Gene loci information

Transcript annotation

  • This transcript has been annotated as Tyrosine–tRNA ligase, cytoplasmic.

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_3 g1213 g1213.t6 TSS g1213.t6 8797313 8797313
chr_3 g1213 g1213.t6 isoform g1213.t6 8797434 8799190
chr_3 g1213 g1213.t6 exon g1213.t6.exon1 8797434 8797641
chr_3 g1213 g1213.t6 exon g1213.t6.exon2 8797711 8798691
chr_3 g1213 g1213.t6 cds g1213.t6.CDS1 8797753 8798691
chr_3 g1213 g1213.t6 exon g1213.t6.exon3 8798751 8798881
chr_3 g1213 g1213.t6 cds g1213.t6.CDS2 8798751 8798881
chr_3 g1213 g1213.t6 exon g1213.t6.exon4 8798944 8799190
chr_3 g1213 g1213.t6 cds g1213.t6.CDS3 8798944 8799190
chr_3 g1213 g1213.t6 TTS g1213.t6 8799210 8799210

Sequences

>g1213.t6 Gene=g1213 Length=1567
ATGGCAGAAGAATTGACATTTGAAAAGAAACTTGAGTTAATCAAAAGAAATCTGCAAGAG
GTTCTTGGTGAAGAAAATCTGCACAAGATTGTGAAAGAACGAGATTTAAAACTTTATTGG
GGAACTGCCACAACTGGAAAACCTCATATTGCATATTTCGTGCCAATGACAAAAATTGCA
GACTTTCTAAAAGCTGGATGTGAAGTGAGTCACAATCTTGTTTGCAGACTTACATGCATA
TTTAGATAATATGAAAGCACCATGGTCACTTCTAGAAGAGAGAACAAAATATTATGAAGC
TGTTATTAAAGCTATGCTTCAATCACTAGGTGTACCATTGGAGAAACTTAAATTCGTGCA
AGGCACAAGTTTTGAATTGTCTCGTGAATACTCTTTAGATGTTTATAGACTCACATCAAT
TGTGACTCAACATGATGCTAAAAAAGCTGGTGCTGAAGTTGTGAAACAAGTTGAATATCC
TCTTTTATCTGGATTGCTTTATCCTGGCCTTCAGGCACTCGATGAAGAATATTTAAAAGT
TGATGCTCAATTTGGAGGTGTTGATCAAAGAAAAATTTTTACTTTTGCTGAAAAATATCT
TCCACAACTCGGTTATGCAAAGAGAATTCATCTTATGAATCCCATGGTGCCTGGTTTAAC
AGGTGGCAAAATGTCTTCTTCTGAAGAGGACTCTAAAATTGATCTTCTTGATTCAGCTGC
TAATGTTAAGAAAAAAATTAAAAGAGCATTCTGTGAACCAGGAAATATTCAAGACAATGG
ACTTTTATCATTTGTAAAGCACGTTTTATTTTCAATTTTTAAAGAAGATCAAGGATTTGA
AATTAAAAGAAAGGAAGAGAATGGTGGCGATGTAACATTTATGAAATATGAAGATTTAGA
AAAGGCGTTTGCAGAAGAAAAAATTCATCCAGGCGATTTAAAAGCAGCTGTCGAAACTTA
TATCAATTGGCTTTTAGATCCAATTAGGAAAATATTTGATGATCAATATCATCGAGATCT
AACTGAAAGAGCTTATCCTACAAAGAAAGAGGTAGCTCAAAAATCTGATGAAAATTCACC
AGATAAGATGGAATTAAAAGTAGGAAAAATTATAGAAGCTACCAAACATCCAGATGCTGA
CACATTATGCATAATGAAAGTTAATGTTGGAAAAGATGAAATTAGATCGATTGTTAGTAA
TTTAATGTCTTATTATAAACTCGATGAGCTAGTGAACAGAAATGTCGTTGTATTGACAAA
CATGAAATCTTCAAAAATACGCGGAGTAGAAAGCGAAGGTTTAGTGTTGTGTGCATTCAA
CACTGATAAATATGAGCCATTAATTCCACCATTTGATGCAAATGTTGGTGATAGAATCTT
CATTGAAGGCTATAACAATACAACTTCTGATGTAGCTCAATTGAATCCTAAGAAGAAAGT
GTGGGACAAAATTCAGAACGAGTTGAAAACAAATTCAGATGGTGAATGTGTATGGCGAGA
ATTTAGTATGATGTCGATTAATGGTGAAAAAATTACAAGCAGCCTTATTAATTGTAACGT
GAAATAA

>g1213.t6 Gene=g1213 Length=438
MKAPWSLLEERTKYYEAVIKAMLQSLGVPLEKLKFVQGTSFELSREYSLDVYRLTSIVTQ
HDAKKAGAEVVKQVEYPLLSGLLYPGLQALDEEYLKVDAQFGGVDQRKIFTFAEKYLPQL
GYAKRIHLMNPMVPGLTGGKMSSSEEDSKIDLLDSAANVKKKIKRAFCEPGNIQDNGLLS
FVKHVLFSIFKEDQGFEIKRKEENGGDVTFMKYEDLEKAFAEEKIHPGDLKAAVETYINW
LLDPIRKIFDDQYHRDLTERAYPTKKEVAQKSDENSPDKMELKVGKIIEATKHPDADTLC
IMKVNVGKDEIRSIVSNLMSYYKLDELVNRNVVVLTNMKSSKIRGVESEGLVLCAFNTDK
YEPLIPPFDANVGDRIFIEGYNNTTSDVAQLNPKKKVWDKIQNELKTNSDGECVWREFSM
MSINGEKITSSLINCNVK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g1213.t6 Gene3D G3DSA:3.40.50.620 HUPs 1 131 0.000e+00
10 g1213.t6 Gene3D G3DSA:1.10.240.10 - 132 261 0.000e+00
12 g1213.t6 Gene3D G3DSA:2.40.50.140 - 271 438 0.000e+00
3 g1213.t6 PANTHER PTHR42765 SOLEUCYL-TRNA SYNTHETASE 1 301 0.000e+00
4 g1213.t6 PANTHER PTHR42765:SF2 TYROSINE–TRNA LIGASE 1 301 0.000e+00
6 g1213.t6 PRINTS PR01040 Tyrosyl-tRNA synthetase signature 76 91 4.000e-07
5 g1213.t6 PRINTS PR01040 Tyrosyl-tRNA synthetase signature 93 115 4.000e-07
7 g1213.t6 PRINTS PR01040 Tyrosyl-tRNA synthetase signature 126 138 4.000e-07
1 g1213.t6 Pfam PF00579 tRNA synthetases class I (W and Y) 2 242 0.000e+00
2 g1213.t6 Pfam PF01588 Putative tRNA binding domain 282 374 0.000e+00
14 g1213.t6 ProSiteProfiles PS50886 tRNA-binding domain profile. 276 377 2.947e+01
8 g1213.t6 SUPERFAMILY SSF52374 Nucleotidylyl transferase 8 260 0.000e+00
9 g1213.t6 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 276 437 0.000e+00
13 g1213.t6 TIGRFAM TIGR00234 tyrS: tyrosine–tRNA ligase 9 251 0.000e+00

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:0005524 ATP binding MF
GO:0006418 tRNA aminoacylation for protein translation BP
GO:0000166 nucleotide binding MF
GO:0004831 tyrosine-tRNA ligase activity MF
GO:0004812 aminoacyl-tRNA ligase activity MF
GO:0000049 tRNA binding MF
GO:0006437 tyrosyl-tRNA aminoacylation BP

KEGG

Orthology

Pathway

This gene does not belong to any 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