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.t2 TSS g3889.t2 28630164 28630164
chr_3 g3889 g3889.t2 isoform g3889.t2 28630459 28632463
chr_3 g3889 g3889.t2 exon g3889.t2.exon1 28630459 28630574
chr_3 g3889 g3889.t2 cds g3889.t2.CDS1 28630459 28630574
chr_3 g3889 g3889.t2 exon g3889.t2.exon2 28630685 28631216
chr_3 g3889 g3889.t2 cds g3889.t2.CDS2 28630685 28631216
chr_3 g3889 g3889.t2 exon g3889.t2.exon3 28631276 28632463
chr_3 g3889 g3889.t2 cds g3889.t2.CDS3 28631276 28632463
chr_3 g3889 g3889.t2 TTS g3889.t2 28632536 28632536

Sequences

>g3889.t2 Gene=g3889 Length=1836
ATGCTCACTATTTTCCACACAATCCAAAAAGCTACTATTCCAGTATTACTCAAACTAGAA
CGTCATCAGCTGCAATTGCGACAGATTCAAGTAGCGAGTGGATTATGTGGAAAAAGTGAA
TTGAAACGTCGTATGAAAGCGGCACAAAAAGAGAAGGAGAAACAAGAAAAGGAAGCAGCA
GCTGCTGAAAAAGCACAAACTGATGCTAATGCAAATGCTAATAAGGAAAATAAAATTGAT
GAGGCAGATATTTCTCCAAATGAGTACTTCAAATTGCGTTCTGGTGTTGTCAATGAATTA
AAGAAATTGCCAGAGACTCATCCTTATCCACATAAGTTTCATGTGTCAAGTTCACTGGAG
GATTTCATTGCAAAATATAGCAATCTTAAAGATGGTGAAATGCTTGAAAATGAACCATTG
AGTGTTGCTGGAAGAGTTCATGCTATTCGTGCTTCTGGTGCTAAATTAATTTTCTACGAT
GTTCGTGGTGAAGGTGTCAAAATCCAAGTAATGGTGAATGCCAGATTGTACTCATCAGAA
GAAAAGTTCTTTACCGATACTGATCGCATTCGACGTGGTGATATCGTTGGTATTGAAGGA
TATCCTGGCAAAACTAAGAAAGGCGAATTATCAGTTATACCAAAAAATATTAAAATATTG
TCACCATGTTTACATATGCTTCCGCACTTGCATTTCGGTTTAAAGGATAAGGAAACACGT
TTCCGACAACGTTATTTAGATTTGATTCTCAATAATAGAGTTCGTGATATTTTCCATGTT
CGTTCAAAAATTATCTCTTATATTCGACAATTCTTTGATAAAATGGGCTTTTTAGAAGTT
GAAACTCCAATGATGAATATGATTCCGGGTGGTGCAACTGCAAAACCTTTTGTAACACAT
CATAATGATTTGAATATGGATCTTTATATGAGAATTGCACCAGAATTGTACTTGAAAATG
TTAGTAGTTGGTGGTCTTGATCGTGTTTATGAAATTGGTCGACTATTCAGAAATGAAGGC
ATCGATATGACTCATAATCCAGAATTTACAACTTGTGAATTTTACATGGCGTATGCAGAC
TACAATGATTTAATTGAAATAACTGAGAAACTACTTTCGGGTATGGTAAAATCGATTCAT
GGAAGCTATAAAATTAAATATCATCCAAATGGTGAAGAAGGAGAAGAAGTTGAAGTTGAT
TTCACGCCTCCATTCAAGCGTGTACCTATGTTAAAAACTCTTGAAGAAATTCTCAAAGTT
AAATTTCCATCAGCTACTGAATTGCATACTAAAGAATCTAATAAATTCTTTGATCAACTA
TGCATCAAACATCAAGTCGAATGTCCCGCTCCGAGAACGACTGCTCGTCTTTTGGATAAA
TTGGTTGGTCAATTTTTAGAAGAAGATTGTATAAATCCAACTTTCATCACCGATCATCCT
CAATTGATGTCACCATTAGCAAAATATCATAGAAGTCAACCTGGCCTTACTGAACGTTTT
GAGTTATTTGTTATGAAGAAAGAGGTTTGCAATGCATATACTGAATTGAATGATCCGTTT
GTGCAACGTGAAAGATTTATGCAACAAGCATCAGATAAAGCCGCAGGAGATGATGAAGCT
CAGTTAATTGATGAAAACTTTTGTATGTCACTCGAATATGGACTACCACCGACCGGTGGA
TGGGGTCTAGGAATCGATCGATTGACTATGTTCCTCACTGATAATAATAATATAAAAGAA
GTTCTTCTTTTCCCTGCTATGAAGCCCGATTTAGGTGGACCTTCTGAAGAAGCTACATCA
GCTATCACTGCTAATGCGAATGTTGACAAGAAATAA

>g3889.t2 Gene=g3889 Length=611
MLTIFHTIQKATIPVLLKLERHQLQLRQIQVASGLCGKSELKRRMKAAQKEKEKQEKEAA
AAEKAQTDANANANKENKIDEADISPNEYFKLRSGVVNELKKLPETHPYPHKFHVSSSLE
DFIAKYSNLKDGEMLENEPLSVAGRVHAIRASGAKLIFYDVRGEGVKIQVMVNARLYSSE
EKFFTDTDRIRRGDIVGIEGYPGKTKKGELSVIPKNIKILSPCLHMLPHLHFGLKDKETR
FRQRYLDLILNNRVRDIFHVRSKIISYIRQFFDKMGFLEVETPMMNMIPGGATAKPFVTH
HNDLNMDLYMRIAPELYLKMLVVGGLDRVYEIGRLFRNEGIDMTHNPEFTTCEFYMAYAD
YNDLIEITEKLLSGMVKSIHGSYKIKYHPNGEEGEEVEVDFTPPFKRVPMLKTLEEILKV
KFPSATELHTKESNKFFDQLCIKHQVECPAPRTTARLLDKLVGQFLEEDCINPTFITDHP
QLMSPLAKYHRSQPGLTERFELFVMKKEVCNAYTELNDPFVQRERFMQQASDKAAGDDEA
QLIDENFCMSLEYGLPPTGGWGLGIDRLTMFLTDNNNIKEVLLFPAMKPDLGGPSEEATS
AITANANVDKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g3889.t2 CDD cd04322 LysRS_N 140 248 1.12969E-50
17 g3889.t2 CDD cd00775 LysRS_core 251 589 0.0
14 g3889.t2 Coils Coil Coil 38 72 -
13 g3889.t2 Gene3D G3DSA:2.40.50.140 - 77 231 5.6E-46
12 g3889.t2 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 232 606 1.9E-140
4 g3889.t2 Hamap MF_00252 Lysine–tRNA ligase [lysS]. 92 590 37.742466
18 g3889.t2 MobiDBLite mobidb-lite consensus disorder prediction 46 80 -
19 g3889.t2 MobiDBLite mobidb-lite consensus disorder prediction 46 63 -
3 g3889.t2 PANTHER PTHR42918 LYSYL-TRNA SYNTHETASE 36 590 2.2E-265
15 g3889.t2 PIRSF PIRSF039101 LysRS2 20 602 1.3E-265
9 g3889.t2 PRINTS PR00982 Lysyl-tRNA synthetase signature 273 283 1.6E-38
8 g3889.t2 PRINTS PR00982 Lysyl-tRNA synthetase signature 289 305 1.6E-38
6 g3889.t2 PRINTS PR00982 Lysyl-tRNA synthetase signature 318 331 1.6E-38
7 g3889.t2 PRINTS PR00982 Lysyl-tRNA synthetase signature 336 353 1.6E-38
5 g3889.t2 PRINTS PR00982 Lysyl-tRNA synthetase signature 472 488 1.6E-38
1 g3889.t2 Pfam PF01336 OB-fold nucleic acid binding domain 141 220 3.1E-14
2 g3889.t2 Pfam PF00152 tRNA synthetases class II (D, K and N) 236 587 1.2E-80
21 g3889.t2 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 258 589 29.31
11 g3889.t2 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 84 228 4.93E-36
10 g3889.t2 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 236 588 2.19E-117
20 g3889.t2 TIGRFAM TIGR00499 lysS_bact: lysine–tRNA ligase 87 590 2.0E-193

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:0005737 cytoplasm CC
GO:0003676 nucleic acid binding MF
GO:0000166 nucleotide binding MF
GO:0006418 tRNA aminoacylation for protein translation BP
GO:0004824 lysine-tRNA ligase activity MF
GO:0004812 aminoacyl-tRNA ligase activity MF

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