Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable leucine–tRNA ligase, mitochondrial.

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 g4703 g4703.t1 TSS g4703.t1 4315166 4315166
chr_2 g4703 g4703.t1 isoform g4703.t1 4315186 4317860
chr_2 g4703 g4703.t1 exon g4703.t1.exon1 4315186 4315290
chr_2 g4703 g4703.t1 cds g4703.t1.CDS1 4315186 4315290
chr_2 g4703 g4703.t1 exon g4703.t1.exon2 4315347 4317860
chr_2 g4703 g4703.t1 cds g4703.t1.CDS2 4315347 4317860
chr_2 g4703 g4703.t1 TTS g4703.t1 4317908 4317908

Sequences

>g4703.t1 Gene=g4703 Length=2619
ATGTTGACAAAAACATTATTTTTAAGAAATTTTAATTTAAATCATCAAAATTCTCTCAAA
TTACAATGGCGATTATACGCTACAGCAGGATGTCATCATTTGAAGGAGAGAATTTTGGAT
GAAAAGATGAAAATTGAAATTGAAAATCATTGGAAAGATAAGTTGTCATTCAAATTATTT
GATAGAGAAAACATGAAAGACAAGTTTTATGTTCTCTCAATGTTTCCTTATCCGTCTGGT
TCATTGCATATGGGTCATTGTAGAATTTATTCAACTTCTGATGCAATTGCAAGATTTCAC
CGGTTAGAAGGGAAGAATGTCTTTCATCCTATTGGATTTGATGCTTTTGGTCTTCCTGCT
GAAAATGCTGCAATAAAGAGAAAAATACCAGCTGATGAATGGACTCGACAGAATATTAAA
CACATGAAAAAGCAGCTCGATATGCTTGCTTGTTCATTCGATTGGAGTGCAGAATTAGCA
ACTTGTGATTCAGATTATTACAAATGGACACAAAAATTATTTCTTATGTTATTCAATGAT
GGCCTCGCTTATCAAAATGAATCGTTAGTAAATTGGGATCCAGTTGATGAAACAGTGCTA
GCTGATGAACAAGTTGATGAGAATGGTTGTTCATGGCGATCAGGAGCAAAAGTTGAGAAA
CGATTTTTAAAGCAATGGTTTATTAAGACAACAAAATATTCTAAACAACTGTATGATGGT
TTAAGTGATCCAATTCTTAAAAATTGGCGTGATATTGTGCCTATACAACAACATTGGATC
GGTGAATGTGATGGTTGGAATTTTACACTTAAACTTAAAAATGGCAAGAATATTGTCATT
TGGAGTAGCACACCTGAAGATTTCAAAATTGCTTCATTCATTGCAATCAAAAAAGAACAT
CTGCTAAATCATGAAAAGCTTGAAGATGGACTGCTTGAAATTAAAGCAGAAAATCCTTTC
ACTGGACAAAATTTACCAATAATAGTCACAAATGAAGTTGAATTTCCTCCATTCAATGAT
GTTCATTTAGGAGTGACATCAAAAAATGAAAACGATTTAGAAATTGCAAGGAAACATGGG
ATAGAAATAAATAATGCACCATCAAGTGAGTCTGACAGAGAGAATGTAATAAAGACTGCT
CAAGAATCGGGAATCGGTGCTGATTTCAAAACTAGTTCTAAATTGAGAGATTGGTTGATG
TCAAGACAACGCTTTTGGGGAACACCAATTCCAATTATTCATTGTAATAAATGTGGAGCT
GTTCCAGTCGATGAAAAAGATTTACCAATCAAATTACCTGAAAAACGTGAAGATGTCGGA
AAACCATTAAAACAAAATGAAGAATGGCTCAAATGCAATTGTCCAAAATGTGGTGGTGAT
GCCAAACGTGAATCTGACACAATGGATACTTTTGTTGATTCTTCATGGTATTTTCTAAGA
TATTTGGATACGAACAATAATCAAGATCTTGTTGATAAACAAATTAGTAAAGAAATGATG
CCTGTTGACATTTATATCGGAGGAAAAGAACATGCAGCTCTTCATCTTTATTATGCACGA
TTTATCAATCATTTTCTTCATCAAAAAGGATATGTGAAGCATTCAGAGCCATTTGAAAGA
CTTTTAGTTCAAGGAATGGTCAAAGGAAAAACTTTTCGTGCTAAAGGTACAGGAAAATAT
TTGACACCAGTCGAAGTTGATGTGATTGATGAGAAGAAAGGAAAAGTATTTGTTAAAGGA
ACACAAGAGCCAGTTGAAATTTCATGGGAAAAAATGTCAAAGTCAAAATTTAATGGAGTC
GATCCAATTGAAGTCATCAATACACATGGCTGTGACACTACTCGTTTAATAATTTTAGCT
GACGTGGCACCTACATCACATAGAAATTGGTCAGAAGATACTTTTCCTGGAATTATAAAC
TGGCAAAAAAGATTATGGATGACATTGCATGATTTTCATTATATTAGAGAAAAAGTTGGT
GAAATTGAGAAATCTGACAAATTTAATGAACATGAAGAAAAGCTACTCGATGCATGCAAT
TATTTCGCTAGTGGTGCAACTTTTAATTTTAGAGTTTCTTATCAAATCAGTGTGGCTATT
TCACAAATGCAAGGACTTACAAGTGCAATTCGACGAGCACCAACAGATGTTATTGCCTTT
GGTGAACAATATGAACGTGCACTTTCTGCACAAATTATCATGCTTGCAGCACTTGCTCCT
CACTTTGCATCTGAATTATGGAGTAGATTTGTAACAGCTCCAAATCGAGTTTTAGTAAAA
TCAAATTATTTTGACTGGAATTTAGATGTTCTTCAACAGAGATGGCCAAAAGTTGATCCA
GATTATAAAATTAATTTCACAGTAAAAGTCGATAATCATATTGTCCATAAAACTAAAATT
CCATGTAGCATACTCAATCAAATGAGCAAAGAAGAAGCAACAAGAATAGGACTCGAGTAT
CCAAAAGTTATCAAATTTCTCAAAAAGAAATCTGTTATTGAAAGTCATTGGCAATTGTAT
ACAGATTATGGAGGTACATTAAATTTAACAACTGAAAAGAAATCAATAGAAAATTTAGAT
GAGGATTGTAATGAAAAAGAACAGGTAATTAATAAATGA

>g4703.t1 Gene=g4703 Length=872
MLTKTLFLRNFNLNHQNSLKLQWRLYATAGCHHLKERILDEKMKIEIENHWKDKLSFKLF
DRENMKDKFYVLSMFPYPSGSLHMGHCRIYSTSDAIARFHRLEGKNVFHPIGFDAFGLPA
ENAAIKRKIPADEWTRQNIKHMKKQLDMLACSFDWSAELATCDSDYYKWTQKLFLMLFND
GLAYQNESLVNWDPVDETVLADEQVDENGCSWRSGAKVEKRFLKQWFIKTTKYSKQLYDG
LSDPILKNWRDIVPIQQHWIGECDGWNFTLKLKNGKNIVIWSSTPEDFKIASFIAIKKEH
LLNHEKLEDGLLEIKAENPFTGQNLPIIVTNEVEFPPFNDVHLGVTSKNENDLEIARKHG
IEINNAPSSESDRENVIKTAQESGIGADFKTSSKLRDWLMSRQRFWGTPIPIIHCNKCGA
VPVDEKDLPIKLPEKREDVGKPLKQNEEWLKCNCPKCGGDAKRESDTMDTFVDSSWYFLR
YLDTNNNQDLVDKQISKEMMPVDIYIGGKEHAALHLYYARFINHFLHQKGYVKHSEPFER
LLVQGMVKGKTFRAKGTGKYLTPVEVDVIDEKKGKVFVKGTQEPVEISWEKMSKSKFNGV
DPIEVINTHGCDTTRLIILADVAPTSHRNWSEDTFPGIINWQKRLWMTLHDFHYIREKVG
EIEKSDKFNEHEEKLLDACNYFASGATFNFRVSYQISVAISQMQGLTSAIRRAPTDVIAF
GEQYERALSAQIIMLAALAPHFASELWSRFVTAPNRVLVKSNYFDWNLDVLQQRWPKVDP
DYKINFTVKVDNHIVHKTKIPCSILNQMSKEEATRIGLEYPKVIKFLKKKSVIESHWQLY
TDYGGTLNLTTEKKSIENLDEDCNEKEQVINK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g4703.t1 CDD cd00812 LeuRS_core 68 630 7.71375E-104
17 g4703.t1 Coils Coil Coil 849 872 -
14 g4703.t1 Gene3D G3DSA:3.40.50.620 HUPs 66 319 1.8E-68
15 g4703.t1 Gene3D G3DSA:3.40.50.620 HUPs 347 553 8.7E-63
16 g4703.t1 Gene3D G3DSA:1.10.730.10 - 571 836 3.8E-33
3 g4703.t1 PANTHER PTHR43740 LEUCYL-TRNA SYNTHETASE 37 832 1.9E-262
10 g4703.t1 PRINTS PR00985 Leucyl-tRNA synthetase signature 161 178 2.9E-43
5 g4703.t1 PRINTS PR00985 Leucyl-tRNA synthetase signature 187 203 2.9E-43
8 g4703.t1 PRINTS PR00985 Leucyl-tRNA synthetase signature 220 233 2.9E-43
7 g4703.t1 PRINTS PR00985 Leucyl-tRNA synthetase signature 251 270 2.9E-43
9 g4703.t1 PRINTS PR00985 Leucyl-tRNA synthetase signature 463 481 2.9E-43
4 g4703.t1 PRINTS PR00985 Leucyl-tRNA synthetase signature 502 524 2.9E-43
6 g4703.t1 PRINTS PR00985 Leucyl-tRNA synthetase signature 535 545 2.9E-43
2 g4703.t1 Pfam PF00133 tRNA synthetases class I (I, L, M and V) 49 206 5.9E-19
1 g4703.t1 Pfam PF00133 tRNA synthetases class I (I, L, M and V) 395 551 7.2E-11
19 g4703.t1 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature. 76 87 -
11 g4703.t1 SUPERFAMILY SSF52374 Nucleotidylyl transferase 47 639 5.42E-124
13 g4703.t1 SUPERFAMILY SSF50677 ValRS/IleRS/LeuRS editing domain 268 370 6.41E-8
12 g4703.t1 SUPERFAMILY SSF47323 Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 641 782 3.6E-12

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