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.t1 TSS g6570.t1 17671026 17671026
chr_2 g6570 g6570.t1 isoform g6570.t1 17671129 17673020
chr_2 g6570 g6570.t1 exon g6570.t1.exon1 17671129 17671186
chr_2 g6570 g6570.t1 cds g6570.t1.CDS1 17671129 17671186
chr_2 g6570 g6570.t1 exon g6570.t1.exon2 17671256 17672191
chr_2 g6570 g6570.t1 cds g6570.t1.CDS2 17671256 17672191
chr_2 g6570 g6570.t1 exon g6570.t1.exon3 17672244 17672810
chr_2 g6570 g6570.t1 cds g6570.t1.CDS3 17672244 17672810
chr_2 g6570 g6570.t1 exon g6570.t1.exon4 17672869 17673020
chr_2 g6570 g6570.t1 cds g6570.t1.CDS4 17672869 17673020
chr_2 g6570 g6570.t1 TTS g6570.t1 17673081 17673081

Sequences

>g6570.t1 Gene=g6570 Length=1713
ATGCCGACAATTGGAATCAAGCGTGATTTATTATTTGAAACCTTGGGCAAAACTTACACC
GATGATGAATTTCAAGAATTATGCTTTGAATTTGGATTAGAACTTGATGAAGTGACAACT
GAAAAGCAAATGCTTACGAAAGAGCAAGGTGAAGGAGCACAAGCACAAGATGCATCTGAG
GAAATTATTTACAGAATAGAGATTCCAGCAAATCGATACGACCTTTTATGTTTGGAAGGC
TTGAGCAATGGATTGCTAGTCTTTCAGAAAAAACGTGAATCGCCGATATATGAAAAAGTC
ATACCTGAAAAAATTGAAAAATTATTTGTTACAAAGACAACAGCGCAAATAAGACCATAT
GTAGTTGCTGCTATTTTGAGAGATGTAAAACTAAATAAGGATCGTTATGCGAATTTCATT
GATTTACAAGATAAATTACATCAGAATATTTGTCGAAAAAGAACCCTAGTTGCTATCGGA
ACACACGATTTAGACACAATCAAAGGTCCATTTACATATGACGCAAAGAAGCCTCAAGAT
ATTCGTTTTATTCCATTGAATCAAACAAAAGAGATGAATGGGGAGGAGCTAATGAACTTC
TACTCAAATCATGCTCAACTTAAATCTTATCTTCCAATCATAAAAGATTCTCCTGTCTAT
CCAGTTATTTATGATTCAAGAAATACAATTCTTTCACTGCCGCCTATTATCAATGGGGAT
CATTCAAAAATTTCTGTTGACAGTAAAAATATCTTTATAGAATGTACTGCAACTGATTTG
ACAAAGGCAAAAATTGTTCTTGATACAATGGTAACATTATTTTCTCAATACTGTTCAGAG
CCATTTAAAATTGAAGCCGTGGAAGTTCATAATGCTGATGACACAATCATCACTTATCCT
GAATTAAGTGTCCGAAATGAAAAAGTTTTAGTCGATAAATTAAACAAATACATTGGAATC
AATGTTGATGCAGAAAATGTAGCCGACATGTTAAAAATTCCACCTACACGTCACGACGTT
ATACACACTACTGACATTATAGAAGATGTTGCTATCGCTTATGGCTATAATAAAATTGAG
CATACAATTCCAAATATCAATACGGTTGGTGGAATGTTTCCTCTGAATAAACTTACAGAG
TTACTACGTGTAGAGCTTGCTCAATCAGGTTTTACTGAAGGTCTCACTTTTACATTATGC
TCTCGTGATGATGTAGCGAAAAAAATGAACAAAAATATTGATGAAATTCCGGCAGTTCAT
ATTTCAAATCCAAAAACTGCCGAATTTCAGATTGCAAGAACAACATTAATTCCAGGCTTG
CTTAAAACTATTTCTGCAAACAAAAAAATGCCACTACCATTGAAGCTTTTTGAAATTTCT
GACGTTATTTTAAAAGATGATGAGGCAGAAGTCGGTGCACGAAATGAAAGGAGATTATGT
GCTGTAAACTACAATAAACATGCCGGATTTGAGGTCGTACATGGTATCCTTGATCGAATT
ATGCAAGTTTTAGAAGTTCCATGGAATAAATCAAATGGCTATTCGTTAAAAGCAGTAGAC
GATCCTGCTTATTTTCCAAGAAGATGTGCATCTGTCCTTTATAAAGGCATTAGTATAGGA
AAAATTGGAATTTTACATCCAACAGTTTTAGAAGCTTTTGAGCTTGTAAATCCTGTTTCG
GTAGTAGAATTAACAATTGAACCTTTTGTTTAA

>g6570.t1 Gene=g6570 Length=570
MPTIGIKRDLLFETLGKTYTDDEFQELCFEFGLELDEVTTEKQMLTKEQGEGAQAQDASE
EIIYRIEIPANRYDLLCLEGLSNGLLVFQKKRESPIYEKVIPEKIEKLFVTKTTAQIRPY
VVAAILRDVKLNKDRYANFIDLQDKLHQNICRKRTLVAIGTHDLDTIKGPFTYDAKKPQD
IRFIPLNQTKEMNGEELMNFYSNHAQLKSYLPIIKDSPVYPVIYDSRNTILSLPPIINGD
HSKISVDSKNIFIECTATDLTKAKIVLDTMVTLFSQYCSEPFKIEAVEVHNADDTIITYP
ELSVRNEKVLVDKLNKYIGINVDAENVADMLKIPPTRHDVIHTTDIIEDVAIAYGYNKIE
HTIPNINTVGGMFPLNKLTELLRVELAQSGFTEGLTFTLCSRDDVAKKMNKNIDEIPAVH
ISNPKTAEFQIARTTLIPGLLKTISANKKMPLPLKLFEISDVILKDDEAEVGARNERRLC
AVNYNKHAGFEVVHGILDRIMQVLEVPWNKSNGYSLKAVDDPAYFPRRCASVLYKGISIG
KIGILHPTVLEAFELVNPVSVVELTIEPFV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g6570.t1 CDD cd00769 PheRS_beta_core 374 569 0.0000000
14 g6570.t1 Gene3D G3DSA:3.30.56.10 - 1 90 0.0000000
11 g6570.t1 Gene3D G3DSA:3.50.40.10 - 99 303 0.0000000
13 g6570.t1 Gene3D G3DSA:3.30.56.10 - 330 359 0.0000000
12 g6570.t1 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 373 570 0.0000000
5 g6570.t1 PANTHER PTHR10947 PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN AND LEUCINE-RICH REPEAT-CONTAINING PROTEIN 47 1 569 0.0000000
6 g6570.t1 PANTHER PTHR10947:SF0 PHENYLALANINE–TRNA LIGASE BETA SUBUNIT 1 569 0.0000000
2 g6570.t1 Pfam PF18262 Phe-tRNA synthetase beta subunit B1 domain 1 91 0.0000000
3 g6570.t1 Pfam PF03483 B3/4 domain 118 278 0.0000000
1 g6570.t1 Pfam PF03484 tRNA synthetase B5 domain 332 356 0.0000010
4 g6570.t1 Pfam PF17759 Phenylalanyl tRNA synthetase beta chain CLM domain 359 565 0.0000000
18 g6570.t1 ProSiteProfiles PS51483 B5 domain profile. 282 361 11.3330000
17 g6570.t1 SMART SM00873 B3_4_2 117 279 0.0000000
16 g6570.t1 SMART SM00874 B5_2 304 356 0.0000004
8 g6570.t1 SUPERFAMILY SSF46955 Putative DNA-binding domain 6 85 0.0000001
10 g6570.t1 SUPERFAMILY SSF56037 PheT/TilS domain 220 279 0.0000262
9 g6570.t1 SUPERFAMILY SSF46955 Putative DNA-binding domain 309 360 0.0000000
7 g6570.t1 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 353 569 0.0000000
19 g6570.t1 TIGRFAM TIGR00471 pheT_arch: phenylalanine–tRNA ligase, beta subunit 1 569 0.0000000

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:0000287 magnesium ion binding MF
GO:0006432 phenylalanyl-tRNA aminoacylation BP
GO:0004826 phenylalanine-tRNA ligase activity MF
GO:0003723 RNA binding MF
GO:0005524 ATP binding MF
GO:0000166 nucleotide binding MF
GO:0005737 cytoplasm CC

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. There were no conditions that were differentially expressed