General information for g5279.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable arginine–tRNA ligase, mitochondrial.
Parent gene
- The parent gene g5279 is located on chr_2: 8368044..8369669 (+ strand)
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.t4 | TSS | g5279.t4 | 8367857 | 8367857 |
| chr_2 | g5279 | g5279.t4 | isoform | g5279.t4 | 8368044 | 8369669 |
| chr_2 | g5279 | g5279.t4 | exon | g5279.t4.exon1 | 8368044 | 8369669 |
| chr_2 | g5279 | g5279.t4 | cds | g5279.t4.CDS1 | 8368434 | 8369669 |
| chr_2 | g5279 | g5279.t4 | TTS | g5279.t4 | 8369777 | 8369777 |
Sequences
>g5279.t4 Gene=g5279 Length=1626
TTAAATGAGTTATATCCCGGTAATAAATTAAACCTTCAAGGTCTTTTACAAATAAAACAG
AATAAGGATAAATATGAATTAAAACTGCCACTTAAATTGGTCAAAAATTCATTTGCTAGC
ACTGACATATTGAATCATATAAAAAATCCTCACATTGAATCGATTAAAGTTGATACACAA
GAAATTTCATTTTTAATATCCAATGATTCAATTAAAAAGTCATTTTCCAATGCAACTGAT
GTCTCAATATGCAATGAATCAAAGAAATTTATTGTTGAGTTTAGTTCCCCAAACATCGCA
AAACCATTTCATGTGGGTCATTTGAGAAGTACAATTATCGGTAATTTTCTCTCAAATTTA
CTTCAGCGCGTTAATCATCGAGTTATAAAAATGAATTATCTTGGTGATTATGGTACACAG
TTTGGTTTTCTCAAAGCAGGAATTGATATGGAAAATTTGAGTGATGAGAAAATAAAAGAA
AACCCACTTCAAAATCTATTGCGTGTATATGTGGCTGCAAACACATCAGAAGATCCATGT
GTTGCTGAAAAAGCTCGTAAAATTTTTGAAATAATGGAATTTGGAGAAAATGCTGAGATC
ATAGAGCAATGGAATAAAATTAGAGAATATACACTTAATGAACTTAAATTAATTTATGAG
AGATTAAATGTAATTTACGATAGCTATGAGTTTGAATCAATGTATCGTCGTAAAAATATT
GAGGACGTCATTTCATTGATGCAAGAAATGAAATTACTTGAGCGTGAAACTGATGAAAAA
ATTATAGTTAAAGTTGAAAATCGACGAGTTCCTTTTATAAAAAGCGATTCAACGACTTTA
TATTTAACTCGTGACATTGCAGCATTTTTAAAACGAAAAGAAAAATATGAGATGGATAGA
ATATTTTATGTTGTTGATAATGGACAGAATGATCATTTCACAGCTATTAAAAGTGTTGTT
AATCAACTAGGATTCGATAGTGACAGTTTTATTCATCATATAAAATTTGGACGTATCAAA
GGAATGAGCACACGAAAGGGAAAGATTGTGTTTCTCAAGGACATCTTAGACGAAGCTAAA
GAATTGATGTATAAAAAACAACAAGAATCTAAAACAACAAAAGTCGATCTCTCACAATGT
GGCGAATCTATTGCAGATATCTTAGGCACATCAGCAATCATTGTGAATGATTTGAAACAA
CGTAGACAACGTGATTATGAATTTGATTGGAATAAAATTCTTCAAGTAACTGGTGATACA
GGAATAAAATTTCAATACACGCATTGTCGTCTCTATAGTTTACAAAATCAAAACTCACAC
ATTCAAGAAGCTGAAGAATTAAATTTTGATTTGCTTAAAGAACAAGAAGCACAACAGTTG
ATATTTCTTATACTTAAATATCCTGAAATAATTTATCATTCTTACGAAGAATTAGAATCG
TGTATTTTGGTTAAATATACATTCGATCTATGCAATGTTGTTAGTCGAGCATGGAAAGTA
CTGTCAGTAAAAAATTGTGAATGTAAAGAAACAGCATCACAACGTCTTTATCTTTTTAAT
ACAACACGAAAAGTACTGAAACATAGTTTAGATATTCTAGGCTTAAAAGTTTTAAATGAG
ATGTAA
>g5279.t4 Gene=g5279 Length=411
MNYLGDYGTQFGFLKAGIDMENLSDEKIKENPLQNLLRVYVAANTSEDPCVAEKARKIFE
IMEFGENAEIIEQWNKIREYTLNELKLIYERLNVIYDSYEFESMYRRKNIEDVISLMQEM
KLLERETDEKIIVKVENRRVPFIKSDSTTLYLTRDIAAFLKRKEKYEMDRIFYVVDNGQN
DHFTAIKSVVNQLGFDSDSFIHHIKFGRIKGMSTRKGKIVFLKDILDEAKELMYKKQQES
KTTKVDLSQCGESIADILGTSAIIVNDLKQRRQRDYEFDWNKILQVTGDTGIKFQYTHCR
LYSLQNQNSHIQEAEELNFDLLKEQEAQQLIFLILKYPEIIYHSYEELESCILVKYTFDL
CNVVSRAWKVLSVKNCECKETASQRLYLFNTTRKVLKHSLDILGLKVLNEM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g5279.t4 | Coils | Coil | Coil | 304 | 324 | - |
| 8 | g5279.t4 | Gene3D | G3DSA:3.40.50.620 | HUPs | 1 | 287 | 3.9E-75 |
| 9 | g5279.t4 | Gene3D | G3DSA:1.10.730.10 | - | 288 | 411 | 2.7E-27 |
| 3 | g5279.t4 | PANTHER | PTHR11956 | ARGINYL-TRNA SYNTHETASE | 1 | 411 | 2.4E-90 |
| 4 | g5279.t4 | PANTHER | PTHR11956:SF5 | ARGININE–TRNA LIGASE, CYTOPLASMIC-RELATED | 1 | 411 | 2.4E-90 |
| 2 | g5279.t4 | Pfam | PF00750 | tRNA synthetases class I (R) | 1 | 280 | 8.2E-54 |
| 1 | g5279.t4 | Pfam | PF05746 | DALR anticodon binding domain | 295 | 411 | 4.5E-20 |
| 7 | g5279.t4 | SMART | SM00836 | dalr_1_4 | 294 | 411 | 1.6E-28 |
| 5 | g5279.t4 | SUPERFAMILY | SSF52374 | Nucleotidylyl transferase | 2 | 288 | 8.7E-44 |
| 6 | g5279.t4 | SUPERFAMILY | SSF47323 | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 288 | 411 | 1.57E-23 |
| 11 | g5279.t4 | TIGRFAM | TIGR00456 | argS: arginine–tRNA ligase | 1 | 411 | 1.6E-79 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5279/g5279.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5279.t4.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
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.
