General information for g3988.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Phenylalanine–tRNA ligase alpha subunit.
Parent gene
- The parent gene g3988 is located on chr_3: 29396607..29399724 (+ 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_3 | g3988 | g3988.t1 | TSS | g3988.t1 | 29394985 | 29394985 |
| chr_3 | g3988 | g3988.t1 | isoform | g3988.t1 | 29395061 | 29396607 |
| chr_3 | g3988 | g3988.t1 | exon | g3988.t1.exon1 | 29395061 | 29395342 |
| chr_3 | g3988 | g3988.t1 | cds | g3988.t1.CDS1 | 29395061 | 29395342 |
| chr_3 | g3988 | g3988.t1 | exon | g3988.t1.exon2 | 29395399 | 29396607 |
| chr_3 | g3988 | g3988.t1 | cds | g3988.t1.CDS2 | 29395399 | 29396607 |
| chr_3 | g3988 | g3988.t1 | TTS | g3988.t1 | 29396662 | 29396662 |
Sequences
>g3988.t1 Gene=g3988 Length=1491
ATGCAGCTAGAGTTGACCGAACAAATTCTTCATTTCATTGAGCATCATAAGAAAGCTGAT
TCAATTGATTTAGCAGCTGAATTCAAAGAAGATCATCAAAAAGTAATTGGAGCATTAAAA
AGTATCGAAGCTCATGGTGAAATTTTAAAGTCTGAGACTACAACAAAAAAAGTTTGGGAT
CTAACTAATGAAGGACATTATGTCATAGAGCATGGATCACATGAAGCTACTGTTTTTAAT
GCTATTCCCAATGCAGGAATTTTGCAAGCCGATTTGATGAAAACATCACCAAATGCAAAA
GTAGGATTTTCAAAAGCAATGAATGCAGGATGGATTGTTATTGACAAATCGGGCAAAACT
CCTTTAGTAAAAAGAAAAGTCGAATCGATTGATGATGTTGTGCAACAGCATTTAATTGAA
ATTCAAAGTGGAAAAAGTACAAACATTCCTGATAACATCAAAGCTGATTATAAGAAACGA
AAACTTTTAGTTGAAAATACTATTAAAAGTTTTATTATTACAAAGGGTCCTGAATTTACA
ACGACACTTACGAAACTTGAAACAGACTTAACTTCTGACATGCTCACTTCAGGTGCTTGG
AAAAATCTTAAATTCAAGGAATATAATTTCGATGCCCTTGGTGCAGTGCCACAAGCTGGA
TATCAACATCCACTTCTTAAAGTTCGCACCGAAGTATCAGAAATTTTCACTCAAATGGGA
TTTGTTGAAATGCCAACAAATAATTATGTTGAGGCATCTTTCTGGAATTTTGATGCACTC
TTTCAACCACAAATGCATCCTGCTAGAGACGCTCAAGATACATTCTTCCTTTCAATTCCT
GAAAAGAGTTATAAATTTCCCACATCATATCTCGAACGAGTGAAAAATGCTCATGAAAAT
GGTGGTAATGGATCAATCGGTTATAGATACAATTGGAAAATAGAAGAGGCACAAAAAAAT
ATTTTAAGAACTCATACTACAGGTGTATCTGCACGAATGCTCTATAAATTAGCAAATCAA
GAAGGTGGATTTAAGCCTGTTAAATATTTTTCAATTGATAAAGTTTTCCGTAATGAAACA
TTAGATGCTACTCATCTTGCTGAATTCCATCAAGTCGAAGGTGTCATTGCTGGCGTTGAT
ATAAGCTTAGGAGGTCTTAAAGGAATAATTTCAGAATTTTTCTCTAAAATGGGTCTCACT
GATGTGCAGTTCAAACCTGCATATAATCCATATACTGAACCTTCTATGGAAATTTTCGCA
TATCATAAAGGTCTCGGAAAATTGATTGAAATTGGAAATAGTGGAATGTTTAGAAGAGAA
ATGTTAGATCCAATGAATATCCCAAGTAATGTAAATGTATATGGATATGGTCTCTCATTA
GAAAGACCTACAATGATAAAATATGGCATTAAAAATATCCGTGAATTAATTGGACCTAAA
GTTGATTTGAAAATGGTGCAAGAATCTGCATTATGTCGCTTAGATAAATAA
>g3988.t1 Gene=g3988 Length=496
MQLELTEQILHFIEHHKKADSIDLAAEFKEDHQKVIGALKSIEAHGEILKSETTTKKVWD
LTNEGHYVIEHGSHEATVFNAIPNAGILQADLMKTSPNAKVGFSKAMNAGWIVIDKSGKT
PLVKRKVESIDDVVQQHLIEIQSGKSTNIPDNIKADYKKRKLLVENTIKSFIITKGPEFT
TTLTKLETDLTSDMLTSGAWKNLKFKEYNFDALGAVPQAGYQHPLLKVRTEVSEIFTQMG
FVEMPTNNYVEASFWNFDALFQPQMHPARDAQDTFFLSIPEKSYKFPTSYLERVKNAHEN
GGNGSIGYRYNWKIEEAQKNILRTHTTGVSARMLYKLANQEGGFKPVKYFSIDKVFRNET
LDATHLAEFHQVEGVIAGVDISLGGLKGIISEFFSKMGLTDVQFKPAYNPYTEPSMEIFA
YHKGLGKLIEIGNSGMFRREMLDPMNIPSNVNVYGYGLSLERPTMIKYGIKNIRELIGPK
VDLKMVQESALCRLDK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g3988.t1 | CDD | cd00496 | PheRS_alpha_core | 223 | 482 | 0.000 |
| 10 | g3988.t1 | Gene3D | G3DSA:1.10.10.2310 | - | 15 | 206 | 0.000 |
| 9 | g3988.t1 | Gene3D | G3DSA:1.10.10.2320 | - | 61 | 163 | 0.000 |
| 11 | g3988.t1 | Gene3D | G3DSA:1.10.10.2330 | - | 74 | 130 | 0.000 |
| 8 | g3988.t1 | Gene3D | G3DSA:3.30.930.10 | Bira Bifunctional Protein; Domain 2 | 223 | 496 | 0.000 |
| 5 | g3988.t1 | PANTHER | PTHR11538 | PHENYLALANYL-TRNA SYNTHETASE | 6 | 495 | 0.000 |
| 6 | g3988.t1 | PANTHER | PTHR11538:SF40 | PHENYLALANINE–TRNA LIGASE ALPHA SUBUNIT | 6 | 495 | 0.000 |
| 3 | g3988.t1 | Pfam | PF18552 | PheRS DNA binding domain 1 | 1 | 59 | 0.000 |
| 1 | g3988.t1 | Pfam | PF18553 | PheRS DNA binding domain 3 | 73 | 130 | 0.000 |
| 2 | g3988.t1 | Pfam | PF18554 | PheRS DNA binding domain 2 | 132 | 163 | 0.000 |
| 4 | g3988.t1 | Pfam | PF01409 | tRNA synthetases class II core domain (F) | 208 | 486 | 0.000 |
| 13 | g3988.t1 | ProSiteProfiles | PS50862 | Aminoacyl-transfer RNA synthetases class-II family profile. | 346 | 479 | 17.161 |
| 7 | g3988.t1 | SUPERFAMILY | SSF55681 | Class II aaRS and biotin synthetases | 208 | 482 | 0.000 |
| 12 | g3988.t1 | TIGRFAM | TIGR00468 | pheS: phenylalanine–tRNA ligase, alpha subunit | 154 | 482 | 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.
