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.t6 TSS g2726.t6 19900887 19900887
chr_3 g2726 g2726.t6 isoform g2726.t6 19901288 19902019
chr_3 g2726 g2726.t6 exon g2726.t6.exon1 19901288 19902019
chr_3 g2726 g2726.t6 cds g2726.t6.CDS1 19901310 19902017
chr_3 g2726 g2726.t6 TTS g2726.t6 19902555 19902555

Sequences

>g2726.t6 Gene=g2726 Length=732
AATCGCAAATGAAAGAAAACAAATGAGTAGTTCATCAAATTCACCAACTGAAGTGATTTC
CATTATTAAACATCTTTATGACATTTTTTATAATACAACAAAAGCTATATTTCCTCAATT
TGAAGATCCAATTTGTGTAATATCAAGTCAAACTAATAAGTCAGATTATCAATGCAACAG
TGCTATGCCATTGAGTTCAAAGCTGAAGCAATTGAATGTGCAAATGTCATCATTAGATAT
TGCAAAGAAACTTGTCGAAAATCTTCCATATTCGCCTCTTATTGAAAGAACTGAAATAAC
TGGACCTGGTTTCATCTCAATCTTTTTAACAAAGGATTATGCCAAGACATTTATCTCTCT
AATTTTGAATGAAGGTGTAAAACCACCGCCTATGAAAAAATTGCGAGTTGTTGTTGATTT
CTCTTCACCGAATATTGCCAAGCAAATGCATGTAGGACATTTACGCTCGACTATCATCGG
AGATTCAATTTCGCGACTTCTTGAATTCTTAGGACATGATGTGTTGAGAATTAATCATTT
AGGAGATTGGGGAACACAATTTGGAATGCTTATTGCTCATCTTGAAGACATTTTTCCCAA
TTATGTCAATGAATCGCCACCAATTGCAGATTTGCAAGCATTCTATAAAGAGTCAAAAAA
ACGTTTTGATGAAGACGAAGAGTTTAAGAAGCGTGCATATGATCGAGTTGTGAAATTACA
ATCAGGTGAAAA

>g2726.t6 Gene=g2726 Length=236
MSSSSNSPTEVISIIKHLYDIFYNTTKAIFPQFEDPICVISSQTNKSDYQCNSAMPLSSK
LKQLNVQMSSLDIAKKLVENLPYSPLIERTEITGPGFISIFLTKDYAKTFISLILNEGVK
PPPMKKLRVVVDFSSPNIAKQMHVGHLRSTIIGDSISRLLEFLGHDVLRINHLGDWGTQF
GMLIAHLEDIFPNYVNESPPIADLQAFYKESKKRFDEDEEFKKRAYDRVVKLQSGE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g2726.t6 Gene3D G3DSA:3.30.1360.70 - 10 118 5.7E-17
12 g2726.t6 Gene3D G3DSA:3.40.50.620 HUPs 127 236 1.8E-41
3 g2726.t6 PANTHER PTHR11956 ARGINYL-TRNA SYNTHETASE 15 236 4.3E-77
4 g2726.t6 PANTHER PTHR11956:SF5 ARGININE–TRNA LIGASE, CYTOPLASMIC-RELATED 15 236 4.3E-77
6 g2726.t6 PRINTS PR01038 Arginyl-tRNA synthetase signature 128 143 1.1E-19
5 g2726.t6 PRINTS PR01038 Arginyl-tRNA synthetase signature 143 159 1.1E-19
7 g2726.t6 PRINTS PR01038 Arginyl-tRNA synthetase signature 167 180 1.1E-19
1 g2726.t6 Pfam PF03485 Arginyl tRNA synthetase N terminal domain 21 102 3.9E-15
2 g2726.t6 Pfam PF00750 tRNA synthetases class I (R) 122 236 4.5E-57
11 g2726.t6 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature. 136 147 -
10 g2726.t6 SMART SM01016 Arg_tRNA_synt_N_2 16 102 2.9E-15
9 g2726.t6 SUPERFAMILY SSF55190 Arginyl-tRNA synthetase (ArgRS), N-terminal ‘additional’ domain 12 118 3.14E-14
8 g2726.t6 SUPERFAMILY SSF52374 Nucleotidylyl transferase 122 235 7.82E-39

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

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