Gene loci information

Transcript annotation

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

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 g3969 g3969.t4 TTS g3969.t4 29322391 29322391
chr_3 g3969 g3969.t4 isoform g3969.t4 29322392 29323677
chr_3 g3969 g3969.t4 exon g3969.t4.exon1 29322392 29323677
chr_3 g3969 g3969.t4 cds g3969.t4.CDS1 29322420 29323256
chr_3 g3969 g3969.t4 TSS g3969.t4 29323887 29323887

Sequences

>g3969.t4 Gene=g3969 Length=1286
AGGAAAAATTCAAGCTGAACTCGGTAAAAGTGAACAAACGATTTATGCAGGCTTCGATCC
AACGAGTGATAGTCTTCATGTTGGTAATTTATTAGTAATAATAGGATTACTTCATGCACA
ACGTGGACAACATCGAACAATTGCATTGATAGGAGGTGCAACAGGAAAAATCGGAGATCC
AAGTGGAAGATCTAAAGAAAGAAATCTACTTGAAAACAATGTAATTGATCATAATTTAAA
ATCAATAAGCATTCAAATTAAAAAAATTTTTGATAATCATCGAGAATATTTTTGGGAGAA
ACAAAATCAAAAGAAAGAAGAATTGAAAGAGTTGCTAATTGTTAATAATGCTGATTGGTA
TAGTGACATTAGTTTTATCGACTTTATTTCTAAAGTAGGCAGACATTTTCGACTTGGTCA
AATGTTATCAAGAGCATCAGTTAGAAGTAGACTGGAAAGTGAAGAAGGAATGAGTTTTAC
AGAATTTACTTATCAAGTATTTCAAGCTTATGATTGGCTACAATTATTTCAAAAATATAA
TTGTCGTTATCAAATGGGAGGTCTTGATCAGATGGGAAATCTAATGACTGGATGTGAATT
TATTACAAGAGTTTTAAAGAAACAAGCATACGGCATTACATTACCAATTATAACTAATGA
AGAAGGTAACAAATTTGGTAAATCAGCTGGAAATGCTGTTTGGCTTGATGCCAATAAAAC
ATCAGAATTTGGATTTTATCAGTTTTTCTTGAGGCAACCTGATACAGAAGCAGAAAAATT
ATTTAAACTTTTCTCTCTTCTTCGAACGAATGAAGTTTTTGATCAAATTGATAAACATAA
ACGAGCACCTGAATTAAGAGGACTTCAAATAGCATTAGCCGATCAATTGACTCTATTAAT
TCATGGTGAAAAGGGTTTAGAGAAGGCTAAAAAAATTTCAAACGCCTTATATAATGGTGA
TGTTCATGCATTAGGTTCGATGAATAAAAACGAAGTACAAGAGGTATTTTCAGGAGCACC
CTATAAAGAACTCATTCTTGAACCAGGAATGACCATTTTAAATATTGGTATGAGGGTTGG
TTGCTTTAAACATGAAAATGATGCTAAAAGAATAATATCAGCTGGAGGATTTTACATTAA
TATGAAACGCTCAAATAATCCTTCTGAAATTTTAACACCAAATGTTCATATTTTACCTAA
TGACATTACACTTATAAGAGTAGGAAAAAGAAATTTCTATATTATTAAGTGGGTATAAAT
AAATATTAGTTTATTTATAGAAATTT

>g3969.t4 Gene=g3969 Length=278
MLSRASVRSRLESEEGMSFTEFTYQVFQAYDWLQLFQKYNCRYQMGGLDQMGNLMTGCEF
ITRVLKKQAYGITLPIITNEEGNKFGKSAGNAVWLDANKTSEFGFYQFFLRQPDTEAEKL
FKLFSLLRTNEVFDQIDKHKRAPELRGLQIALADQLTLLIHGEKGLEKAKKISNALYNGD
VHALGSMNKNEVQEVFSGAPYKELILEPGMTILNIGMRVGCFKHENDAKRIISAGGFYIN
MKRSNNPSEILTPNVHILPNDITLIRVGKRNFYIIKWV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g3969.t4 Gene3D G3DSA:3.40.50.620 HUPs 1 76 0
9 g3969.t4 Gene3D G3DSA:1.10.240.10 - 77 182 0
11 g3969.t4 Gene3D G3DSA:3.10.290.10 - 183 278 0
2 g3969.t4 PANTHER PTHR11766:SF0 TYROSINE–TRNA LIGASE, MITOCHONDRIAL 1 278 0
3 g3969.t4 PANTHER PTHR11766 TYROSYL-TRNA SYNTHETASE 1 278 0
4 g3969.t4 PRINTS PR01040 Tyrosyl-tRNA synthetase signature 16 31 0
5 g3969.t4 PRINTS PR01040 Tyrosyl-tRNA synthetase signature 37 59 0
6 g3969.t4 PRINTS PR01040 Tyrosyl-tRNA synthetase signature 70 82 0
1 g3969.t4 Pfam PF00579 tRNA synthetases class I (W and Y) 1 177 0
8 g3969.t4 SUPERFAMILY SSF52374 Nucleotidylyl transferase 1 177 0
7 g3969.t4 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif 186 277 0
12 g3969.t4 TIGRFAM TIGR00234 tyrS: tyrosine–tRNA ligase 1 277 0

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:0003723 RNA binding MF
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:0006437 tyrosyl-tRNA aminoacylation BP

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