General information for g2399.t1
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.t1 | TTS | g2399.t1 | 17637045 | 17637045 |
| chr_3 | g2399 | g2399.t1 | isoform | g2399.t1 | 17637103 | 17639502 |
| chr_3 | g2399 | g2399.t1 | exon | g2399.t1.exon1 | 17637103 | 17639088 |
| chr_3 | g2399 | g2399.t1 | cds | g2399.t1.CDS1 | 17637103 | 17639088 |
| chr_3 | g2399 | g2399.t1 | exon | g2399.t1.exon2 | 17639143 | 17639502 |
| chr_3 | g2399 | g2399.t1 | cds | g2399.t1.CDS2 | 17639143 | 17639502 |
| chr_3 | g2399 | g2399.t1 | TSS | g2399.t1 | 17640433 | 17640433 |
Sequences
>g2399.t1 Gene=g2399 Length=2346
ATGGATGAAGCAACTTTTATTTCTAAATTTATTGCACTTGGTTTTAATGAGCAAAAAGCA
AAGGAGACTTTAAAGAATGCAACTCTAACAAAGAATATTACAGCAGCATTTAATTCATTA
GATAATCATAATAAGAAAATTGAAGAATTGACAAAAGGATCTGGAGCATTAGTCTATCAT
TTATGCTCAAAAATCAAGCCTCAATCGCTTCAATATTTAGATCTTCTTATATCTCTCATC
ACTGAGAATAAGTTGGATAATAATCTTCGAGTTGATTTAGCATTAGAATTTGTACTTTCA
CATAGTGTCAGTAATACAACAATCAACGTGGCAGATCTTGAAAAGCATTGTGGAGTGAAT
GTTGTTGTAACACCTGAAGAAATTGAAGAAGTAGTTGCTGAAGTAATAAAAAAGAACAAG
AAAGAGCTCGAAGAACAACGTTATCGCTTCAATACCGGCAAAATGCTTGCAGAAATTCGT
TCAAAAATTCCTTTTGCCGATGGAAAAGCTATCAAGTCAGAAGTTGATTGCCAGATATTT
TATCTTCTTGGTGCAAAAACTGAAGCTGACTTGGCTCCACAGCCAAAGAAGAAGGCAGCT
CCATCAAATAATACTGCAACTTCAAAATCCGTCAAGCCAAAAGAAGAAGAGGAAGTTTCA
AATGATGACACTGCATTAACAATCACAGAATTGATGAAGAAAGTTAAATTTCATGCGCCA
GGTGAAAATTACAAAACTGATGGTTATGTTACGACACCAGAAACCGAACGATTACTTAAA
GAGCATTTAAAAATCACTGGAGGTCAAGTTAGAACAAGATTTCCTCCCGAACCTAATGGA
ATCCTTCATATCGGTCATGCAAAAGCTATTAACATCAATTTTGGATATGCTGCTGCTAAA
AATGGAATTTGTTTTCTTCGATATGACGATACAAATCCTGAAAAAGAGGAAGAAAAGTTT
TTCATTGCCATCAAAGACATGGTAGAGTGGCTTGGTTACAAACCTCACAAAATCACTCAT
TCTTCTGATAATTTTCAACAACTTTATGAATGGGCAGTTGTTCTTATTAAAAAAGGACTT
GCATATGTGTGTCATCAAACAGCCGATGAAATGAAAGGTTTCAATACTATTTTGAGCCCA
TGGCGTGATCGTCCAATTGAAGAAAGTTTGCAACTTTTCGAAGATATGAAGAATGGAAAA
ATTGATGAAGGTGCTGCTACATTAAGAATGAAAATTACTTTAGAAGAAGGAAAAGTTGAT
CCTGTGGCATATAGAATCAAATTCATAGCGCATCATCGTACTTGTAATGATTGGTGTATT
TATCCAACTTATGATTACACGCATTGTTTATGCGATAGTATTGAGCATATTACACATTCA
TTATGCACAAAAGAATTCCAAACGAGACGTTCTAGTTACTATTGGTTGTGCAATGCTCTT
AATATTTATTGCCCTGTACAATGGGAATATGGACGACTAAATGTAAATTATACAGTTGTT
TCAAAACGAAAAATTGCTAAGCTCATCACTGAAAAAATTGTTGCTGATTGGGATGATCCG
AGATTGTTTACGTTGACTGCATTAAGACGTCGTGGTTTTCCATCAGAAGCAATTAATAAT
TTCTGTGCTCTTATGGGTGTCACTGGTTCTCAAGGCTCAGTTGATCCTAGTATGCTTGAA
GCTTGTGTTCGAGATGTTCTCAATGTTACTGCTCCTAGAAAATTGGTTGTGCTTGAACCA
TTAAAAATTACAATTACAAATTTTATCAGCGATAAGCCAATCATCTTAACTGTTCCTGAC
TTTCCATCTCAGCCAGATAATAAATCATCGCACAATATTACTTTTGATCGTGTAGTTTAT
ATTGAACAAAGCGATTTCAAAGAGTCTCCTGAGAAAGGTTATCGTCGTCTTTCTCCAAAT
CAAACTGTTGGTCTTCGTCATGCAGGTGTTGTAATTAAAGTTGTAGAAATTAAAAGAGAT
TCTAATGGAAAACCAATTGAATTATTTTGTACTTGCGAAAAAAGCGAAACTGCTGAGAAG
CCAAAAGCATATATTCAATGGGTTTCTGTTCCTCAAATAATTGAAGTGAGACTCTATGAA
AGACTATTTTTACACAAAAATCCTGAGGATATAAATGAAGTGCCTAACGGATTTTTAAGT
GATTGTAATAAGGATACACTAAAAATATTGAAATCTTATGCTGATAAATCTATTACTACT
GCAAAAGTTTATGATAAATTTCAATTTGAGAGAATTGGCTTTTTCTCTGTTGATCCTGAT
TCTACGAGCGATAAACTTGTTTTCAATCGTACAGTATCATTAAAAGAAGATTCTGGAAAA
GAATAA
>g2399.t1 Gene=g2399 Length=781
MDEATFISKFIALGFNEQKAKETLKNATLTKNITAAFNSLDNHNKKIEELTKGSGALVYH
LCSKIKPQSLQYLDLLISLITENKLDNNLRVDLALEFVLSHSVSNTTINVADLEKHCGVN
VVVTPEEIEEVVAEVIKKNKKELEEQRYRFNTGKMLAEIRSKIPFADGKAIKSEVDCQIF
YLLGAKTEADLAPQPKKKAAPSNNTATSKSVKPKEEEEVSNDDTALTITELMKKVKFHAP
GENYKTDGYVTTPETERLLKEHLKITGGQVRTRFPPEPNGILHIGHAKAININFGYAAAK
NGICFLRYDDTNPEKEEEKFFIAIKDMVEWLGYKPHKITHSSDNFQQLYEWAVVLIKKGL
AYVCHQTADEMKGFNTILSPWRDRPIEESLQLFEDMKNGKIDEGAATLRMKITLEEGKVD
PVAYRIKFIAHHRTCNDWCIYPTYDYTHCLCDSIEHITHSLCTKEFQTRRSSYYWLCNAL
NIYCPVQWEYGRLNVNYTVVSKRKIAKLITEKIVADWDDPRLFTLTALRRRGFPSEAINN
FCALMGVTGSQGSVDPSMLEACVRDVLNVTAPRKLVVLEPLKITITNFISDKPIILTVPD
FPSQPDNKSSHNITFDRVVYIEQSDFKESPEKGYRRLSPNQTVGLRHAGVVIKVVEIKRD
SNGKPIELFCTCEKSETAEKPKAYIQWVSVPQIIEVRLYERLFLHKNPEDINEVPNGFLS
DCNKDTLKILKSYADKSITTAKVYDKFQFERIGFFSVDPDSTSDKLVFNRTVSLKEDSGK
E
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g2399.t1 | CDD | cd00807 | GlnRS_core | 269 | 573 | 3.90319E-155 |
| 16 | g2399.t1 | Gene3D | G3DSA:1.10.8.1290 | - | 2 | 121 | 1.0E-18 |
| 15 | g2399.t1 | Gene3D | G3DSA:1.10.10.2420 | - | 122 | 192 | 1.7E-22 |
| 12 | g2399.t1 | Gene3D | G3DSA:3.40.50.620 | HUPs | 235 | 573 | 9.5E-141 |
| 13 | g2399.t1 | Gene3D | G3DSA:2.40.240.10 | Ribosomal Protein L25; Chain P | 574 | 776 | 2.5E-67 |
| 14 | g2399.t1 | Gene3D | G3DSA:2.40.240.10 | Ribosomal Protein L25; Chain P | 579 | 708 | 2.5E-67 |
| 19 | g2399.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 191 | 222 | - |
| 5 | g2399.t1 | PANTHER | PTHR43097 | GLUTAMINE-TRNA LIGASE | 7 | 780 | 0.0 |
| 6 | g2399.t1 | PANTHER | PTHR43097:SF2 | GLUTAMINE–TRNA LIGASE | 7 | 780 | 0.0 |
| 9 | g2399.t1 | PRINTS | PR00987 | Glutamyl-tRNA synthetase signature | 273 | 285 | 8.1E-7 |
| 8 | g2399.t1 | PRINTS | PR00987 | Glutamyl-tRNA synthetase signature | 302 | 315 | 8.1E-7 |
| 7 | g2399.t1 | PRINTS | PR00987 | Glutamyl-tRNA synthetase signature | 442 | 452 | 8.1E-7 |
| 2 | g2399.t1 | Pfam | PF04558 | Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1 | 6 | 168 | 1.3E-44 |
| 3 | g2399.t1 | Pfam | PF04557 | Glutaminyl-tRNA synthetase, non-specific RNA binding region part 2 | 171 | 260 | 3.6E-26 |
| 1 | g2399.t1 | Pfam | PF00749 | tRNA synthetases class I (E and Q), catalytic domain | 269 | 568 | 3.8E-109 |
| 4 | g2399.t1 | Pfam | PF03950 | tRNA synthetases class I (E and Q), anti-codon binding domain | 571 | 758 | 2.2E-41 |
| 18 | g2399.t1 | ProSitePatterns | PS00178 | Aminoacyl-transfer RNA synthetases class-I signature. | 276 | 287 | - |
| 10 | g2399.t1 | SUPERFAMILY | SSF52374 | Nucleotidylyl transferase | 269 | 575 | 3.66E-84 |
| 11 | g2399.t1 | SUPERFAMILY | SSF50715 | Ribosomal protein L25-like | 571 | 777 | 1.26E-52 |
| 20 | g2399.t1 | TIGRFAM | TIGR00440 | glnS: glutamine–tRNA ligase | 270 | 778 | 1.3E-182 |
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 transcript has been annotated with K01886 (glutaminyl-tRNA synthetase)
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.
