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.t5 TSS g3889.t5 28630164 28630164
chr_3 g3889 g3889.t5 isoform g3889.t5 28630459 28632463
chr_3 g3889 g3889.t5 exon g3889.t5.exon1 28630459 28631216
chr_3 g3889 g3889.t5 cds g3889.t5.CDS1 28630563 28631216
chr_3 g3889 g3889.t5 exon g3889.t5.exon2 28631276 28632463
chr_3 g3889 g3889.t5 cds g3889.t5.CDS2 28631276 28632463
chr_3 g3889 g3889.t5 TTS g3889.t5 28632536 28632536

Sequences

>g3889.t5 Gene=g3889 Length=1946
ATGCTCACTATTTTCCACACAATCCAAAAAGCTACTATTCCAGTATTACTCAAACTAGAA
CGTCATCAGCTGCAATTGCGACAGATTCAAGTAGCGAGTGGATTATGTGGAAAAAGGTTA
GAGAAAACAATGCAAAAAATTCATGGAACGTGATGATGATGATGAAAATGCTCTATCAAA
ATGATAAAAAATATTGTTTAATAAACTTTATTCTTCTTTTTATTAGTGAATTGAAACGTC
GTATGAAAGCGGCACAAAAAGAGAAGGAGAAACAAGAAAAGGAAGCAGCAGCTGCTGAAA
AAGCACAAACTGATGCTAATGCAAATGCTAATAAGGAAAATAAAATTGATGAGGCAGATA
TTTCTCCAAATGAGTACTTCAAATTGCGTTCTGGTGTTGTCAATGAATTAAAGAAATTGC
CAGAGACTCATCCTTATCCACATAAGTTTCATGTGTCAAGTTCACTGGAGGATTTCATTG
CAAAATATAGCAATCTTAAAGATGGTGAAATGCTTGAAAATGAACCATTGAGTGTTGCTG
GAAGAGTTCATGCTATTCGTGCTTCTGGTGCTAAATTAATTTTCTACGATGTTCGTGGTG
AAGGTGTCAAAATCCAAGTAATGGTGAATGCCAGATTGTACTCATCAGAAGAAAAGTTCT
TTACCGATACTGATCGCATTCGACGTGGTGATATCGTTGGTATTGAAGGATATCCTGGCA
AAACTAAGAAAGGCGAATTATCAGTTATACCAAAAAATATTAAAATATTGTCACCATGTT
TACATATGCTTCCGCACTTGCATTTCGGTTTAAAGGATAAGGAAACACGTTTCCGACAAC
GTTATTTAGATTTGATTCTCAATAATAGAGTTCGTGATATTTTCCATGTTCGTTCAAAAA
TTATCTCTTATATTCGACAATTCTTTGATAAAATGGGCTTTTTAGAAGTTGAAACTCCAA
TGATGAATATGATTCCGGGTGGTGCAACTGCAAAACCTTTTGTAACACATCATAATGATT
TGAATATGGATCTTTATATGAGAATTGCACCAGAATTGTACTTGAAAATGTTAGTAGTTG
GTGGTCTTGATCGTGTTTATGAAATTGGTCGACTATTCAGAAATGAAGGCATCGATATGA
CTCATAATCCAGAATTTACAACTTGTGAATTTTACATGGCGTATGCAGACTACAATGATT
TAATTGAAATAACTGAGAAACTACTTTCGGGTATGGTAAAATCGATTCATGGAAGCTATA
AAATTAAATATCATCCAAATGGTGAAGAAGGAGAAGAAGTTGAAGTTGATTTCACGCCTC
CATTCAAGCGTGTACCTATGTTAAAAACTCTTGAAGAAATTCTCAAAGTTAAATTTCCAT
CAGCTACTGAATTGCATACTAAAGAATCTAATAAATTCTTTGATCAACTATGCATCAAAC
ATCAAGTCGAATGTCCCGCTCCGAGAACGACTGCTCGTCTTTTGGATAAATTGGTTGGTC
AATTTTTAGAAGAAGATTGTATAAATCCAACTTTCATCACCGATCATCCTCAATTGATGT
CACCATTAGCAAAATATCATAGAAGTCAACCTGGCCTTACTGAACGTTTTGAGTTATTTG
TTATGAAGAAAGAGGTTTGCAATGCATATACTGAATTGAATGATCCGTTTGTGCAACGTG
AAAGATTTATGCAACAAGCATCAGATAAAGCCGCAGGAGATGATGAAGCTCAGTTAATTG
ATGAAAACTTTTGTATGTCACTCGAATATGGACTACCACCGACCGGTGGATGGGGTCTAG
GAATCGATCGATTGACTATGTTCCTCACTGATAATAATAATATAAAAGAAGTTCTTCTTT
TCCCTGCTATGAAGCCCGATTTAGGTGGACCTTCTGAAGAAGCTACATCAGCTATCACTG
CTAATGCGAATGTTGACAAGAAATAA

>g3889.t5 Gene=g3889 Length=613
MWKKVRENNAKNSWNVMMMMKMLYQNDKKYCLINFILLFISELKRRMKAAQKEKEKQEKE
AAAAEKAQTDANANANKENKIDEADISPNEYFKLRSGVVNELKKLPETHPYPHKFHVSSS
LEDFIAKYSNLKDGEMLENEPLSVAGRVHAIRASGAKLIFYDVRGEGVKIQVMVNARLYS
SEEKFFTDTDRIRRGDIVGIEGYPGKTKKGELSVIPKNIKILSPCLHMLPHLHFGLKDKE
TRFRQRYLDLILNNRVRDIFHVRSKIISYIRQFFDKMGFLEVETPMMNMIPGGATAKPFV
THHNDLNMDLYMRIAPELYLKMLVVGGLDRVYEIGRLFRNEGIDMTHNPEFTTCEFYMAY
ADYNDLIEITEKLLSGMVKSIHGSYKIKYHPNGEEGEEVEVDFTPPFKRVPMLKTLEEIL
KVKFPSATELHTKESNKFFDQLCIKHQVECPAPRTTARLLDKLVGQFLEEDCINPTFITD
HPQLMSPLAKYHRSQPGLTERFELFVMKKEVCNAYTELNDPFVQRERFMQQASDKAAGDD
EAQLIDENFCMSLEYGLPPTGGWGLGIDRLTMFLTDNNNIKEVLLFPAMKPDLGGPSEEA
TSAITANANVDKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
21 g3889.t5 CDD cd04322 LysRS_N 142 250 5.74547E-51
22 g3889.t5 CDD cd00775 LysRS_core 253 591 0.0
14 g3889.t5 Coils Coil Coil 40 74 -
13 g3889.t5 Gene3D G3DSA:2.40.50.140 - 79 233 5.7E-46
12 g3889.t5 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 234 608 1.9E-140
4 g3889.t5 Hamap MF_00252 Lysine–tRNA ligase [lysS]. 94 592 37.742466
23 g3889.t5 MobiDBLite mobidb-lite consensus disorder prediction 51 65 -
24 g3889.t5 MobiDBLite mobidb-lite consensus disorder prediction 51 80 -
3 g3889.t5 PANTHER PTHR42918 LYSYL-TRNA SYNTHETASE 42 592 1.4E-264
20 g3889.t5 PIRSF PIRSF039101 LysRS2 17 604 8.2E-265
6 g3889.t5 PRINTS PR00982 Lysyl-tRNA synthetase signature 275 285 1.6E-38
8 g3889.t5 PRINTS PR00982 Lysyl-tRNA synthetase signature 291 307 1.6E-38
5 g3889.t5 PRINTS PR00982 Lysyl-tRNA synthetase signature 320 333 1.6E-38
9 g3889.t5 PRINTS PR00982 Lysyl-tRNA synthetase signature 338 355 1.6E-38
7 g3889.t5 PRINTS PR00982 Lysyl-tRNA synthetase signature 474 490 1.6E-38
1 g3889.t5 Pfam PF01336 OB-fold nucleic acid binding domain 143 222 3.1E-14
2 g3889.t5 Pfam PF00152 tRNA synthetases class II (D, K and N) 238 589 1.2E-80
16 g3889.t5 Phobius SIGNAL_PEPTIDE Signal peptide region 1 49 -
17 g3889.t5 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 30 -
18 g3889.t5 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 31 41 -
19 g3889.t5 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 42 49 -
15 g3889.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 50 613 -
26 g3889.t5 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 260 591 29.31
11 g3889.t5 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 86 230 4.93E-36
10 g3889.t5 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 238 590 2.19E-117
25 g3889.t5 TIGRFAM TIGR00499 lysS_bact: lysine–tRNA ligase 89 592 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