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.t3 TSS g2726.t3 19900887 19900887
chr_3 g2726 g2726.t3 isoform g2726.t3 19900964 19903103
chr_3 g2726 g2726.t3 exon g2726.t3.exon1 19900964 19901008
chr_3 g2726 g2726.t3 exon g2726.t3.exon2 19901080 19901219
chr_3 g2726 g2726.t3 exon g2726.t3.exon3 19901286 19903103
chr_3 g2726 g2726.t3 cds g2726.t3.CDS1 19901310 19903103
chr_3 g2726 g2726.t3 TTS g2726.t3 19903172 19903172

Sequences

>g2726.t3 Gene=g2726 Length=2003
ATGGAAGAACAAATAGCAAAAGAAAGTCATCGCTTATCATCAATTGAAGCAGAAATTGCT
CAAGTTGAAAATTCAATCAAAAATATAAAGGAAGGCAATTTTGGAGATGAAAGCGCAGAA
TTGAGCTCATTGTTGACCGAAAATAGTAAATTAAAATTCCGTTTGGAAATTCTTAATAAG
GTTGTGCAATCGCAAATGAAAGAAAACAAATGAGTAGTTCATCAAATTCACCAACTGAAG
TGATTTCCATTATTAAACATCTTTATGACATTTTTTATAATACAACAAAAGCTATATTTC
CTCAATTTGAAGATCCAATTTGTGTAATATCAAGTCAAACTAATAAGTCAGATTATCAAT
GCAACAGTGCTATGCCATTGAGTTCAAAGCTGAAGCAATTGAATGTGCAAATGTCATCAT
TAGATATTGCAAAGAAACTTGTCGAAAATCTTCCATATTCGCCTCTTATTGAAAGAACTG
AAATAACTGGACCTGGTTTCATCTCAATCTTTTTAACAAAGGATTATGCCAAGACATTTA
TCTCTCTAATTTTGAATGAAGGTGTAAAACCACCGCCTATGAAAAAATTGCGAGTTGTTG
TTGATTTCTCTTCACCGAATATTGCCAAGCAAATGCATGTAGGACATTTACGCTCGACTA
TCATCGGAGATTCAATTTCGCGACTTCTTGAATTCTTAGGACATGATGTGTTGAGAATTA
ATCATTTAGGAGATTGGGGAACACAATTTGGAATGCTTATTGCTCATCTTGAAGACATTT
TTCCCAATTATGTCAATGAATCGCCACCAATTGCAGATTTGCAAGCATTCTATAAAGAGT
CAAAAAAACGTTTTGATGAAGACGAAGAGTTTAAGAAGCGTGCATATGATCGAGTTGTGA
AATTACAATCAGGTGAAAAAAATTCTACTAAGGCATGGCAATTAATTTGTGATGTATCAC
GTCGTGAATTTCAACATATTTATGATTTGCTTGATGTAAAAATAGTTGAACGTGGTGAAT
CGTTTTATCAATCACGAATGGAGTCATTAGTTAAAGAACTAGATGAGCAAGGACTTTTAG
AAGAAGATGAAGGACGAAAAATTATGTGGGGTGAAAAAACTGAAGGTGAAATACCTTTGA
CTATTGTTAAATCTGGCGGTGGTTTCACTTATGATACATCAGATATGGCGACTATTAAAC
AAAGAATTGAAGAAGAAAAGGCTGACTGGATAATTTATGTTACTGATGCCGGTCAAGCTA
CTCATTTTAAATCAATTTTTGCATGCGCAAAACGTGCTGGTATTTTAGATCCCTCAAAAA
TTCGTATTGATCACTTAGGTTTTGGCGTTGTACTTGGTGAAGATGGCAAAAAATTTAAAA
CTCGTTCAGGTGATACTGTTAAACTTTCGGATTTACTTGAAGAGGGTACACGACGATCAT
TAGAAAAACTTAAAGAAAAAGAAAGAGATAAGATTTTGAATGAACAAGAAATAATTGATG
CTACCAATAATGTTGCATATGGATGCATTAAATATGCTGATTTATCCAAGAGTTCTAGAA
ATGACTATGTTTTCAGTTTCGATCGAATGTTGGATGACCGAGGAAATACTGCCGTTTATT
TATTGTATGCATATGTTCGCATTTGCTCAATTGCACGCAATTTGGGAGAAGAATTTAATA
AGCAGATGCCTAAACTAAAAAAAGAAACACCTATTGTACTTGACCATGAAAAGGAATGGA
AATTAGCAAAAGTTTTGATTCAATTTCCTGATATCATTGAGAAAATTTTGCGAGAATTGA
ATATTCACTATTTGTGCGATTTTCTCTATCATATTGCCACTACATTTACAGAATTTTACG
ATTCTTGCTATTGTATTCAAAAGAACAAGCAAGGAGAAGTTGTCAAAATTGATGTAAGTC
GAGTGCTCTTATGTGAAGCAACAGCAGCAATCATGGCTCAATGCTTCGATATCCTTGGCA
TTAAAACATTAAAGAAAGTTTAA

>g2726.t3 Gene=g2726 Length=597
MSSSSNSPTEVISIIKHLYDIFYNTTKAIFPQFEDPICVISSQTNKSDYQCNSAMPLSSK
LKQLNVQMSSLDIAKKLVENLPYSPLIERTEITGPGFISIFLTKDYAKTFISLILNEGVK
PPPMKKLRVVVDFSSPNIAKQMHVGHLRSTIIGDSISRLLEFLGHDVLRINHLGDWGTQF
GMLIAHLEDIFPNYVNESPPIADLQAFYKESKKRFDEDEEFKKRAYDRVVKLQSGEKNST
KAWQLICDVSRREFQHIYDLLDVKIVERGESFYQSRMESLVKELDEQGLLEEDEGRKIMW
GEKTEGEIPLTIVKSGGGFTYDTSDMATIKQRIEEEKADWIIYVTDAGQATHFKSIFACA
KRAGILDPSKIRIDHLGFGVVLGEDGKKFKTRSGDTVKLSDLLEEGTRRSLEKLKEKERD
KILNEQEIIDATNNVAYGCIKYADLSKSSRNDYVFSFDRMLDDRGNTAVYLLYAYVRICS
IARNLGEEFNKQMPKLKKETPIVLDHEKEWKLAKVLIQFPDIIEKILRELNIHYLCDFLY
HIATTFTEFYDSCYCIQKNKQGEVVKIDVSRVLLCEATAAIMAQCFDILGIKTLKKV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g2726.t3 CDD cd00671 ArgRS_core 128 394 4.27958E-80
15 g2726.t3 Gene3D G3DSA:3.30.1360.70 - 10 118 3.2E-16
13 g2726.t3 Gene3D G3DSA:3.40.50.620 HUPs 127 469 2.7E-111
14 g2726.t3 Gene3D G3DSA:1.10.730.10 - 470 597 1.7E-27
5 g2726.t3 Hamap MF_00123 Arginine–tRNA ligase [argS]. 16 597 23.410683
4 g2726.t3 PANTHER PTHR11956 ARGINYL-TRNA SYNTHETASE 15 596 3.4E-224
8 g2726.t3 PRINTS PR01038 Arginyl-tRNA synthetase signature 128 143 5.7E-26
7 g2726.t3 PRINTS PR01038 Arginyl-tRNA synthetase signature 143 159 5.7E-26
9 g2726.t3 PRINTS PR01038 Arginyl-tRNA synthetase signature 167 180 5.7E-26
6 g2726.t3 PRINTS PR01038 Arginyl-tRNA synthetase signature 311 332 5.7E-26
2 g2726.t3 Pfam PF03485 Arginyl tRNA synthetase N terminal domain 22 102 1.9E-14
3 g2726.t3 Pfam PF00750 tRNA synthetases class I (R) 122 457 4.7E-138
1 g2726.t3 Pfam PF05746 DALR anticodon binding domain 471 596 3.4E-29
17 g2726.t3 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature. 136 147 -
19 g2726.t3 SMART SM01016 Arg_tRNA_synt_N_2 16 102 2.9E-15
18 g2726.t3 SMART SM00836 dalr_1_4 471 597 5.0E-34
12 g2726.t3 SUPERFAMILY SSF55190 Arginyl-tRNA synthetase (ArgRS), N-terminal ‘additional’ domain 12 118 1.96E-13
10 g2726.t3 SUPERFAMILY SSF52374 Nucleotidylyl transferase 122 465 3.1E-88
11 g2726.t3 SUPERFAMILY SSF47323 Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 465 596 4.45E-31
20 g2726.t3 TIGRFAM TIGR00456 argS: arginine–tRNA ligase 24 596 2.0E-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