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.t1 TSS g1213.t1 8797313 8797313
chr_3 g1213 g1213.t1 isoform g1213.t1 8797434 8799190
chr_3 g1213 g1213.t1 exon g1213.t1.exon1 8797434 8797637
chr_3 g1213 g1213.t1 cds g1213.t1.CDS1 8797434 8797637
chr_3 g1213 g1213.t1 exon g1213.t1.exon2 8797711 8798691
chr_3 g1213 g1213.t1 cds g1213.t1.CDS2 8797711 8798691
chr_3 g1213 g1213.t1 exon g1213.t1.exon3 8798751 8798881
chr_3 g1213 g1213.t1 cds g1213.t1.CDS3 8798751 8798881
chr_3 g1213 g1213.t1 exon g1213.t1.exon4 8798944 8799190
chr_3 g1213 g1213.t1 cds g1213.t1.CDS4 8798944 8799190
chr_3 g1213 g1213.t1 TTS g1213.t1 8799210 8799210

Sequences

>g1213.t1 Gene=g1213 Length=1563
ATGGCAGAAGAATTGACATTTGAAAAGAAACTTGAGTTAATCAAAAGAAATCTGCAAGAG
GTTCTTGGTGAAGAAAATCTGCACAAGATTGTGAAAGAACGAGATTTAAAACTTTATTGG
GGAACTGCCACAACTGGAAAACCTCATATTGCATATTTCGTGCCAATGACAAAAATTGCA
GACTTTCTAAAAGCTGGATGTGAAGTCACAATCTTGTTTGCAGACTTACATGCATATTTA
GATAATATGAAAGCACCATGGTCACTTCTAGAAGAGAGAACAAAATATTATGAAGCTGTT
ATTAAAGCTATGCTTCAATCACTAGGTGTACCATTGGAGAAACTTAAATTCGTGCAAGGC
ACAAGTTTTGAATTGTCTCGTGAATACTCTTTAGATGTTTATAGACTCACATCAATTGTG
ACTCAACATGATGCTAAAAAAGCTGGTGCTGAAGTTGTGAAACAAGTTGAATATCCTCTT
TTATCTGGATTGCTTTATCCTGGCCTTCAGGCACTCGATGAAGAATATTTAAAAGTTGAT
GCTCAATTTGGAGGTGTTGATCAAAGAAAAATTTTTACTTTTGCTGAAAAATATCTTCCA
CAACTCGGTTATGCAAAGAGAATTCATCTTATGAATCCCATGGTGCCTGGTTTAACAGGT
GGCAAAATGTCTTCTTCTGAAGAGGACTCTAAAATTGATCTTCTTGATTCAGCTGCTAAT
GTTAAGAAAAAAATTAAAAGAGCATTCTGTGAACCAGGAAATATTCAAGACAATGGACTT
TTATCATTTGTAAAGCACGTTTTATTTTCAATTTTTAAAGAAGATCAAGGATTTGAAATT
AAAAGAAAGGAAGAGAATGGTGGCGATGTAACATTTATGAAATATGAAGATTTAGAAAAG
GCGTTTGCAGAAGAAAAAATTCATCCAGGCGATTTAAAAGCAGCTGTCGAAACTTATATC
AATTGGCTTTTAGATCCAATTAGGAAAATATTTGATGATCAATATCATCGAGATCTAACT
GAAAGAGCTTATCCTACAAAGAAAGAGGTAGCTCAAAAATCTGATGAAAATTCACCAGAT
AAGATGGAATTAAAAGTAGGAAAAATTATAGAAGCTACCAAACATCCAGATGCTGACACA
TTATGCATAATGAAAGTTAATGTTGGAAAAGATGAAATTAGATCGATTGTTAGTAATTTA
ATGTCTTATTATAAACTCGATGAGCTAGTGAACAGAAATGTCGTTGTATTGACAAACATG
AAATCTTCAAAAATACGCGGAGTAGAAAGCGAAGGTTTAGTGTTGTGTGCATTCAACACT
GATAAATATGAGCCATTAATTCCACCATTTGATGCAAATGTTGGTGATAGAATCTTCATT
GAAGGCTATAACAATACAACTTCTGATGTAGCTCAATTGAATCCTAAGAAGAAAGTGTGG
GACAAAATTCAGAACGAGTTGAAAACAAATTCAGATGGTGAATGTGTATGGCGAGAATTT
AGTATGATGTCGATTAATGGTGAAAAAATTACAAGCAGCCTTATTAATTGTAACGTGAAA
TAA

>g1213.t1 Gene=g1213 Length=520
MAEELTFEKKLELIKRNLQEVLGEENLHKIVKERDLKLYWGTATTGKPHIAYFVPMTKIA
DFLKAGCEVTILFADLHAYLDNMKAPWSLLEERTKYYEAVIKAMLQSLGVPLEKLKFVQG
TSFELSREYSLDVYRLTSIVTQHDAKKAGAEVVKQVEYPLLSGLLYPGLQALDEEYLKVD
AQFGGVDQRKIFTFAEKYLPQLGYAKRIHLMNPMVPGLTGGKMSSSEEDSKIDLLDSAAN
VKKKIKRAFCEPGNIQDNGLLSFVKHVLFSIFKEDQGFEIKRKEENGGDVTFMKYEDLEK
AFAEEKIHPGDLKAAVETYINWLLDPIRKIFDDQYHRDLTERAYPTKKEVAQKSDENSPD
KMELKVGKIIEATKHPDADTLCIMKVNVGKDEIRSIVSNLMSYYKLDELVNRNVVVLTNM
KSSKIRGVESEGLVLCAFNTDKYEPLIPPFDANVGDRIFIEGYNNTTSDVAQLNPKKKVW
DKIQNELKTNSDGECVWREFSMMSINGEKITSSLINCNVK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g1213.t1 CDD cd00805 TyrRS_core 36 321 0.00
12 g1213.t1 Gene3D G3DSA:3.40.50.620 HUPs 5 213 0.00
11 g1213.t1 Gene3D G3DSA:1.10.240.10 - 214 343 0.00
13 g1213.t1 Gene3D G3DSA:2.40.50.140 - 353 520 0.00
3 g1213.t1 PANTHER PTHR42765 SOLEUCYL-TRNA SYNTHETASE 5 383 0.00
4 g1213.t1 PANTHER PTHR42765:SF2 TYROSINE–TRNA LIGASE 5 383 0.00
7 g1213.t1 PRINTS PR01040 Tyrosyl-tRNA synthetase signature 47 69 0.00
6 g1213.t1 PRINTS PR01040 Tyrosyl-tRNA synthetase signature 158 173 0.00
5 g1213.t1 PRINTS PR01040 Tyrosyl-tRNA synthetase signature 175 197 0.00
8 g1213.t1 PRINTS PR01040 Tyrosyl-tRNA synthetase signature 208 220 0.00
1 g1213.t1 Pfam PF00579 tRNA synthetases class I (W and Y) 33 324 0.00
2 g1213.t1 Pfam PF01588 Putative tRNA binding domain 364 456 0.00
15 g1213.t1 ProSiteProfiles PS50886 tRNA-binding domain profile. 358 459 29.47
9 g1213.t1 SUPERFAMILY SSF52374 Nucleotidylyl transferase 3 342 0.00
10 g1213.t1 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 358 519 0.00
16 g1213.t1 TIGRFAM TIGR00234 tyrS: tyrosine–tRNA ligase 10 333 0.00

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 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