Gene loci information

Transcript annotation

  • This transcript has been annotated as Phenylalanine–tRNA ligase beta subunit.

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_2 g6570 g6570.t2 TSS g6570.t2 17671026 17671026
chr_2 g6570 g6570.t2 isoform g6570.t2 17671129 17672191
chr_2 g6570 g6570.t2 exon g6570.t2.exon1 17671129 17671186
chr_2 g6570 g6570.t2 cds g6570.t2.CDS1 17671129 17671186
chr_2 g6570 g6570.t2 exon g6570.t2.exon2 17671256 17672191
chr_2 g6570 g6570.t2 cds g6570.t2.CDS2 17671256 17672190
chr_2 g6570 g6570.t2 TTS g6570.t2 17673081 17673081

Sequences

>g6570.t2 Gene=g6570 Length=994
ATGCCGACAATTGGAATCAAGCGTGATTTATTATTTGAAACCTTGGGCAAAACTTACACC
GATGATGAATTTCAAGAATTATGCTTTGAATTTGGATTAGAACTTGATGAAGTGACAACT
GAAAAGCAAATGCTTACGAAAGAGCAAGGTGAAGGAGCACAAGCACAAGATGCATCTGAG
GAAATTATTTACAGAATAGAGATTCCAGCAAATCGATACGACCTTTTATGTTTGGAAGGC
TTGAGCAATGGATTGCTAGTCTTTCAGAAAAAACGTGAATCGCCGATATATGAAAAAGTC
ATACCTGAAAAAATTGAAAAATTATTTGTTACAAAGACAACAGCGCAAATAAGACCATAT
GTAGTTGCTGCTATTTTGAGAGATGTAAAACTAAATAAGGATCGTTATGCGAATTTCATT
GATTTACAAGATAAATTACATCAGAATATTTGTCGAAAAAGAACCCTAGTTGCTATCGGA
ACACACGATTTAGACACAATCAAAGGTCCATTTACATATGACGCAAAGAAGCCTCAAGAT
ATTCGTTTTATTCCATTGAATCAAACAAAAGAGATGAATGGGGAGGAGCTAATGAACTTC
TACTCAAATCATGCTCAACTTAAATCTTATCTTCCAATCATAAAAGATTCTCCTGTCTAT
CCAGTTATTTATGATTCAAGAAATACAATTCTTTCACTGCCGCCTATTATCAATGGGGAT
CATTCAAAAATTTCTGTTGACAGTAAAAATATCTTTATAGAATGTACTGCAACTGATTTG
ACAAAGGCAAAAATTGTTCTTGATACAATGGTAACATTATTTTCTCAATACTGTTCAGAG
CCATTTAAAATTGAAGCCGTGGAAGTTCATAATGCTGATGACACAATCATCACTTATCCT
GAATTAAGTGTCCGAAATGAAAAAGTTTTAGTCGATAAATTAAACAAATACATTGGAATC
AATGTTGATGCAGAAAATGTAGCCGACATGTTAA

>g6570.t2 Gene=g6570 Length=331
MPTIGIKRDLLFETLGKTYTDDEFQELCFEFGLELDEVTTEKQMLTKEQGEGAQAQDASE
EIIYRIEIPANRYDLLCLEGLSNGLLVFQKKRESPIYEKVIPEKIEKLFVTKTTAQIRPY
VVAAILRDVKLNKDRYANFIDLQDKLHQNICRKRTLVAIGTHDLDTIKGPFTYDAKKPQD
IRFIPLNQTKEMNGEELMNFYSNHAQLKSYLPIIKDSPVYPVIYDSRNTILSLPPIINGD
HSKISVDSKNIFIECTATDLTKAKIVLDTMVTLFSQYCSEPFKIEAVEVHNADDTIITYP
ELSVRNEKVLVDKLNKYIGINVDAENVADML

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g6570.t2 Gene3D G3DSA:3.30.56.10 - 1 90 0.0e+00
8 g6570.t2 Gene3D G3DSA:3.50.40.10 - 99 303 0.0e+00
3 g6570.t2 PANTHER PTHR10947 PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN AND LEUCINE-RICH REPEAT-CONTAINING PROTEIN 47 1 331 0.0e+00
4 g6570.t2 PANTHER PTHR10947:SF0 PHENYLALANINE–TRNA LIGASE BETA SUBUNIT 1 331 0.0e+00
1 g6570.t2 Pfam PF18262 Phe-tRNA synthetase beta subunit B1 domain 1 91 0.0e+00
2 g6570.t2 Pfam PF03483 B3/4 domain 118 278 0.0e+00
7 g6570.t2 SMART SM00873 B3_4_2 117 279 0.0e+00
5 g6570.t2 SUPERFAMILY SSF46955 Putative DNA-binding domain 6 85 1.0e-07
6 g6570.t2 SUPERFAMILY SSF56037 PheT/TilS domain 220 279 9.7e-06

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.

Raw TPM values