Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable arginine–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 g2726 g2726.t2 TSS g2726.t2 19900887 19900887
chr_3 g2726 g2726.t2 isoform g2726.t2 19900964 19903103
chr_3 g2726 g2726.t2 exon g2726.t2.exon1 19900964 19901008
chr_3 g2726 g2726.t2 cds g2726.t2.CDS1 19900964 19901008
chr_3 g2726 g2726.t2 exon g2726.t2.exon2 19901080 19901217
chr_3 g2726 g2726.t2 cds g2726.t2.CDS2 19901080 19901217
chr_3 g2726 g2726.t2 exon g2726.t2.exon3 19901286 19903103
chr_3 g2726 g2726.t2 cds g2726.t2.CDS3 19901286 19903103
chr_3 g2726 g2726.t2 TTS g2726.t2 19903172 19903172

Sequences

>g2726.t2 Gene=g2726 Length=2001
ATGGAAGAACAAATAGCAAAAGAAAGTCATCGCTTATCATCAATTGAAGCAGAAATTGCT
CAAGTTGAAAATTCAATCAAAAATATAAAGGAAGGCAATTTTGGAGATGAAAGCGCAGAA
TTGAGCTCATTGTTGACCGAAAATAGTAAATTAAAATTCCGTTTGGAAATTCTTAATAAG
GTTGCAATCGCAAATGAAAGAAAACAAATGAGTAGTTCATCAAATTCACCAACTGAAGTG
ATTTCCATTATTAAACATCTTTATGACATTTTTTATAATACAACAAAAGCTATATTTCCT
CAATTTGAAGATCCAATTTGTGTAATATCAAGTCAAACTAATAAGTCAGATTATCAATGC
AACAGTGCTATGCCATTGAGTTCAAAGCTGAAGCAATTGAATGTGCAAATGTCATCATTA
GATATTGCAAAGAAACTTGTCGAAAATCTTCCATATTCGCCTCTTATTGAAAGAACTGAA
ATAACTGGACCTGGTTTCATCTCAATCTTTTTAACAAAGGATTATGCCAAGACATTTATC
TCTCTAATTTTGAATGAAGGTGTAAAACCACCGCCTATGAAAAAATTGCGAGTTGTTGTT
GATTTCTCTTCACCGAATATTGCCAAGCAAATGCATGTAGGACATTTACGCTCGACTATC
ATCGGAGATTCAATTTCGCGACTTCTTGAATTCTTAGGACATGATGTGTTGAGAATTAAT
CATTTAGGAGATTGGGGAACACAATTTGGAATGCTTATTGCTCATCTTGAAGACATTTTT
CCCAATTATGTCAATGAATCGCCACCAATTGCAGATTTGCAAGCATTCTATAAAGAGTCA
AAAAAACGTTTTGATGAAGACGAAGAGTTTAAGAAGCGTGCATATGATCGAGTTGTGAAA
TTACAATCAGGTGAAAAAAATTCTACTAAGGCATGGCAATTAATTTGTGATGTATCACGT
CGTGAATTTCAACATATTTATGATTTGCTTGATGTAAAAATAGTTGAACGTGGTGAATCG
TTTTATCAATCACGAATGGAGTCATTAGTTAAAGAACTAGATGAGCAAGGACTTTTAGAA
GAAGATGAAGGACGAAAAATTATGTGGGGTGAAAAAACTGAAGGTGAAATACCTTTGACT
ATTGTTAAATCTGGCGGTGGTTTCACTTATGATACATCAGATATGGCGACTATTAAACAA
AGAATTGAAGAAGAAAAGGCTGACTGGATAATTTATGTTACTGATGCCGGTCAAGCTACT
CATTTTAAATCAATTTTTGCATGCGCAAAACGTGCTGGTATTTTAGATCCCTCAAAAATT
CGTATTGATCACTTAGGTTTTGGCGTTGTACTTGGTGAAGATGGCAAAAAATTTAAAACT
CGTTCAGGTGATACTGTTAAACTTTCGGATTTACTTGAAGAGGGTACACGACGATCATTA
GAAAAACTTAAAGAAAAAGAAAGAGATAAGATTTTGAATGAACAAGAAATAATTGATGCT
ACCAATAATGTTGCATATGGATGCATTAAATATGCTGATTTATCCAAGAGTTCTAGAAAT
GACTATGTTTTCAGTTTCGATCGAATGTTGGATGACCGAGGAAATACTGCCGTTTATTTA
TTGTATGCATATGTTCGCATTTGCTCAATTGCACGCAATTTGGGAGAAGAATTTAATAAG
CAGATGCCTAAACTAAAAAAAGAAACACCTATTGTACTTGACCATGAAAAGGAATGGAAA
TTAGCAAAAGTTTTGATTCAATTTCCTGATATCATTGAGAAAATTTTGCGAGAATTGAAT
ATTCACTATTTGTGCGATTTTCTCTATCATATTGCCACTACATTTACAGAATTTTACGAT
TCTTGCTATTGTATTCAAAAGAACAAGCAAGGAGAAGTTGTCAAAATTGATGTAAGTCGA
GTGCTCTTATGTGAAGCAACAGCAGCAATCATGGCTCAATGCTTCGATATCCTTGGCATT
AAAACATTAAAGAAAGTTTAA

>g2726.t2 Gene=g2726 Length=666
MEEQIAKESHRLSSIEAEIAQVENSIKNIKEGNFGDESAELSSLLTENSKLKFRLEILNK
VAIANERKQMSSSSNSPTEVISIIKHLYDIFYNTTKAIFPQFEDPICVISSQTNKSDYQC
NSAMPLSSKLKQLNVQMSSLDIAKKLVENLPYSPLIERTEITGPGFISIFLTKDYAKTFI
SLILNEGVKPPPMKKLRVVVDFSSPNIAKQMHVGHLRSTIIGDSISRLLEFLGHDVLRIN
HLGDWGTQFGMLIAHLEDIFPNYVNESPPIADLQAFYKESKKRFDEDEEFKKRAYDRVVK
LQSGEKNSTKAWQLICDVSRREFQHIYDLLDVKIVERGESFYQSRMESLVKELDEQGLLE
EDEGRKIMWGEKTEGEIPLTIVKSGGGFTYDTSDMATIKQRIEEEKADWIIYVTDAGQAT
HFKSIFACAKRAGILDPSKIRIDHLGFGVVLGEDGKKFKTRSGDTVKLSDLLEEGTRRSL
EKLKEKERDKILNEQEIIDATNNVAYGCIKYADLSKSSRNDYVFSFDRMLDDRGNTAVYL
LYAYVRICSIARNLGEEFNKQMPKLKKETPIVLDHEKEWKLAKVLIQFPDIIEKILRELN
IHYLCDFLYHIATTFTEFYDSCYCIQKNKQGEVVKIDVSRVLLCEATAAIMAQCFDILGI
KTLKKV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g2726.t2 CDD cd00671 ArgRS_core 197 463 1.44681E-79
16 g2726.t2 Coils Coil Coil 5 32 -
15 g2726.t2 Gene3D G3DSA:3.30.1360.70 - 79 187 3.8E-16
13 g2726.t2 Gene3D G3DSA:3.40.50.620 HUPs 196 538 3.6E-111
14 g2726.t2 Gene3D G3DSA:1.10.730.10 - 539 666 2.0E-27
5 g2726.t2 Hamap MF_00123 Arginine–tRNA ligase [argS]. 85 666 23.410683
4 g2726.t2 PANTHER PTHR11956 ARGINYL-TRNA SYNTHETASE 83 665 4.4E-224
8 g2726.t2 PRINTS PR01038 Arginyl-tRNA synthetase signature 197 212 8.5E-26
7 g2726.t2 PRINTS PR01038 Arginyl-tRNA synthetase signature 212 228 8.5E-26
9 g2726.t2 PRINTS PR01038 Arginyl-tRNA synthetase signature 236 249 8.5E-26
6 g2726.t2 PRINTS PR01038 Arginyl-tRNA synthetase signature 380 401 8.5E-26
2 g2726.t2 Pfam PF03485 Arginyl tRNA synthetase N terminal domain 91 171 2.2E-14
3 g2726.t2 Pfam PF00750 tRNA synthetases class I (R) 191 526 6.3E-138
1 g2726.t2 Pfam PF05746 DALR anticodon binding domain 540 665 4.0E-29
20 g2726.t2 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature. 205 216 -
19 g2726.t2 SMART SM01016 Arg_tRNA_synt_N_2 85 171 2.9E-15
18 g2726.t2 SMART SM00836 dalr_1_4 540 666 5.0E-34
12 g2726.t2 SUPERFAMILY SSF55190 Arginyl-tRNA synthetase (ArgRS), N-terminal ‘additional’ domain 77 187 1.15E-13
10 g2726.t2 SUPERFAMILY SSF52374 Nucleotidylyl transferase 191 534 3.94E-88
11 g2726.t2 SUPERFAMILY SSF47323 Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 534 665 5.36E-31
21 g2726.t2 TIGRFAM TIGR00456 argS: arginine–tRNA ligase 93 665 2.9E-136

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:0004814 arginine-tRNA ligase activity MF
GO:0005524 ATP binding MF
GO:0006418 tRNA aminoacylation for protein translation BP
GO:0000166 nucleotide binding MF
GO:0004812 aminoacyl-tRNA ligase activity MF
GO:0006420 arginyl-tRNA aminoacylation BP
GO:0005737 cytoplasm CC

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