General information for g5594.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable cysteine–tRNA ligase, mitochondrial.
Parent gene
- The parent gene g5594 is located on chr_2: 10446699..10448950 (+ 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 | g5594 | g5594.t4 | isoform | g5594.t4 | 10445338 | 10446699 |
| chr_2 | g5594 | g5594.t4 | exon | g5594.t4.exon1 | 10445338 | 10446699 |
| chr_2 | g5594 | g5594.t4 | cds | g5594.t4.CDS1 | 10445446 | 10446699 |
| chr_2 | g5594 | g5594.t4 | TSS | g5594.t4 | 10446513 | 10446513 |
| chr_2 | g5594 | g5594.t4 | TTS | g5594.t4 | 10446724 | 10446724 |
Sequences
>g5594.t4 Gene=g5594 Length=1362
CCAACAGTTTATGATTCTGCTCACATTGGTCATGGTTCAACATATGTTCGACTTGATATC
ATTCAACGCATTCTTAGAAATTATTTTAATATCAACTTAGTAACATGCATGAACATCACA
AATATCGATGATAAAATTATAAAAAGAAGTAATGAATTAGGAAAAGATTGGAATTTATTA
GCAGAAGAATATGAAATTGAATTTTGGGATGATTTAAATAAATTGAATATCATGCAACCA
GATATAAAACTAAGAGTGACTGATAAAATCCCAGAAATAATTAAATTCATAGAAGAAATT
GAAAAGAAAGGATATACAACTATCTCAACAAATGGATCAGTGAATTTCAAAACTTCTGCC
TACAGTAAATATGGAAAACTGCATAATGTCGTTCTTGAAGATGTTTCAACAGCAGAATTT
GCTCTTTGGAAGGCAGCAAAAGAGAACGAACCTTGGTGGGATTCAAAATGGGGAAGAGGA
AGACCAGGATGGCATATCGAGTGTTCAACATTAGCAAGTCTTGTTTTTGGTTCACATTTA
GATTTTCATGCAGGTGGAATTGATTTGAAATTTCCACATCATGAAAATGAAGAAGCACAA
AGCTGCGTGTTTCATAATTGTAACGATTGGGTTCAAAATTGGATACATACTGGACATTTA
CATTTAAAAGGACAAAGTGAAAAGATGTCAAAATCACTTAAAAATACAATTTCAATAAGA
GATTTTTTGAAAGATTATACAGCAGAAAAATTTCGAATGGCATGCTTATTATCACATTAT
CGTTCATCAATTGAGTTTGGTCCAGAATTAATGTTTGCTGCTGATTCTATTCTCAAACGG
GTCAAATCATTTAAAGAAGACGTTAAAGCATTTATTAGTGGTGCAAAAATTGATGGATAT
GTCAATGAAGAAGAATTGAGAAAACATTTTCAAGAATCTAGAAATAATATTGATGAAGCT
CTAAGAGATGATTTTCATACTGCTGCATGCATTGGTCAATTATCTGATTTGATGCGACTT
ATAAGTAAAACAATAAATAATGTGGATAAAAAAAATGAACAGAGGTCATCAAATGGAAAT
GAAAAAGCGCTTTTATATGCTGTAGTAAATTATATTGATCACATGCTACAAATTTTTGGA
ATTGGCGATGAAATTCAATTTAGTGAATCATATGATGAGGGTCGAATGGAAAATTTAGTT
AATTCGATTATAAAAGTTAGAAATGACATTCGATTAAGAGCTAAAGAAACTAAAAGTAAA
GAGCTATTTCAAGTGTGCGATGAAATAAGGCAATCAATGAGAGAGAATTTAATAGAAATC
AAAGACCATGGAAATTTATCGTCATGGAGTAAAGTAAAATAA
>g5594.t4 Gene=g5594 Length=417
MNITNIDDKIIKRSNELGKDWNLLAEEYEIEFWDDLNKLNIMQPDIKLRVTDKIPEIIKF
IEEIEKKGYTTISTNGSVNFKTSAYSKYGKLHNVVLEDVSTAEFALWKAAKENEPWWDSK
WGRGRPGWHIECSTLASLVFGSHLDFHAGGIDLKFPHHENEEAQSCVFHNCNDWVQNWIH
TGHLHLKGQSEKMSKSLKNTISIRDFLKDYTAEKFRMACLLSHYRSSIEFGPELMFAADS
ILKRVKSFKEDVKAFISGAKIDGYVNEEELRKHFQESRNNIDEALRDDFHTAACIGQLSD
LMRLISKTINNVDKKNEQRSSNGNEKALLYAVVNYIDHMLQIFGIGDEIQFSESYDEGRM
ENLVNSIIKVRNDIRLRAKETKSKELFQVCDEIRQSMRENLIEIKDHGNLSSWSKVK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g5594.t4 | Coils | Coil | Coil | 267 | 287 | - |
| 8 | g5594.t4 | Gene3D | G3DSA:3.40.50.620 | HUPs | 1 | 231 | 5.4E-83 |
| 9 | g5594.t4 | Gene3D | G3DSA:1.20.120.640 | - | 235 | 415 | 1.1E-11 |
| 2 | g5594.t4 | PANTHER | PTHR10890:SF27 | CYSTEINE–TRNA LIGASE, MITOCHONDRIAL-RELATED | 1 | 414 | 2.9E-139 |
| 3 | g5594.t4 | PANTHER | PTHR10890 | CYSTEINYL-TRNA SYNTHETASE | 1 | 414 | 2.9E-139 |
| 5 | g5594.t4 | PRINTS | PR00983 | Cysteinyl-tRNA synthetase signature | 114 | 132 | 8.2E-17 |
| 4 | g5594.t4 | PRINTS | PR00983 | Cysteinyl-tRNA synthetase signature | 145 | 166 | 8.2E-17 |
| 1 | g5594.t4 | Pfam | PF01406 | tRNA synthetases class I (C) catalytic domain | 2 | 237 | 1.7E-79 |
| 6 | g5594.t4 | SUPERFAMILY | SSF52374 | Nucleotidylyl transferase | 1 | 237 | 4.79E-53 |
| 7 | g5594.t4 | SUPERFAMILY | SSF47323 | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 266 | 414 | 2.88E-15 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5594/g5594.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5594.t4.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| 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 |
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.
