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.t3 isoform g3170.t3 23432754 23433643
chr_3 g3170 g3170.t3 exon g3170.t3.exon1 23432754 23433072
chr_3 g3170 g3170.t3 cds g3170.t3.CDS1 23432756 23433072
chr_3 g3170 g3170.t3 exon g3170.t3.exon2 23433129 23433436
chr_3 g3170 g3170.t3 cds g3170.t3.CDS2 23433129 23433436
chr_3 g3170 g3170.t3 exon g3170.t3.exon3 23433501 23433643
chr_3 g3170 g3170.t3 cds g3170.t3.CDS3 23433501 23433643
chr_3 g3170 g3170.t3 TSS g3170.t3 23433686 23433686
chr_3 g3170 g3170.t3 TTS g3170.t3 NA NA

Sequences

>g3170.t3 Gene=g3170 Length=770
ATGTCACTAAAATTAACGAAAGTTGACTTAGAACGCATTCCGGAAAATATAAACTTTTCG
CAGGAAGAAGAGAATGTTCTTAAATATTGGAATGAAGAGAAAGTCTTTGAGAATTGTTTG
AAACAATCAAAAGGAAAACCGAGATATACATTCTATGACGGGCCACCCTTTGCAACAGGT
TTGCCTCACTACGGCCACATCCTAGCAGGCACAATCAAAGATATCGTTACGAGATATGCA
CATCAACAAGGATATCACGTTGAAAGAAGATTTGGATGGGATTGTCATGGACTTCCAGTT
GAATTTGAAATCGACAAAAATCTTGGCATTAAAGGACCAGATGATGTGAATAAGATGGGC
ATTGCTGCATACAATAATGAATGTAGAAAGATTGTTATGCGATATGCAAATGAATGGGAA
CAAATTGTTGGCCGATTAGGAAGATGGATAGACTTTAAAAATGATTATAAAACTCTTTAT
CCTTGGTTTATGGAGTCAGTATGGTGGGTTTTTAAGCAACTTTATACAAAAGGTATGGTT
TATCAAGGCGTGAAAGTTATGCCTTATAGTACAGCTTGTACAACACCACTATCAAATTTC
GAATCTGGTCAAAATTACAAAGATGTTCAAGATCCAATGGTATTTGTTTCAATGCCGCTC
ATTGATGATAAAGATAAAGCTGCTTTAATTGTATGGACAACAACTCCTTGGACTCTTCCT
TCGAATATGGCATGTTGTGTCAATCCAGAGCTTACTTACGTCAAAGTTAA

>g3170.t3 Gene=g3170 Length=256
MSLKLTKVDLERIPENINFSQEEENVLKYWNEEKVFENCLKQSKGKPRYTFYDGPPFATG
LPHYGHILAGTIKDIVTRYAHQQGYHVERRFGWDCHGLPVEFEIDKNLGIKGPDDVNKMG
IAAYNNECRKIVMRYANEWEQIVGRLGRWIDFKNDYKTLYPWFMESVWWVFKQLYTKGMV
YQGVKVMPYSTACTTPLSNFESGQNYKDVQDPMVFVSMPLIDDKDKAALIVWTTTPWTLP
SNMACCVNPELTYVKV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g3170.t3 Gene3D G3DSA:3.40.50.620 HUPs 11 227 2.9E-66
2 g3170.t3 PANTHER PTHR42780:SF1 ISOLEUCINE–TRNA LIGASE, CYTOPLASMIC 12 256 5.4E-138
3 g3170.t3 PANTHER PTHR42780 SOLEUCYL-TRNA SYNTHETASE 12 256 5.4E-138
5 g3170.t3 PRINTS PR00984 Isoleucyl-tRNA synthetase signature 49 60 4.2E-14
4 g3170.t3 PRINTS PR00984 Isoleucyl-tRNA synthetase signature 230 253 4.2E-14
1 g3170.t3 Pfam PF00133 tRNA synthetases class I (I, L, M and V) 26 254 1.2E-94
8 g3170.t3 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature. 56 67 -
6 g3170.t3 SUPERFAMILY SSF52374 Nucleotidylyl transferase 13 235 5.63E-57
7 g3170.t3 SUPERFAMILY SSF50677 ValRS/IleRS/LeuRS editing domain 207 255 2.88E-14

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:0006428 isoleucyl-tRNA aminoacylation BP
GO:0006418 tRNA aminoacylation for protein translation BP
GO:0000166 nucleotide binding MF
GO:0004812 aminoacyl-tRNA ligase activity MF
GO:0004822 isoleucine-tRNA ligase activity MF

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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