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.t1 TSS g3889.t1 28630164 28630164
chr_3 g3889 g3889.t1 isoform g3889.t1 28630309 28632463
chr_3 g3889 g3889.t1 exon g3889.t1.exon1 28630309 28630334
chr_3 g3889 g3889.t1 cds g3889.t1.CDS1 28630309 28630334
chr_3 g3889 g3889.t1 exon g3889.t1.exon2 28630685 28631216
chr_3 g3889 g3889.t1 cds g3889.t1.CDS2 28630685 28631216
chr_3 g3889 g3889.t1 exon g3889.t1.exon3 28631276 28632463
chr_3 g3889 g3889.t1 cds g3889.t1.CDS3 28631276 28632463
chr_3 g3889 g3889.t1 TTS g3889.t1 28632536 28632536

Sequences

>g3889.t1 Gene=g3889 Length=1746
ATGGCTGAAGAGAAATTGTCTAAAAATGAATTGAAACGTCGTATGAAAGCGGCACAAAAA
GAGAAGGAGAAACAAGAAAAGGAAGCAGCAGCTGCTGAAAAAGCACAAACTGATGCTAAT
GCAAATGCTAATAAGGAAAATAAAATTGATGAGGCAGATATTTCTCCAAATGAGTACTTC
AAATTGCGTTCTGGTGTTGTCAATGAATTAAAGAAATTGCCAGAGACTCATCCTTATCCA
CATAAGTTTCATGTGTCAAGTTCACTGGAGGATTTCATTGCAAAATATAGCAATCTTAAA
GATGGTGAAATGCTTGAAAATGAACCATTGAGTGTTGCTGGAAGAGTTCATGCTATTCGT
GCTTCTGGTGCTAAATTAATTTTCTACGATGTTCGTGGTGAAGGTGTCAAAATCCAAGTA
ATGGTGAATGCCAGATTGTACTCATCAGAAGAAAAGTTCTTTACCGATACTGATCGCATT
CGACGTGGTGATATCGTTGGTATTGAAGGATATCCTGGCAAAACTAAGAAAGGCGAATTA
TCAGTTATACCAAAAAATATTAAAATATTGTCACCATGTTTACATATGCTTCCGCACTTG
CATTTCGGTTTAAAGGATAAGGAAACACGTTTCCGACAACGTTATTTAGATTTGATTCTC
AATAATAGAGTTCGTGATATTTTCCATGTTCGTTCAAAAATTATCTCTTATATTCGACAA
TTCTTTGATAAAATGGGCTTTTTAGAAGTTGAAACTCCAATGATGAATATGATTCCGGGT
GGTGCAACTGCAAAACCTTTTGTAACACATCATAATGATTTGAATATGGATCTTTATATG
AGAATTGCACCAGAATTGTACTTGAAAATGTTAGTAGTTGGTGGTCTTGATCGTGTTTAT
GAAATTGGTCGACTATTCAGAAATGAAGGCATCGATATGACTCATAATCCAGAATTTACA
ACTTGTGAATTTTACATGGCGTATGCAGACTACAATGATTTAATTGAAATAACTGAGAAA
CTACTTTCGGGTATGGTAAAATCGATTCATGGAAGCTATAAAATTAAATATCATCCAAAT
GGTGAAGAAGGAGAAGAAGTTGAAGTTGATTTCACGCCTCCATTCAAGCGTGTACCTATG
TTAAAAACTCTTGAAGAAATTCTCAAAGTTAAATTTCCATCAGCTACTGAATTGCATACT
AAAGAATCTAATAAATTCTTTGATCAACTATGCATCAAACATCAAGTCGAATGTCCCGCT
CCGAGAACGACTGCTCGTCTTTTGGATAAATTGGTTGGTCAATTTTTAGAAGAAGATTGT
ATAAATCCAACTTTCATCACCGATCATCCTCAATTGATGTCACCATTAGCAAAATATCAT
AGAAGTCAACCTGGCCTTACTGAACGTTTTGAGTTATTTGTTATGAAGAAAGAGGTTTGC
AATGCATATACTGAATTGAATGATCCGTTTGTGCAACGTGAAAGATTTATGCAACAAGCA
TCAGATAAAGCCGCAGGAGATGATGAAGCTCAGTTAATTGATGAAAACTTTTGTATGTCA
CTCGAATATGGACTACCACCGACCGGTGGATGGGGTCTAGGAATCGATCGATTGACTATG
TTCCTCACTGATAATAATAATATAAAAGAAGTTCTTCTTTTCCCTGCTATGAAGCCCGAT
TTAGGTGGACCTTCTGAAGAAGCTACATCAGCTATCACTGCTAATGCGAATGTTGACAAG
AAATAA

>g3889.t1 Gene=g3889 Length=581
MAEEKLSKNELKRRMKAAQKEKEKQEKEAAAAEKAQTDANANANKENKIDEADISPNEYF
KLRSGVVNELKKLPETHPYPHKFHVSSSLEDFIAKYSNLKDGEMLENEPLSVAGRVHAIR
ASGAKLIFYDVRGEGVKIQVMVNARLYSSEEKFFTDTDRIRRGDIVGIEGYPGKTKKGEL
SVIPKNIKILSPCLHMLPHLHFGLKDKETRFRQRYLDLILNNRVRDIFHVRSKIISYIRQ
FFDKMGFLEVETPMMNMIPGGATAKPFVTHHNDLNMDLYMRIAPELYLKMLVVGGLDRVY
EIGRLFRNEGIDMTHNPEFTTCEFYMAYADYNDLIEITEKLLSGMVKSIHGSYKIKYHPN
GEEGEEVEVDFTPPFKRVPMLKTLEEILKVKFPSATELHTKESNKFFDQLCIKHQVECPA
PRTTARLLDKLVGQFLEEDCINPTFITDHPQLMSPLAKYHRSQPGLTERFELFVMKKEVC
NAYTELNDPFVQRERFMQQASDKAAGDDEAQLIDENFCMSLEYGLPPTGGWGLGIDRLTM
FLTDNNNIKEVLLFPAMKPDLGGPSEEATSAITANANVDKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g3889.t1 CDD cd04322 LysRS_N 110 218 4.02692E-51
17 g3889.t1 CDD cd00775 LysRS_core 221 559 0.0
14 g3889.t1 Coils Coil Coil 1 42 -
13 g3889.t1 Gene3D G3DSA:2.40.50.140 - 45 201 5.0E-46
12 g3889.t1 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 202 576 1.7E-140
4 g3889.t1 Hamap MF_00252 Lysine–tRNA ligase [lysS]. 62 560 37.742466
18 g3889.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 50 -
19 g3889.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 33 -
3 g3889.t1 PANTHER PTHR42918 LYSYL-TRNA SYNTHETASE 2 560 2.6E-267
15 g3889.t1 PIRSF PIRSF039101 LysRS2 1 572 9.9E-266
5 g3889.t1 PRINTS PR00982 Lysyl-tRNA synthetase signature 243 253 1.3E-38
6 g3889.t1 PRINTS PR00982 Lysyl-tRNA synthetase signature 259 275 1.3E-38
8 g3889.t1 PRINTS PR00982 Lysyl-tRNA synthetase signature 288 301 1.3E-38
9 g3889.t1 PRINTS PR00982 Lysyl-tRNA synthetase signature 306 323 1.3E-38
7 g3889.t1 PRINTS PR00982 Lysyl-tRNA synthetase signature 442 458 1.3E-38
1 g3889.t1 Pfam PF01336 OB-fold nucleic acid binding domain 111 190 2.9E-14
2 g3889.t1 Pfam PF00152 tRNA synthetases class II (D, K and N) 206 557 1.0E-80
21 g3889.t1 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 228 559 29.31
11 g3889.t1 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 54 198 4.5E-36
10 g3889.t1 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 206 558 1.81E-117
20 g3889.t1 TIGRFAM TIGR00499 lysS_bact: lysine–tRNA ligase 57 560 1.6E-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