Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable arginine–tRNA ligase, mitochondrial.

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_2 g5279 g5279.t1 TSS g5279.t1 8367857 8367857
chr_2 g5279 g5279.t1 isoform g5279.t1 8367950 8369669
chr_2 g5279 g5279.t1 exon g5279.t1.exon1 8367950 8367985
chr_2 g5279 g5279.t1 cds g5279.t1.CDS1 8367950 8367985
chr_2 g5279 g5279.t1 exon g5279.t1.exon2 8368044 8369669
chr_2 g5279 g5279.t1 cds g5279.t1.CDS2 8368044 8369669
chr_2 g5279 g5279.t1 TTS g5279.t1 8369777 8369777

Sequences

>g5279.t1 Gene=g5279 Length=1662
ATGTCAGTCAAATTAAGAAACATAATTAGTGCAACGTTAAATGAGTTATATCCCGGTAAT
AAATTAAACCTTCAAGGTCTTTTACAAATAAAACAGAATAAGGATAAATATGAATTAAAA
CTGCCACTTAAATTGGTCAAAAATTCATTTGCTAGCACTGACATATTGAATCATATAAAA
AATCCTCACATTGAATCGATTAAAGTTGATACACAAGAAATTTCATTTTTAATATCCAAT
GATTCAATTAAAAAGTCATTTTCCAATGCAACTGATGTCTCAATATGCAATGAATCAAAG
AAATTTATTGTTGAGTTTAGTTCCCCAAACATCGCAAAACCATTTCATGTGGGTCATTTG
AGAAGTACAATTATCGGTAATTTTCTCTCAAATTTACTTCAGCGCGTTAATCATCGAGTT
ATAAAAATGAATTATCTTGGTGATTATGGTACACAGTTTGGTTTTCTCAAAGCAGGAATT
GATATGGAAAATTTGAGTGATGAGAAAATAAAAGAAAACCCACTTCAAAATCTATTGCGT
GTATATGTGGCTGCAAACACATCAGAAGATCCATGTGTTGCTGAAAAAGCTCGTAAAATT
TTTGAAATAATGGAATTTGGAGAAAATGCTGAGATCATAGAGCAATGGAATAAAATTAGA
GAATATACACTTAATGAACTTAAATTAATTTATGAGAGATTAAATGTAATTTACGATAGC
TATGAGTTTGAATCAATGTATCGTCGTAAAAATATTGAGGACGTCATTTCATTGATGCAA
GAAATGAAATTACTTGAGCGTGAAACTGATGAAAAAATTATAGTTAAAGTTGAAAATCGA
CGAGTTCCTTTTATAAAAAGCGATTCAACGACTTTATATTTAACTCGTGACATTGCAGCA
TTTTTAAAACGAAAAGAAAAATATGAGATGGATAGAATATTTTATGTTGTTGATAATGGA
CAGAATGATCATTTCACAGCTATTAAAAGTGTTGTTAATCAACTAGGATTCGATAGTGAC
AGTTTTATTCATCATATAAAATTTGGACGTATCAAAGGAATGAGCACACGAAAGGGAAAG
ATTGTGTTTCTCAAGGACATCTTAGACGAAGCTAAAGAATTGATGTATAAAAAACAACAA
GAATCTAAAACAACAAAAGTCGATCTCTCACAATGTGGCGAATCTATTGCAGATATCTTA
GGCACATCAGCAATCATTGTGAATGATTTGAAACAACGTAGACAACGTGATTATGAATTT
GATTGGAATAAAATTCTTCAAGTAACTGGTGATACAGGAATAAAATTTCAATACACGCAT
TGTCGTCTCTATAGTTTACAAAATCAAAACTCACACATTCAAGAAGCTGAAGAATTAAAT
TTTGATTTGCTTAAAGAACAAGAAGCACAACAGTTGATATTTCTTATACTTAAATATCCT
GAAATAATTTATCATTCTTACGAAGAATTAGAATCGTGTATTTTGGTTAAATATACATTC
GATCTATGCAATGTTGTTAGTCGAGCATGGAAAGTACTGTCAGTAAAAAATTGTGAATGT
AAAGAAACAGCATCACAACGTCTTTATCTTTTTAATACAACACGAAAAGTACTGAAACAT
AGTTTAGATATTCTAGGCTTAAAAGTTTTAAATGAGATGTAA

>g5279.t1 Gene=g5279 Length=553
MSVKLRNIISATLNELYPGNKLNLQGLLQIKQNKDKYELKLPLKLVKNSFASTDILNHIK
NPHIESIKVDTQEISFLISNDSIKKSFSNATDVSICNESKKFIVEFSSPNIAKPFHVGHL
RSTIIGNFLSNLLQRVNHRVIKMNYLGDYGTQFGFLKAGIDMENLSDEKIKENPLQNLLR
VYVAANTSEDPCVAEKARKIFEIMEFGENAEIIEQWNKIREYTLNELKLIYERLNVIYDS
YEFESMYRRKNIEDVISLMQEMKLLERETDEKIIVKVENRRVPFIKSDSTTLYLTRDIAA
FLKRKEKYEMDRIFYVVDNGQNDHFTAIKSVVNQLGFDSDSFIHHIKFGRIKGMSTRKGK
IVFLKDILDEAKELMYKKQQESKTTKVDLSQCGESIADILGTSAIIVNDLKQRRQRDYEF
DWNKILQVTGDTGIKFQYTHCRLYSLQNQNSHIQEAEELNFDLLKEQEAQQLIFLILKYP
EIIYHSYEELESCILVKYTFDLCNVVSRAWKVLSVKNCECKETASQRLYLFNTTRKVLKH
SLDILGLKVLNEM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g5279.t1 Coils Coil Coil 446 466 -
11 g5279.t1 Gene3D G3DSA:3.40.50.620 HUPs 95 429 1.3E-102
12 g5279.t1 Gene3D G3DSA:1.10.730.10 - 430 553 4.6E-27
3 g5279.t1 PANTHER PTHR11956 ARGINYL-TRNA SYNTHETASE 51 553 2.9E-119
4 g5279.t1 PANTHER PTHR11956:SF5 ARGININE–TRNA LIGASE, CYTOPLASMIC-RELATED 51 553 2.9E-119
7 g5279.t1 PRINTS PR01038 Arginyl-tRNA synthetase signature 101 116 2.3E-23
8 g5279.t1 PRINTS PR01038 Arginyl-tRNA synthetase signature 116 132 2.3E-23
5 g5279.t1 PRINTS PR01038 Arginyl-tRNA synthetase signature 140 153 2.3E-23
6 g5279.t1 PRINTS PR01038 Arginyl-tRNA synthetase signature 283 304 2.3E-23
2 g5279.t1 Pfam PF00750 tRNA synthetases class I (R) 96 422 6.2E-80
1 g5279.t1 Pfam PF05746 DALR anticodon binding domain 437 553 7.6E-20
14 g5279.t1 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature. 109 120 -
15 g5279.t1 SMART SM00836 dalr_1_4 436 553 1.6E-28
9 g5279.t1 SUPERFAMILY SSF52374 Nucleotidylyl transferase 97 430 2.51E-67
10 g5279.t1 SUPERFAMILY SSF47323 Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 430 553 2.75E-23
16 g5279.t1 TIGRFAM TIGR00456 argS: arginine–tRNA ligase 39 553 2.3E-104

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5279/g5279.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5279.t1.fa.iupred3.txt does not exist

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

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