Gene loci information

Transcript annotation

  • This transcript has been annotated as Leucine–tRNA ligase, cytoplasmic.

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_2 g4655 g4655.t1 TTS g4655.t1 3961787 3961787
chr_2 g4655 g4655.t1 isoform g4655.t1 3961872 3965678
chr_2 g4655 g4655.t1 exon g4655.t1.exon1 3961872 3962522
chr_2 g4655 g4655.t1 cds g4655.t1.CDS1 3961872 3962522
chr_2 g4655 g4655.t1 exon g4655.t1.exon2 3962581 3964143
chr_2 g4655 g4655.t1 cds g4655.t1.CDS2 3962581 3964143
chr_2 g4655 g4655.t1 exon g4655.t1.exon3 3964204 3965412
chr_2 g4655 g4655.t1 cds g4655.t1.CDS3 3964204 3965412
chr_2 g4655 g4655.t1 exon g4655.t1.exon4 3965494 3965577
chr_2 g4655 g4655.t1 cds g4655.t1.CDS4 3965494 3965577
chr_2 g4655 g4655.t1 exon g4655.t1.exon5 3965676 3965678
chr_2 g4655 g4655.t1 cds g4655.t1.CDS5 3965676 3965678
chr_2 g4655 g4655.t1 TSS g4655.t1 3965812 3965812

Sequences

>g4655.t1 Gene=g4655 Length=3510
ATGGCTACTGAAAGGAAAGGAACATTTAAAGTTGAGTTTCTGCAAAAGATAGAACGTGAA
ATTCAAGAAAAATGGGAACGAGAGAAGATTCACGACTCGGATGCACCAAAAGAAGCTCGC
AAATCTCTCGATGAAAAATTCTTTGTCACTTTTCCTTATCCTTACATGAATGGACGTCTT
CATTTAGGTCATACTTTCTCTTTATCAAAAGCTGAATTTGGTGTTCGTTATTTTCGATTG
AAAGGAAAGAATGTTTTATTTCCACTTGGATTTCATTGTACTGGAATGCCAATCAAGGCT
TGTGCTGATAAGTTGAAACGTGAAATTGAGACATTTGGCTATCCTCCAAACTTTCCAATT
GAAGAAGAAACAACAGCTGTTGAAGTTGAACGCGATGTTGTGCCAAAAGATAAGTCAAAA
AGTAAAAAGAGCAAAGCTGTCGCAAAAGCTGGATCAACTAAATATCAATGGCAAATTATG
CAAAGTCTTGGTCTTGAAGATGAAGAGATTAAAAAGTTTGCTGACACCGATCATTGGCTT
GAATATTTCCCTCCTCTCGCTATTCAAGATTTAAAAAAGATGGGATCGCACATTGATTTT
CGTCGAACATTCGTTACAACTGATGTCAATCCATTCTATGATTCGTTTGTTCGATGGCAA
TTTTGTCTATTAAAGGAACGTGGAAAAATTATGTACGGAAAACGTCATACAATCTTCTCA
CCAAAAGATGGTCAACCCTGTATGGACCATGATCGTTCTTCAGGTGAAGGTGTTGGACCA
CAAGAGTATACTCTTATCAAAATGAAAGTTATTGGAAATATTCCAGAGAAATTGAAAAAT
GTCAAAACTGAAATTTTCATGGTTGCAGCAACTCTTCGTCCTGAAACAATGTATGGTCAA
ACAAACTGCTGGTTACATCCTGATATTAAATATATCGCTTTCGAAACAGTTAAGCAAGGT
GAAGTTTGGATTTGCACAAGAAGGGCTGCTAGAAATATGTCATATCAAGATTTTACTGCT
AAAGTTGGTGAAGTAAAAGTCGTTGCTGAACTTACTGGTCATGAGTTGATGGGAGTTCAA
TTATCTGCACCACTTACATCGAACAAAGTTATTTATACTCTTCCAATGTTGACAATCAAG
GAGGATAAAGGTACTGGTGTTGTAACTTCTGTTCCTTCAGATTCGCCTGATGACTATGCT
GCTCTTACTGACTTACAAAAGAAACAACCACTTCGTGAGAAATATGGAATTAAAGATGAA
ATGGTTTTACCTTATAATCCAATTCCAATTATTGAGGTTCCTGGCTTAGGAAACCTTAGT
GCAGTTACAGTTTGTGAGCAACTCAAAGTTCAATCGCAAAATGATCGTGATAAGTTAGCA
GAAGCAAAAGAACTTGTCTATCTTAAAGGTTTTTATGATGGTGTTTTGCTTGTTGGAGAT
CATAAAGGAAAGAAAGTTCAAGATGTCAAAAAAGATTTGAAGAATTATCTTGTTCAAAGA
AATGAAGCTGATACTTATTATGAGCCAGAAAAGACAATTATATCACGTTCAGCTGATGAA
TGTGTCGTAGCTCTATGTAATCAATGGTATATAACTTATGGAGAAGAAGAATGGCTTAAA
AAGACGCAAGGATTGTTGAAAAATATTGAAACTTATCATGAAGAATCTCGCAAGAGTTTT
GAACATTGTCTTGGTTGGTTACATGAATATGCGTGCTCAAGAACATATGGTTTAGGAACA
AAACTTCCTTGGGATGAACAATGGTTGATTGAGTCTCTATCTGATTCAACAATTTACATG
GCTTTTTACACAATCGTTCATCTACTACAAAGTGGAAGCTTTAGAGGTGAAAAACCAAGT
CCATTGGGAATAAAAGCTGAAATGATGACACCTGAAGTTTGGAATTATATTTTCTTTGCT
GATGCCAAATATCCATCAAAATCAAAAATTAGCAAAGATAAATTGGATATTCTTAAACGT
GAATTTAATTATTGGTATCCGATGGATTTAAGAGTATCTGGTAAAGATCTCATTAATAAC
CATCTTACATTCATGCTTTACAATCACACTGCAATTTGGCAAAATGAACCAGATAAATGG
CCACTCGGTGTTCGTGCTAATGGACATTTGCTTCTAAATTCTGCTAAAATGTCAAAATCT
GATGGAAATTTCTTGACCCTTTATGAAGCTGTTGAGAAGTTTTCAGCTGATGGCACACGT
CTTTGTCTCGCGGATGCTGGTGATTCAGTTGAAGATGCCAATTTTGTTGAGATCACTGCT
GATGCAGGTATTTTGAGACTTTATACATTGATTGAATGGGTGAAAGAAATGATTGCTGGA
AAACTTTTATTGAGAACTGGTTCAAAAGATGCTTTTTATGATCGTGTTTTCATTAGTGAA
ATGAATAGTTTCATTAAACAAACTGATGAGAACTATAACAAAATGCTTTACAAAGAAGCA
TTGAGAACAGGTGTTTTCGAATTTCAACGTGCAAGAGATACTTATCGTGAACTTTGTGGT
GCAAACAACATGCATGTTGATTTAGTTTTTCAATTTATCGAAAATCAAGCACTTTTAATG
GCACCAATTTGTCCGCATGTTGCTGAACATATTTGGGGCTTGTTAGGAAAATCAGGAAGC
ATTGTAAATGCCAAATTCCCTGTAGCTGGACCAATTGATGAGAAACTTATCAAATGTTCT
GATTATCTGATGGAAGCAGCTCACAATTTCCGCTTACTCTACAAAAAAAACTTTTCAGCT
AAAGGTGCACAAAAACCAACGGGTGCAACTATCTGGATTGCTAAAACTTTTCCACCATGG
CAGAGTTGTGTAATTGATACAATGAGAAATCTTTATGAGAAAAATAATTCTGTTCTTCCG
GATAATAAACTTGTTAGTGCTGAGTTAATGAAAATAGAATCGCTCAAAAAATATCAGAAG
AAAGCAATGCCATTTGTGCAGAGAATTAGAGATCGTGTGAGTGTTTTGGGAAAATCAGCA
ATGGCAGTTACTGTCGATTTTGATGAGCATGGAGTTATTGAAACAAATTTACAGTACTTG
AAAGGAACACTCGATTTGGAGCAAATTGAAATTCGATTCACTGATGATCCATCAGCAACT
GAAAATACAAGAGAGAGTGTACAACCAGGAAGTCCTTTCATTTCTTATATTGTAAAGCCA
TCAGTTAGAGTAAATTTTGAGAACCCAATCCCACGTTCGGGCCTTTTTACTCAGCAAATA
AACGTGGGAGAAGGTGACACTTTAAATACACTAAAAGAAAAGCTCGCTAAAGGATTAGGA
CTTAAAGTCACGACAGCAATTCAATTATGGAGATTTGAAGATCATGTTTTAGGGCCAAGA
AAAATGCCAATTTTTAATGATTTTAAGACAGGAAAGAAACAGATAGAAGAAGGAATATTC
TCAGTTGATGCTAAAGATTCAAAAGTTTTCATCACAAATAATGAAAGTAAAATCGAAGTT
GGAACAAATTTCATCTATGTTGTTGAATGA

>g4655.t1 Gene=g4655 Length=1169
MATERKGTFKVEFLQKIEREIQEKWEREKIHDSDAPKEARKSLDEKFFVTFPYPYMNGRL
HLGHTFSLSKAEFGVRYFRLKGKNVLFPLGFHCTGMPIKACADKLKREIETFGYPPNFPI
EEETTAVEVERDVVPKDKSKSKKSKAVAKAGSTKYQWQIMQSLGLEDEEIKKFADTDHWL
EYFPPLAIQDLKKMGSHIDFRRTFVTTDVNPFYDSFVRWQFCLLKERGKIMYGKRHTIFS
PKDGQPCMDHDRSSGEGVGPQEYTLIKMKVIGNIPEKLKNVKTEIFMVAATLRPETMYGQ
TNCWLHPDIKYIAFETVKQGEVWICTRRAARNMSYQDFTAKVGEVKVVAELTGHELMGVQ
LSAPLTSNKVIYTLPMLTIKEDKGTGVVTSVPSDSPDDYAALTDLQKKQPLREKYGIKDE
MVLPYNPIPIIEVPGLGNLSAVTVCEQLKVQSQNDRDKLAEAKELVYLKGFYDGVLLVGD
HKGKKVQDVKKDLKNYLVQRNEADTYYEPEKTIISRSADECVVALCNQWYITYGEEEWLK
KTQGLLKNIETYHEESRKSFEHCLGWLHEYACSRTYGLGTKLPWDEQWLIESLSDSTIYM
AFYTIVHLLQSGSFRGEKPSPLGIKAEMMTPEVWNYIFFADAKYPSKSKISKDKLDILKR
EFNYWYPMDLRVSGKDLINNHLTFMLYNHTAIWQNEPDKWPLGVRANGHLLLNSAKMSKS
DGNFLTLYEAVEKFSADGTRLCLADAGDSVEDANFVEITADAGILRLYTLIEWVKEMIAG
KLLLRTGSKDAFYDRVFISEMNSFIKQTDENYNKMLYKEALRTGVFEFQRARDTYRELCG
ANNMHVDLVFQFIENQALLMAPICPHVAEHIWGLLGKSGSIVNAKFPVAGPIDEKLIKCS
DYLMEAAHNFRLLYKKNFSAKGAQKPTGATIWIAKTFPPWQSCVIDTMRNLYEKNNSVLP
DNKLVSAELMKIESLKKYQKKAMPFVQRIRDRVSVLGKSAMAVTVDFDEHGVIETNLQYL
KGTLDLEQIEIRFTDDPSATENTRESVQPGSPFISYIVKPSVRVNFENPIPRSGLFTQQI
NVGEGDTLNTLKEKLAKGLGLKVTTAIQLWRFEDHVLGPRKMPIFNDFKTGKKQIEEGIF
SVDAKDSKVFITNNESKIEVGTNFIYVVE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g4655.t1 CDD cd07959 Anticodon_Ia_Leu_AEc 755 875 1.33724E-40
10 g4655.t1 Coils Coil Coil 445 465 -
9 g4655.t1 Gene3D G3DSA:1.10.730.10 - 765 876 1.9E-10
4 g4655.t1 PANTHER PTHR45794 LEUCYL-TRNA SYNTHETASE 4 1056 0.0
5 g4655.t1 PANTHER PTHR45794:SF1 LEUCINE–TRNA LIGASE, CYTOPLASMIC 4 1056 0.0
2 g4655.t1 Pfam PF00133 tRNA synthetases class I (I, L, M and V) 21 104 1.8E-11
1 g4655.t1 Pfam PF00133 tRNA synthetases class I (I, L, M and V) 178 755 4.6E-26
3 g4655.t1 Pfam PF08264 Anticodon-binding domain of tRNA ligase 794 911 5.8E-15
12 g4655.t1 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature. 54 65 -
6 g4655.t1 SUPERFAMILY SSF52374 Nucleotidylyl transferase 9 755 1.13E-85
8 g4655.t1 SUPERFAMILY SSF50677 ValRS/IleRS/LeuRS editing domain 266 509 4.6E-29
7 g4655.t1 SUPERFAMILY SSF47323 Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 766 980 3.55E-26
13 g4655.t1 TIGRFAM TIGR00395 leuS_arch: leucine–tRNA ligase 16 1054 3.6E-280

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:0004823 leucine-tRNA ligase activity MF
GO:0005524 ATP binding MF
GO:0002161 aminoacyl-tRNA editing activity MF
GO:0006418 tRNA aminoacylation for protein translation BP
GO:0000166 nucleotide binding MF
GO:0006429 leucyl-tRNA aminoacylation BP
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