General information for g2399.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable glutamine–tRNA ligase.
Parent gene
- The parent gene g2399 is located on chr_3: 17638780..17639608 (- 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_3 | g2399 | g2399.t2 | TTS | g2399.t2 | 17637045 | 17637045 |
| chr_3 | g2399 | g2399.t2 | isoform | g2399.t2 | 17637103 | 17638339 |
| chr_3 | g2399 | g2399.t2 | exon | g2399.t2.exon1 | 17637103 | 17638339 |
| chr_3 | g2399 | g2399.t2 | cds | g2399.t2.CDS1 | 17637103 | 17638338 |
| chr_3 | g2399 | g2399.t2 | TSS | g2399.t2 | NA | NA |
Sequences
>g2399.t2 Gene=g2399 Length=1237
AATGAAAGGTTTCAATACTATTTTGAGCCCATGGCGTGATCGTCCAATTGAAGAAAGTTT
GCAACTTTTCGAAGATATGAAGAATGGAAAAATTGATGAAGGTGCTGCTACATTAAGAAT
GAAAATTACTTTAGAAGAAGGAAAAGTTGATCCTGTGGCATATAGAATCAAATTCATAGC
GCATCATCGTACTTGTAATGATTGGTGTATTTATCCAACTTATGATTACACGCATTGTTT
ATGCGATAGTATTGAGCATATTACACATTCATTATGCACAAAAGAATTCCAAACGAGACG
TTCTAGTTACTATTGGTTGTGCAATGCTCTTAATATTTATTGCCCTGTACAATGGGAATA
TGGACGACTAAATGTAAATTATACAGTTGTTTCAAAACGAAAAATTGCTAAGCTCATCAC
TGAAAAAATTGTTGCTGATTGGGATGATCCGAGATTGTTTACGTTGACTGCATTAAGACG
TCGTGGTTTTCCATCAGAAGCAATTAATAATTTCTGTGCTCTTATGGGTGTCACTGGTTC
TCAAGGCTCAGTTGATCCTAGTATGCTTGAAGCTTGTGTTCGAGATGTTCTCAATGTTAC
TGCTCCTAGAAAATTGGTTGTGCTTGAACCATTAAAAATTACAATTACAAATTTTATCAG
CGATAAGCCAATCATCTTAACTGTTCCTGACTTTCCATCTCAGCCAGATAATAAATCATC
GCACAATATTACTTTTGATCGTGTAGTTTATATTGAACAAAGCGATTTCAAAGAGTCTCC
TGAGAAAGGTTATCGTCGTCTTTCTCCAAATCAAACTGTTGGTCTTCGTCATGCAGGTGT
TGTAATTAAAGTTGTAGAAATTAAAAGAGATTCTAATGGAAAACCAATTGAATTATTTTG
TACTTGCGAAAAAAGCGAAACTGCTGAGAAGCCAAAAGCATATATTCAATGGGTTTCTGT
TCCTCAAATAATTGAAGTGAGACTCTATGAAAGACTATTTTTACACAAAAATCCTGAGGA
TATAAATGAAGTGCCTAACGGATTTTTAAGTGATTGTAATAAGGATACACTAAAAATATT
GAAATCTTATGCTGATAAATCTATTACTACTGCAAAAGTTTATGATAAATTTCAATTTGA
GAGAATTGGCTTTTTCTCTGTTGATCCTGATTCTACGAGCGATAAACTTGTTTTCAATCG
TACAGTATCATTAAAAGAAGATTCTGGAAAAGAATAA
>g2399.t2 Gene=g2399 Length=411
MKGFNTILSPWRDRPIEESLQLFEDMKNGKIDEGAATLRMKITLEEGKVDPVAYRIKFIA
HHRTCNDWCIYPTYDYTHCLCDSIEHITHSLCTKEFQTRRSSYYWLCNALNIYCPVQWEY
GRLNVNYTVVSKRKIAKLITEKIVADWDDPRLFTLTALRRRGFPSEAINNFCALMGVTGS
QGSVDPSMLEACVRDVLNVTAPRKLVVLEPLKITITNFISDKPIILTVPDFPSQPDNKSS
HNITFDRVVYIEQSDFKESPEKGYRRLSPNQTVGLRHAGVVIKVVEIKRDSNGKPIELFC
TCEKSETAEKPKAYIQWVSVPQIIEVRLYERLFLHKNPEDINEVPNGFLSDCNKDTLKIL
KSYADKSITTAKVYDKFQFERIGFFSVDPDSTSDKLVFNRTVSLKEDSGKE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g2399.t2 | Gene3D | G3DSA:3.40.50.620 | HUPs | 2 | 203 | 0 |
| 9 | g2399.t2 | Gene3D | G3DSA:2.40.240.10 | Ribosomal Protein L25; Chain P | 204 | 406 | 0 |
| 8 | g2399.t2 | Gene3D | G3DSA:2.40.240.10 | Ribosomal Protein L25; Chain P | 209 | 338 | 0 |
| 3 | g2399.t2 | PANTHER | PTHR43097 | GLUTAMINE-TRNA LIGASE | 1 | 410 | 0 |
| 4 | g2399.t2 | PANTHER | PTHR43097:SF2 | GLUTAMINE–TRNA LIGASE | 1 | 410 | 0 |
| 1 | g2399.t2 | Pfam | PF00749 | tRNA synthetases class I (E and Q), catalytic domain | 9 | 198 | 0 |
| 2 | g2399.t2 | Pfam | PF03950 | tRNA synthetases class I (E and Q), anti-codon binding domain | 201 | 388 | 0 |
| 5 | g2399.t2 | SUPERFAMILY | SSF52374 | Nucleotidylyl transferase | 5 | 205 | 0 |
| 6 | g2399.t2 | SUPERFAMILY | SSF50715 | Ribosomal protein L25-like | 201 | 407 | 0 |
| 10 | g2399.t2 | TIGRFAM | TIGR00440 | glnS: glutamine–tRNA ligase | 9 | 408 | 0 |
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:0005524 | ATP binding | MF |
| GO:0004819 | glutamine-tRNA ligase activity | MF |
| GO:0005737 | cytoplasm | CC |
| GO:0006425 | glutaminyl-tRNA aminoacylation | BP |
| GO:0000166 | nucleotide binding | MF |
| GO:0006418 | tRNA aminoacylation for protein translation | BP |
| GO:0043039 | tRNA aminoacylation | BP |
| GO:0006412 | translation | BP |
| 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.
