Gene loci information

Transcript annotation

  • This transcript has been annotated as Lysine–tRNA ligase.

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 g3889 g3889.t6 isoform g3889.t6 28631216 28632463
chr_3 g3889 g3889.t6 exon g3889.t6.exon1 28631216 28632463
chr_3 g3889 g3889.t6 cds g3889.t6.CDS1 28631303 28632463
chr_3 g3889 g3889.t6 TTS g3889.t6 28632536 28632536
chr_3 g3889 g3889.t6 TSS g3889.t6 NA NA

Sequences

>g3889.t6 Gene=g3889 Length=1248
TGTATGTTATATAAAAGATTTTGTAAAGTTTAATATTTATTAAGCATAATTTTATTTTAG
ATTAAAATATTGTCACCATGTTTACATATGCTTCCGCACTTGCATTTCGGTTTAAAGGAT
AAGGAAACACGTTTCCGACAACGTTATTTAGATTTGATTCTCAATAATAGAGTTCGTGAT
ATTTTCCATGTTCGTTCAAAAATTATCTCTTATATTCGACAATTCTTTGATAAAATGGGC
TTTTTAGAAGTTGAAACTCCAATGATGAATATGATTCCGGGTGGTGCAACTGCAAAACCT
TTTGTAACACATCATAATGATTTGAATATGGATCTTTATATGAGAATTGCACCAGAATTG
TACTTGAAAATGTTAGTAGTTGGTGGTCTTGATCGTGTTTATGAAATTGGTCGACTATTC
AGAAATGAAGGCATCGATATGACTCATAATCCAGAATTTACAACTTGTGAATTTTACATG
GCGTATGCAGACTACAATGATTTAATTGAAATAACTGAGAAACTACTTTCGGGTATGGTA
AAATCGATTCATGGAAGCTATAAAATTAAATATCATCCAAATGGTGAAGAAGGAGAAGAA
GTTGAAGTTGATTTCACGCCTCCATTCAAGCGTGTACCTATGTTAAAAACTCTTGAAGAA
ATTCTCAAAGTTAAATTTCCATCAGCTACTGAATTGCATACTAAAGAATCTAATAAATTC
TTTGATCAACTATGCATCAAACATCAAGTCGAATGTCCCGCTCCGAGAACGACTGCTCGT
CTTTTGGATAAATTGGTTGGTCAATTTTTAGAAGAAGATTGTATAAATCCAACTTTCATC
ACCGATCATCCTCAATTGATGTCACCATTAGCAAAATATCATAGAAGTCAACCTGGCCTT
ACTGAACGTTTTGAGTTATTTGTTATGAAGAAAGAGGTTTGCAATGCATATACTGAATTG
AATGATCCGTTTGTGCAACGTGAAAGATTTATGCAACAAGCATCAGATAAAGCCGCAGGA
GATGATGAAGCTCAGTTAATTGATGAAAACTTTTGTATGTCACTCGAATATGGACTACCA
CCGACCGGTGGATGGGGTCTAGGAATCGATCGATTGACTATGTTCCTCACTGATAATAAT
AATATAAAAGAAGTTCTTCTTTTCCCTGCTATGAAGCCCGATTTAGGTGGACCTTCTGAA
GAAGCTACATCAGCTATCACTGCTAATGCGAATGTTGACAAGAAATAA

>g3889.t6 Gene=g3889 Length=386
MLPHLHFGLKDKETRFRQRYLDLILNNRVRDIFHVRSKIISYIRQFFDKMGFLEVETPMM
NMIPGGATAKPFVTHHNDLNMDLYMRIAPELYLKMLVVGGLDRVYEIGRLFRNEGIDMTH
NPEFTTCEFYMAYADYNDLIEITEKLLSGMVKSIHGSYKIKYHPNGEEGEEVEVDFTPPF
KRVPMLKTLEEILKVKFPSATELHTKESNKFFDQLCIKHQVECPAPRTTARLLDKLVGQF
LEEDCINPTFITDHPQLMSPLAKYHRSQPGLTERFELFVMKKEVCNAYTELNDPFVQRER
FMQQASDKAAGDDEAQLIDENFCMSLEYGLPPTGGWGLGIDRLTMFLTDNNNIKEVLLFP
AMKPDLGGPSEEATSAITANANVDKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g3889.t6 CDD cd00775 LysRS_core 26 364 0.00
9 g3889.t6 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 7 381 0.00
2 g3889.t6 PANTHER PTHR42918 LYSYL-TRNA SYNTHETASE 1 365 0.00
5 g3889.t6 PRINTS PR00982 Lysyl-tRNA synthetase signature 48 58 0.00
3 g3889.t6 PRINTS PR00982 Lysyl-tRNA synthetase signature 64 80 0.00
4 g3889.t6 PRINTS PR00982 Lysyl-tRNA synthetase signature 93 106 0.00
7 g3889.t6 PRINTS PR00982 Lysyl-tRNA synthetase signature 111 128 0.00
6 g3889.t6 PRINTS PR00982 Lysyl-tRNA synthetase signature 247 263 0.00
1 g3889.t6 Pfam PF00152 tRNA synthetases class II (D, K and N) 11 362 0.00
11 g3889.t6 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 33 364 29.31
8 g3889.t6 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 11 363 0.00
12 g3889.t6 TIGRFAM TIGR00499 lysS_bact: lysine–tRNA ligase 1 365 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:0006430 lysyl-tRNA aminoacylation BP
GO:0005524 ATP binding MF
GO:0006418 tRNA aminoacylation for protein translation BP
GO:0000166 nucleotide binding MF
GO:0004824 lysine-tRNA ligase activity MF
GO:0004812 aminoacyl-tRNA ligase activity MF
GO:0005737 cytoplasm CC

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