Gene loci information

Transcript annotation

  • This transcript has been annotated as Isoleucine–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_3 g1105 g1105.t1 TSS g1105.t1 8203842 8203842
chr_3 g1105 g1105.t1 isoform g1105.t1 8203988 8209573
chr_3 g1105 g1105.t1 exon g1105.t1.exon1 8203988 8204179
chr_3 g1105 g1105.t1 cds g1105.t1.CDS1 8203988 8204179
chr_3 g1105 g1105.t1 exon g1105.t1.exon2 8204235 8204360
chr_3 g1105 g1105.t1 cds g1105.t1.CDS2 8204235 8204360
chr_3 g1105 g1105.t1 exon g1105.t1.exon3 8204416 8206698
chr_3 g1105 g1105.t1 cds g1105.t1.CDS3 8204416 8206698
chr_3 g1105 g1105.t1 exon g1105.t1.exon4 8206761 8206945
chr_3 g1105 g1105.t1 cds g1105.t1.CDS4 8206761 8206945
chr_3 g1105 g1105.t1 exon g1105.t1.exon5 8209126 8209205
chr_3 g1105 g1105.t1 cds g1105.t1.CDS5 8209126 8209205
chr_3 g1105 g1105.t1 exon g1105.t1.exon6 8209426 8209444
chr_3 g1105 g1105.t1 cds g1105.t1.CDS6 8209426 8209444
chr_3 g1105 g1105.t1 exon g1105.t1.exon7 8209525 8209573
chr_3 g1105 g1105.t1 cds g1105.t1.CDS7 8209525 8209573
chr_3 g1105 g1105.t1 TTS g1105.t1 NA NA

Sequences

>g1105.t1 Gene=g1105 Length=2934
ATGATTTCACTAAATGCACGTCTTTGTCAAATAAATGCAAAATTTTGGAAAATTTTAAAC
CGGAATATAAAAACAAAAGTCGATGAAAGTAAAAAAGTTAAATTTACTGACACAATAAAC
TTGCCCAAAACAAAATTTCCTACTCGATTAAATCAACAGCAACGAGCAGATGTAGAAGAA
ATTATCAGAACGAAACATTTAAATGTGTTGTACAATTGGCAAAGAGAAAATTTACAAACT
CAATCAGACGACTATGTTCTTCATGATGGTCCACCTTATGCAAATGGCAATCTTCATATG
GGACATGCTGTTAATAAAATTCTTAAAGATATAATTTTAAAACAAAAGATTATAAGCGGT
AAAAGAGTGCATTATGTTCCTGGATGGGATTGTCATGGACTGCCTATAGAATTAAAAGCT
TTAGGAAATATAAAAGAAAAATCACCACTAAAAATAAGAGAAAAGGCAAAAAAGTTTGCA
ATAGAAGCTATTAAAAATCAAAAGGCTTCATTTGAATCGTGGGGAGTAACAGGAACATGG
AATGACAATAATCATACTTATAGAACGTTTGATAAAAACTACATCAAAAATCAACTGAAA
ATGTTTCATAAAATGTATAAAAGAGAACTCATTTATCGCGATTTGAAGCCTGTATACTTT
TCTCCTTCATCTGGGACAGCATTAGCAGAAGCCGAATTAGAATATGATGAAAATTTCAAA
AGCCCATCACTATATTTTCGATGTGAGCTTTTAAATTCACAAGATATTTCAAATGAAAAA
GTTTATGCTCTTATTTGGACCACTACACCATGGACTCTGCCTGCCAATCAAGCGATTTGC
TTCAATAAAGATCTTCGATATAATTTAGTGAAAATAAATGGAAGCAATTTCATCATATGT
GCAGACACAATACAAAATCTTAAAAGCGAACTTGAAACTGATATTGAAATAGTTAAAGAA
GTAAGTGCAGAATTTTTAAAGAATCTGCTTTATCGACATCCAGTGAATACCGACGAAGTT
CTTCCATTTTATGCTGCAACACATGTTCAGTCAGATAAAGGCACTGGATTGGTTCACACA
GCACCCACTCATGGCCAAGATGACTTTCTAGTATTTCTCAATAAGAAAATTCCTTTAAAA
TGTCTTGTAAATGAGAAAGGATGTTACAATGAATTGGCACCTGATTTTTTAAAACACAAA
GAAGTTCTTGGTGATGGAAATAAACTTGTGTTGCAACATGTTGAGAAAATGAATAATATA
GTTAAATTAAAAGAATTTAAACATTCATATCCAATTGATTGGAGAACAAAAAGTCCAGTA
ATTATTTTGGCAAGCGAGCAATGGTTTATCAATACTGAAAAGATTAAAACAAAAGCAATC
CAAGAAATCGAAAATGTTAAAATCTATCCTGAGAAATCATCTAAAATTTCAAAGAGTGTT
TTAAAGACTCAATTAGAAAAGAGACCATATTGGTGTATAAGCAGACAAAGGTGTTGGGGT
GTTCCTATACCTGTTCTATATAATGATCAAAAACAAGCGATTATCAATGATGATTTAATA
AATAATTATATAAAATTAATAGAAGAAACAGGCTCAATTGATTTTTGGTGGGAAAAAGAT
GTTGAAAAATTAGTTCCTAAAAATTTTGATTCGTCAGGTTTAAGGAAAGGAAATGATATT
CTTGATATCTGGTTTGATTCTGGGATAAGTTGGTCATATGCTTTAGAAAAAAATCAAATT
GCAGATCTTTATCTTGAAGGTGTCGATCAATTCACTGGATGGTTTCAATCATCACTTATG
ACAAGTGTTGGTATTCGAGATAAAGCGCCTTATAAAAACATCTTTGTTCATGGCTTTACA
GTGGATGAGACAGGAAGAAAAATGTCAAAATCGCTGGGAAATATCATAAGCCCCGATTCA
ATTGTAAAAAAATATGGCATCGATGTTATGAGATTTTGGATTGCAGCTCATGCTACGCAA
CATTCATTAATTCCAGTCAGTAATAAGCTTCTCGATGACAGTGCAAATAATTTAATTAAA
ATAAGGTCAACATTAAAGTACTTGCTCGGAGTTATTGGCAGCATTGAGGACGATTGTGCA
ATTGATGAAACACAATTGACGCATTTGGACAGATTTATTCTCCATCAACTGAGCGATTAT
GTCAGCAATGCGAAAAATGCCTATGAAAGCTTTCAATTCAATCGCATTATTGCGCTCACC
AATAACTTTGTAAACACTGATCTATCAAGTTGCTATCTTCACTTAATCAAAGATCGACTC
TATTGCGGCTATGACAGTGAGCATCAACGATTTAGAAAGATCTTATCGAATTGTTATAGT
CAATTAGCGAAAACTTTATGGCCAATTACGCCATTTTTGGTAGAAGAAAGTTGGAATTAC
TTGGAATCATCATATTCGTTTTTTAAACGACTAAGAAATAACAGCGATGAAAAGACAATG
TGGAATTTTAGTGAGAGTAAGGAAATTGTTGAATTCGCATTAAATTTGAAGAAAAGTTTC
TGCTCTCAACTAACTGACATGAACACGACAAAATTAAATGTGACAATTGAGGGAAATGAT
GATGATCTTAAGGTGCTGATGAACCTTCATCCAACATTCAACAAGGTACACCATGATTCA
CAGTTGTGTGAAATCCTCCAAGTGTCTTCGATCGTTCTCAAGCATTCACCTTTGAAAGAA
ATGAAAATATCATATGAGACAGCATCAGACAATTTCTGTCCAAGATGTAGGAGATTTCAA
GCGGGTGCAAATGGTATTTGCATAAGATCAAGTTTAAGTTCAACAATTAGTGACAAAAAC
GTGACTGTGCGAACGTGCAAAATTACAAAAAAATTAAAAAAAATAGCTATAATTCACGGA
GGCAGCAAGTGGGATCTGCCAGTAAATGTCAACTTAGTCATATCCCACAACTAA

>g1105.t1 Gene=g1105 Length=977
MISLNARLCQINAKFWKILNRNIKTKVDESKKVKFTDTINLPKTKFPTRLNQQQRADVEE
IIRTKHLNVLYNWQRENLQTQSDDYVLHDGPPYANGNLHMGHAVNKILKDIILKQKIISG
KRVHYVPGWDCHGLPIELKALGNIKEKSPLKIREKAKKFAIEAIKNQKASFESWGVTGTW
NDNNHTYRTFDKNYIKNQLKMFHKMYKRELIYRDLKPVYFSPSSGTALAEAELEYDENFK
SPSLYFRCELLNSQDISNEKVYALIWTTTPWTLPANQAICFNKDLRYNLVKINGSNFIIC
ADTIQNLKSELETDIEIVKEVSAEFLKNLLYRHPVNTDEVLPFYAATHVQSDKGTGLVHT
APTHGQDDFLVFLNKKIPLKCLVNEKGCYNELAPDFLKHKEVLGDGNKLVLQHVEKMNNI
VKLKEFKHSYPIDWRTKSPVIILASEQWFINTEKIKTKAIQEIENVKIYPEKSSKISKSV
LKTQLEKRPYWCISRQRCWGVPIPVLYNDQKQAIINDDLINNYIKLIEETGSIDFWWEKD
VEKLVPKNFDSSGLRKGNDILDIWFDSGISWSYALEKNQIADLYLEGVDQFTGWFQSSLM
TSVGIRDKAPYKNIFVHGFTVDETGRKMSKSLGNIISPDSIVKKYGIDVMRFWIAAHATQ
HSLIPVSNKLLDDSANNLIKIRSTLKYLLGVIGSIEDDCAIDETQLTHLDRFILHQLSDY
VSNAKNAYESFQFNRIIALTNNFVNTDLSSCYLHLIKDRLYCGYDSEHQRFRKILSNCYS
QLAKTLWPITPFLVEESWNYLESSYSFFKRLRNNSDEKTMWNFSESKEIVEFALNLKKSF
CSQLTDMNTTKLNVTIEGNDDDLKVLMNLHPTFNKVHHDSQLCEILQVSSIVLKHSPLKE
MKISYETASDNFCPRCRRFQAGANGICIRSSLSSTISDKNVTVRTCKITKKLKKIAIIHG
GSKWDLPVNVNLVISHN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g1105.t1 CDD cd00818 IleRS_core 85 656 2.19966E-101
18 g1105.t1 CDD cd07960 Anticodon_Ia_Ile_BEm 666 840 6.45948E-40
16 g1105.t1 Coils Coil Coil 304 324 -
14 g1105.t1 Gene3D G3DSA:3.40.50.620 HUPs 63 654 2.7E-217
15 g1105.t1 Gene3D G3DSA:3.90.740.10 - 228 435 2.7E-217
13 g1105.t1 Gene3D G3DSA:1.10.730.20 - 666 932 2.0E-44
3 g1105.t1 PANTHER PTHR42765:SF1 ISOLEUCINE–TRNA LIGASE, MITOCHONDRIAL 30 928 1.1E-290
4 g1105.t1 PANTHER PTHR42765 SOLEUCYL-TRNA SYNTHETASE 30 928 1.1E-290
8 g1105.t1 PRINTS PR00984 Isoleucyl-tRNA synthetase signature 85 96 3.2E-27
7 g1105.t1 PRINTS PR00984 Isoleucyl-tRNA synthetase signature 264 287 3.2E-27
6 g1105.t1 PRINTS PR00984 Isoleucyl-tRNA synthetase signature 428 443 3.2E-27
5 g1105.t1 PRINTS PR00984 Isoleucyl-tRNA synthetase signature 556 569 3.2E-27
9 g1105.t1 PRINTS PR00984 Isoleucyl-tRNA synthetase signature 586 595 3.2E-27
1 g1105.t1 Pfam PF00133 tRNA synthetases class I (I, L, M and V) 71 659 2.1E-155
2 g1105.t1 Pfam PF08264 Anticodon-binding domain of tRNA ligase 710 811 7.8E-20
19 g1105.t1 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature. 92 103 -
10 g1105.t1 SUPERFAMILY SSF52374 Nucleotidylyl transferase 34 674 2.48E-109
12 g1105.t1 SUPERFAMILY SSF50677 ValRS/IleRS/LeuRS editing domain 239 430 1.83E-43
11 g1105.t1 SUPERFAMILY SSF47323 Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 680 920 3.36E-32
20 g1105.t1 TIGRFAM TIGR00392 ileS: isoleucine–tRNA ligase 59 850 4.4E-223

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:0005524 ATP binding MF
GO:0002161 aminoacyl-tRNA editing activity MF
GO:0000049 tRNA binding MF
GO:0004822 isoleucine-tRNA ligase activity MF
GO:0000166 nucleotide binding MF
GO:0006418 tRNA aminoacylation for protein translation BP
GO:0006428 isoleucyl-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