Gene loci information

Transcript annotation

  • This transcript has been annotated as Isoleucine–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_3 g3170 g3170.t1 TTS g3170.t1 23429751 23429751
chr_3 g3170 g3170.t1 isoform g3170.t1 23429830 23433643
chr_3 g3170 g3170.t1 exon g3170.t1.exon1 23429830 23432077
chr_3 g3170 g3170.t1 cds g3170.t1.CDS1 23429830 23432077
chr_3 g3170 g3170.t1 exon g3170.t1.exon2 23432136 23433072
chr_3 g3170 g3170.t1 cds g3170.t1.CDS2 23432136 23433072
chr_3 g3170 g3170.t1 exon g3170.t1.exon3 23433129 23433436
chr_3 g3170 g3170.t1 cds g3170.t1.CDS3 23433129 23433436
chr_3 g3170 g3170.t1 exon g3170.t1.exon4 23433501 23433643
chr_3 g3170 g3170.t1 cds g3170.t1.CDS4 23433501 23433643
chr_3 g3170 g3170.t1 TSS g3170.t1 23433686 23433686

Sequences

>g3170.t1 Gene=g3170 Length=3636
ATGTCACTAAAATTAACGAAAGTTGACTTAGAACGCATTCCGGAAAATATAAACTTTTCG
CAGGAAGAAGAGAATGTTCTTAAATATTGGAATGAAGAGAAAGTCTTTGAGAATTGTTTG
AAACAATCAAAAGGAAAACCGAGATATACATTCTATGACGGGCCACCCTTTGCAACAGGT
TTGCCTCACTACGGCCACATCCTAGCAGGCACAATCAAAGATATCGTTACGAGATATGCA
CATCAACAAGGATATCACGTTGAAAGAAGATTTGGATGGGATTGTCATGGACTTCCAGTT
GAATTTGAAATCGACAAAAATCTTGGCATTAAAGGACCAGATGATGTGAATAAGATGGGC
ATTGCTGCATACAATAATGAATGTAGAAAGATTGTTATGCGATATGCAAATGAATGGGAA
CAAATTGTTGGCCGATTAGGAAGATGGATAGACTTTAAAAATGATTATAAAACTCTTTAT
CCTTGGTTTATGGAGTCAGTATGGTGGGTTTTTAAGCAACTTTATACAAAAGGTATGGTT
TATCAAGGCGTGAAAGTTATGCCTTATAGTACAGCTTGTACAACACCACTATCAAATTTC
GAATCTGGTCAAAATTACAAAGATGTTCAAGATCCAATGGTATTTGTTTCAATGCCGCTC
ATTGATGATAAAGATAAAGCTGCTTTAATTGTATGGACAACAACTCCTTGGACTCTTCCT
TCGAATATGGCATGTTGTGTCAATCCAGAGCTTACTTACGTCAAAGTTAAAGAGAAAGCA
ACTGGTGCTATTTATATTATCATGGAATCACGTATTGAATATGTTTTCAAAACAGCTGAT
GCAGTTGAAGTTTTAGAGAAATTTCCTGGAAAAAATCTTAAAGGACTTTGTTATGAGCCA
CCATTTGATTACTTCAAAAAATATAAAGACACAGCTTTTCGTGTATTGTGCGACAATTAT
GTGACAGAAGGTTCAGGTTCTGGAGTTGTTCATCAAGCTCCATACTTTGGTGAAGACGAT
TATCGGGTTTGCTTGGAAAATAATGTTGTTAAACGTGATCAAGAAATAATTTGTCCACTC
GATCCTAATGGAAGATTTACAAAAGAAGTTACTGATTTTGTTGGTCAATATGTAAAAGAT
GCCGATAAAAATATCATGAAACTATTGAAGGAAAAAGGACGTTTAGTTCGCTCTGGTCAG
CATATGCACAGTTATCCATTCTGCTGGCGTTCAGATACACCATTGATTTATAAAGCTGTT
CCATCATGGTTTGTTCGTGTTGAACATATGACAAAACAATTGCTCGCTAGTTGTGCTCAA
ACTTATTGGGTTCCTGATAATGTTAAAGAAAAACGATTTGGTAATTGGCTCAAAGAAGCA
AGAGATTGGGCTATAAGTCGTAATCGTTATTGGGGAACACCAATTCCTTTATGGATGTCA
CCATCTGGTGATGAAATTGTTTGCATTGGTTCAATTGAAGAACTTGAAAAGTTATCTGGT
GTTAAAGTCACAGACTTGCATCGAGAATTCGTAGATGTCATTGAAATTCCATCGAAAATT
CCAGGCAACCCACCTTTAAAACGTGTTCCAGAAGTTTTTGACTGTTGGTTTGAATCTGGT
TCAATGCCTTATGCTCAACAACATTATCCATTTGAAAATCCACAAGATTTTATCAACAAT
TTCCCAGCTGATTTTATTGCCGAAGGTATCGATCAAACACGTGGTTGGTTCTATACACTT
CTTGTCATCTCAACAGCTCTTTTCAATAAGCCACCATTTAAAAATTTAATTGCTAATGGA
CTTGTGCTTGCTGCTGATGGACAAAAAATGTCTAAAAGAAAACAAAATTATCCTGATCCA
AAGTTATTGGTTGATAAATATGGAGCTGATGCAGTTCGACTTTATCTCATTAATTCACCA
GTTGTTCGTGCTGAGAACTTAAAGTTCAAAGAAGAAGGTGTTCGTGATATAATCAAAGAT
GTATTCTTACCTTGGTTTAATGCTTATCGATTCTTATTCCAAAATATTCATCGTTTAGAA
GCAGAAGAAAAGGTTGTCTATAAATATGATCCAAAACGTCGTGAACGTGAAGGTTCAGAC
AATGTGATGGATGTATGGATTGCAAGTTTCAAGGAATCACTTCTCGATTTTATTGCAAAA
GAAATGAAAGCTTATCGTCTGTATACTGTTGTGCCTCGTCTCACAAAATACATCGATCAA
TTGACTAATTGGTATGTTCGCATGAATCGACGTCGTCTTAAAGGTGAAGGTGGTATTAAA
GATTGTTATAATGCACTCGATACGCTCTATGATGTTCTAATGGCTATGGTTAAAATGATG
GCTCCTTTTACGCCATTTTTGACAGAATACATGTATCAGCGTTTGAGACTTTTAGATGAT
AATGCATCAAATGGAAGTGTTCATTATGAAATGATGCCAGCAGCAAATATGTCAAACATC
AATGTCAATATTGAAAGAGCTGTATCAAGAATGCAAGCAGTTGTAGAACTTGGTCGAGTT
ATGCGTGATCGTCGTACTGTACCAATAAAATATCCATTAACTGAAGTTGTAGTTATTCAT
CAACAACAAGAATATCTTGATGATGTTAAATCATTGCAAGAATTCATTACTGGAGAACTT
AATGTTCGATCAATTGTATTGAGTCAAGATAAGAAGAAATATGGTGTTACATTACGTGCT
GAACCTGATAGTAAACTTCTTGGAATTCGACTTAAAGGCGATGCAAAAGTTGTCTCTCAA
AAGATTAGAGAATTGACAGACAGTGAAATTCAAGAACAATCAAAACATGGTTACTTTGAA
GTTGCTGGTCATCGATTAGAATTGAATGAGGTTCGAGTTATTTATCAATTTGGAGGCGAA
ACAGCAGGAAAAGATTCCGATTATGAAGCGCACAGCGATAATGATGTTCTCGTTTTGTTA
AACATGAAACCCAATCAAGAACTTGTAGATGAAGGCTTAGCACGTGAAATTATCAATAGA
GTACAGAAACTCAAGAAAAAAGCACAATTGATTCCTACTGATCCTGTCATCATTACATTC
AGTGTGTCAAATACAAACAGTGACATAATGAGAATTGCCAAAAGTCATCAAGCATTTATT
GAAAATGTCATTAAATCAAAATTTGTTGAACATGATGCTTCTGCTGATAAGCGTGAGTTA
TTGATTGAAGAAACTCAAGAATTGAAAGATGTTCAATTGCGTTTGAAAATCACTGGACTT
AAAGAGCGAGCTGTGCCAAAATTACCATGGATTAACATTGCTGTGGCTGATGATATAGAA
TTACGATATGTTGAAAATAAATCTGCACGATCAGCGTCATTCAATCTTGAAGACTTTAAT
GGAAATTTGTTAACGTTAGATCAATTGAAAAGCGAAATTGAAGGTGTATTTGGATTTTAT
GGAACCAATTATATTATCACTCTTTCGTTAACTGACAGGAAAGAACTAGATAAAGTAACA
AAAGAGTTAGCTGGAAAGACATTGTTTGTTTTAAAAGGCGCTAAAAGCACCATAGCATCA
CATCTCCTTAACAAGAATTATCCATTTAGCAAATTTACGAACAAAAATGTTAATGGAAAT
GAAGTTACGGTTTATCTTGAAAATCCTGCAAACTAA

>g3170.t1 Gene=g3170 Length=1211
MSLKLTKVDLERIPENINFSQEEENVLKYWNEEKVFENCLKQSKGKPRYTFYDGPPFATG
LPHYGHILAGTIKDIVTRYAHQQGYHVERRFGWDCHGLPVEFEIDKNLGIKGPDDVNKMG
IAAYNNECRKIVMRYANEWEQIVGRLGRWIDFKNDYKTLYPWFMESVWWVFKQLYTKGMV
YQGVKVMPYSTACTTPLSNFESGQNYKDVQDPMVFVSMPLIDDKDKAALIVWTTTPWTLP
SNMACCVNPELTYVKVKEKATGAIYIIMESRIEYVFKTADAVEVLEKFPGKNLKGLCYEP
PFDYFKKYKDTAFRVLCDNYVTEGSGSGVVHQAPYFGEDDYRVCLENNVVKRDQEIICPL
DPNGRFTKEVTDFVGQYVKDADKNIMKLLKEKGRLVRSGQHMHSYPFCWRSDTPLIYKAV
PSWFVRVEHMTKQLLASCAQTYWVPDNVKEKRFGNWLKEARDWAISRNRYWGTPIPLWMS
PSGDEIVCIGSIEELEKLSGVKVTDLHREFVDVIEIPSKIPGNPPLKRVPEVFDCWFESG
SMPYAQQHYPFENPQDFINNFPADFIAEGIDQTRGWFYTLLVISTALFNKPPFKNLIANG
LVLAADGQKMSKRKQNYPDPKLLVDKYGADAVRLYLINSPVVRAENLKFKEEGVRDIIKD
VFLPWFNAYRFLFQNIHRLEAEEKVVYKYDPKRREREGSDNVMDVWIASFKESLLDFIAK
EMKAYRLYTVVPRLTKYIDQLTNWYVRMNRRRLKGEGGIKDCYNALDTLYDVLMAMVKMM
APFTPFLTEYMYQRLRLLDDNASNGSVHYEMMPAANMSNINVNIERAVSRMQAVVELGRV
MRDRRTVPIKYPLTEVVVIHQQQEYLDDVKSLQEFITGELNVRSIVLSQDKKKYGVTLRA
EPDSKLLGIRLKGDAKVVSQKIRELTDSEIQEQSKHGYFEVAGHRLELNEVRVIYQFGGE
TAGKDSDYEAHSDNDVLVLLNMKPNQELVDEGLAREIINRVQKLKKKAQLIPTDPVIITF
SVSNTNSDIMRIAKSHQAFIENVIKSKFVEHDASADKRELLIEETQELKDVQLRLKITGL
KERAVPKLPWINIAVADDIELRYVENKSARSASFNLEDFNGNLLTLDQLKSEIEGVFGFY
GTNYIITLSLTDRKELDKVTKELAGKTLFVLKGAKSTIASHLLNKNYPFSKFTNKNVNGN
EVTVYLENPAN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g3170.t1 CDD cd00818 IleRS_core 47 189 1.68224E-83
17 g3170.t1 CDD cd00818 IleRS_core 384 649 2.34601E-106
19 g3170.t1 CDD cd07961 Anticodon_Ia_Ile_ABEc 649 839 1.10337E-78
14 g3170.t1 Gene3D G3DSA:3.40.50.620 HUPs 23 635 1.7E-238
16 g3170.t1 Gene3D G3DSA:3.90.740.10 - 205 409 1.7E-238
15 g3170.t1 Gene3D G3DSA:1.10.730.10 - 651 847 6.5E-50
5 g3170.t1 Hamap MF_02003 Isoleucine–tRNA ligase [ileS]. 11 1069 12.758949
3 g3170.t1 PANTHER PTHR42780:SF1 ISOLEUCINE–TRNA LIGASE, CYTOPLASMIC 12 1078 0.0
4 g3170.t1 PANTHER PTHR42780 SOLEUCYL-TRNA SYNTHETASE 12 1078 0.0
9 g3170.t1 PRINTS PR00984 Isoleucyl-tRNA synthetase signature 49 60 1.8E-31
6 g3170.t1 PRINTS PR00984 Isoleucyl-tRNA synthetase signature 230 253 1.8E-31
10 g3170.t1 PRINTS PR00984 Isoleucyl-tRNA synthetase signature 403 418 1.8E-31
8 g3170.t1 PRINTS PR00984 Isoleucyl-tRNA synthetase signature 528 541 1.8E-31
7 g3170.t1 PRINTS PR00984 Isoleucyl-tRNA synthetase signature 568 577 1.8E-31
1 g3170.t1 Pfam PF00133 tRNA synthetases class I (I, L, M and V) 26 647 2.0E-233
2 g3170.t1 Pfam PF08264 Anticodon-binding domain of tRNA ligase 704 853 4.6E-21
20 g3170.t1 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature. 56 67 -
11 g3170.t1 SUPERFAMILY SSF52374 Nucleotidylyl transferase 13 659 1.64E-134
13 g3170.t1 SUPERFAMILY SSF50677 ValRS/IleRS/LeuRS editing domain 207 405 3.77E-51
12 g3170.t1 SUPERFAMILY SSF47323 Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 664 914 2.06E-42
21 g3170.t1 TIGRFAM TIGR00392 ileS: isoleucine–tRNA ligase 14 868 6.5E-284

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