.t1.exon3 10567208 10567380
chr_1 g10589 g10589.t1 cds g10589.t1.CDS3 10567208 10567380
chr_1 g10589 g10589.t1 exon g10589.t1.exon4 10567559 10567909
chr_1 g10589 g10589.t1 cds g10589.t1.CDS4 10567559 10567909
chr_1 g10589 g10589.t1 exon g10589.t1.exon5 10567974 10568127
chr_1 g10589 g10589.t1 cds g10589.t1.CDS5 10567974 10568127
chr_1 g10589 g10589.t1 exon g10589.t1.exon6 10568183 10568274
chr_1 g10589 g10589.t1 cds g10589.t1.CDS6 10568183 10568274
chr_1 g10589 g10589.t1 exon g10589.t1.exon7 10568334 10568909
chr_1 g10589 g10589.t1 cds g10589.t1.CDS7 10568334 10568909
chr_1 g10589 g10589.t1 TTS g10589.t1 10569008 10569008

Sequences

>g10589.t1 Gene=g10589 Length=1518
ATGGCTCAACGTATTGACGCAAACGAAATAAAAATTATTTATTGTAGTTGTGGAAAACGT
CTGTTAGTTTTTTGGAATTATAATATCAATTTTTCAGCAATAAAGTGTTCACAATGCCTC
GCCAAAGAACTTTCTCGAAGTTATCAAACATGTCGTTTTCATTTTCCTATAGCAGACATG
ATTTTCAAAATATCGCGGTTTAGTGGAATTAAATGTGCTTCTCAGACACTTTATCGTCTT
TTGAGTACTCAACCAATACAAAGTGTCATTGAATTACATAACAACAAGTACGAGTCAGAC
GATTATTTTAATCTAACACCAAAAATTTTGACTTATCTTGATCAGAACTTACATCTTAAA
AAGAATCATCCACTTTCATTAATAAGGCAGAGAATTGTCAATTTCTTCTACAATGAATAT
GCTAATCCCAAAGGAACCCCATTGTTTAGTGTTTTTGATAGAATGAGTCCAATTGTTACT
GTCAAACAAAATTTTGATTCACTTCTAATTCCTGAGAATCATCCAAGTCGTGCTAAAAGT
GATTGCTATTATATTAATAGAGAATATATGTTGAGGGCTCATTGCACAGCACATCAAGTG
GAATTGTTAAGATCTGGACTCGACAACTTTTTAATTGTAGGTGATGTTTATCGAAGAGAT
GAAATTGATGCCACTCATTTTCCAGTTTTTCATCAAGTTGATGCTGTAAGAGTAATTCAT
AATGACAAACTATTCAAAAATAATCCAGATTTGGAAATATTTGAGAAAAATTATAGTGAA
AATCATAATTCAACTTCAATTGGTTCATCAGAAAAATGTATTGATCAAGTGAAACAACCA
TGTCATACAGTTGAGTCAGTTAAATTGGTTGAATATGAAATGAAAAATGCTTTAGAACGA
CTCGTAATAACACTTTTTGGAAAAAAACTCAAATTCAGATGGGTTGATGCCTATTTTCCC
TTTACTCAACCGTCGTGGGAGTTAGAGATTTATCACAATGACAAATGGTTTGAAATCCTT
GGTTGTGGAATAATGCGAAATGAAATTCTTAGCAAAGCAGGAATTCATAATTCGATAGGT
TATGCTTTCGGTTTAGGTTTAGAAAGATTAGCAATGATTATTTATGATATTCCAGATATA
AGACTTTTCTGGAGCCAAGATTCGGGTTTTCTTAATCAGTTTAATGAGAAAGATCTTAAT
AAAACTATAAAATATAAACCTATTTCGCAATTTCCACAATGCTCCAATGATATCTCGTTT
TGGTTGCCATCTGAATTGTCATTTGAAACATTCTCTTTAAATGATGTGTATGATGTAGTA
AGGAATATTGGTGGTGATATTGTTGAACAAGTAACATTACTCGATAAATTCACTCATCCA
AAAACTGGTAAAAATAGTCTTACATTTCGCATAATATATCGTCATATGGAGCGGACTTTG
ACACAGAAAGAAGTTAATGAAGTCCATGAAGCTATTTCAAATGAACTGATTAAAAAATAT
AATATTAAAATTCGTTAA

>g10589.t1 Gene=g10589 Length=505
MAQRIDANEIKIIYCSCGKRLLVFWNYNINFSAIKCSQCLAKELSRSYQTCRFHFPIADM
IFKISRFSGIKCASQTLYRLLSTQPIQSVIELHNNKYESDDYFNLTPKILTYLDQNLHLK
KNHPLSLIRQRIVNFFYNEYANPKGTPLFSVFDRMSPIVTVKQNFDSLLIPENHPSRAKS
DCYYINREYMLRAHCTAHQVELLRSGLDNFLIVGDVYRRDEIDATHFPVFHQVDAVRVIH
NDKLFKNNPDLEIFEKNYSENHNSTSIGSSEKCIDQVKQPCHTVESVKLVEYEMKNALER
LVITLFGKKLKFRWVDAYFPFTQPSWELEIYHNDKWFEILGCGIMRNEILSKAGIHNSIG
YAFGLGLERLAMIIYDIPDIRLFWSQDSGFLNQFNEKDLNKTIKYKPISQFPQCSNDISF
WLPSELSFETFSLNDVYDVVRNIGGDIVEQVTLLDKFTHPKTGKNSLTFRIIYRHMERTL
TQKEVNEVHEAISNELIKKYNIKIR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g10589.t1 CDD cd00496 PheRS_alpha_core 123 387 0.000
8 g10589.t1 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 78 404 0.000
9 g10589.t1 Gene3D G3DSA:3.30.70.380 - 405 505 0.000
4 g10589.t1 PANTHER PTHR11538 PHENYLALANYL-TRNA SYNTHETASE 83 498 0.000
5 g10589.t1 PANTHER PTHR11538:SF41 PHENYLALANINE–TRNA LIGASE, MITOCHONDRIAL 83 498 0.000
3 g10589.t1 Pfam PF01409 tRNA synthetases class II core domain (F) 121 241 0.000
2 g10589.t1 Pfam PF01409 tRNA synthetases class II core domain (F) 293 394 0.000
1 g10589.t1 Pfam PF03147 Ferredoxin-fold anticodon binding domain 409 505 0.000
12 g10589.t1 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 128 407 12.747
13 g10589.t1 ProSiteProfiles PS51447 Ferredoxin-fold anticodon binding (FDX-ACB) domain profile. 409 505 27.479
11 g10589.t1 SMART SM00896 FDX_ACB_2 409 505 0.000
6 g10589.t1 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 116 395 0.000
7 g10589.t1 SUPERFAMILY SSF54991 Anticodon-binding domain of PheRS 404 505 0.000
14 g10589.t1 TIGRFAM TIGR00469 pheS_mito: phenylalanine–tRNA ligase 90 504 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

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.

Raw TPM values