General information for g2530.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Asparagine–tRNA ligase, cytoplasmic.
Parent gene
- The parent gene g2530 is located on chr_3: 18489019..18490766 (+ 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 | g2530 | g2530.t3 | TSS | g2530.t3 | 18488703 | 18488703 |
| chr_3 | g2530 | g2530.t3 | isoform | g2530.t3 | 18488758 | 18490272 |
| chr_3 | g2530 | g2530.t3 | exon | g2530.t3.exon1 | 18488758 | 18488791 |
| chr_3 | g2530 | g2530.t3 | cds | g2530.t3.CDS1 | 18488758 | 18488791 |
| chr_3 | g2530 | g2530.t3 | exon | g2530.t3.exon2 | 18488967 | 18490018 |
| chr_3 | g2530 | g2530.t3 | cds | g2530.t3.CDS2 | 18488967 | 18490018 |
| chr_3 | g2530 | g2530.t3 | exon | g2530.t3.exon3 | 18490064 | 18490272 |
| chr_3 | g2530 | g2530.t3 | cds | g2530.t3.CDS3 | 18490064 | 18490270 |
| chr_3 | g2530 | g2530.t3 | TTS | g2530.t3 | NA | NA |
Sequences
>g2530.t3 Gene=g2530 Length=1295
ATGGCTACAGAAGCTCTAGAAAAACTGTCGCTAAGTGAACTATATACATCTGAGAAACGT
GGTAGTGATGAGACGGGAGATGGAAGTGAGAAAAAACCATTTAAGACAATTTTGCAGGCG
ATGAGACATGCAGGGAAGGAACCATTTCCAACTATTTATTCTGATGCAAAAGATGAGAAA
TCTGAAAGTTTATATGAGCCAGCGGCTAAATCACAATTAAAGAAAGTAAAGAAACAATGG
CTTACAGAGTTACAAAAAATGGCAGAAAAGTCAAAACGTGATGAAGAAGAAGCTGCTCAA
AGAGAGAAAAATTTAGAAGAAGCAAAGTTGATCAAAATTGCAGAAGATCCATCCTGGCCT
GTTGCTAAACAAATAAGAATTAATGAAGGATTGCAAAATCGTGGCATTCGAGTTAAAATA
TATGGTTGGATTCATCGTCTTAGACGTCAAGGAAAGGGTTTGATGTTTGCAACATTACGT
GATGGCTATGGCTATTTGCAATGTGTTTTAAGCGACTTGCTATGTCAAACTTATGAAGGA
TTATTACTTTCAACTGAATCATCCGTGCTTTTCTTTGGCACTTTGAAAGAAGTTCCTGAG
GGAAAAACTGCACCAGATCAGCATGAATTGCATGTTGATTATTATGAAGTAGTAGGTCAT
TCACCAGCTGGTGGTGCTGATAATTTATTGAACGAATTTGCAAATCCAGATGTAATGCTT
GACAATCGACATATGATGATTCGTGGTGAAAACACATCAAAAATATTAAAAATGCGCAGT
GTAGTGACTCAAGCTTTTCGTAGTCACTTTTATGACAATGGTTACACAGAAGTTTGTCCG
CCAACTCTTGTTCAAACACAAGTCGAAGGAGGCTCAACACTCTTCAAATTTGATTATTTT
GGTGAAGAGGCATATTTAACTCAAAGTTCACAATTATATCTTGAGACATGTATGCCATCA
CTTGGAGACGTTTTCTGCATTGCACAAAGTTATCGAGCAGAGCAATCTCGAACAAGAAGA
CATTTGGCTGAATATAGTCATGTCGAAGCAGAGCGTGCTTTCATCACGTTTGATGATTTA
TTAAATTCACCATATGCTCAACTGGTGAAAGATTTAAATCCTGATTTCAAGCCACCAAAA
AGACCTTTCCGTCGAATGGATTATGCTGAAGCGATTGAATGGTTGAAAACAAATAATGTA
ACAAAAGAGGATGGTTCATTTTACGAATTTGGCGAAGACATTCCTGAAGCACCTGAACGA
AAAATGACCGATACAATTAATGAACCAATTATGCT
>g2530.t3 Gene=g2530 Length=431
MATEALEKLSLSELYTSEKRGSDETGDGSEKKPFKTILQAMRHAGKEPFPTIYSDAKDEK
SESLYEPAAKSQLKKVKKQWLTELQKMAEKSKRDEEEAAQREKNLEEAKLIKIAEDPSWP
VAKQIRINEGLQNRGIRVKIYGWIHRLRRQGKGLMFATLRDGYGYLQCVLSDLLCQTYEG
LLLSTESSVLFFGTLKEVPEGKTAPDQHELHVDYYEVVGHSPAGGADNLLNEFANPDVML
DNRHMMIRGENTSKILKMRSVVTQAFRSHFYDNGYTEVCPPTLVQTQVEGGSTLFKFDYF
GEEAYLTQSSQLYLETCMPSLGDVFCIAQSYRAEQSRTRRHLAEYSHVEAERAFITFDDL
LNSPYAQLVKDLNPDFKPPKRPFRRMDYAEAIEWLKTNNVTKEDGSFYEFGEDIPEAPER
KMTDTINEPIM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g2530.t3 | CDD | cd04323 | AsnRS_cyto_like_N | 137 | 220 | 9.99616E-38 |
| 14 | g2530.t3 | Coils | Coil | Coil | 70 | 108 | - |
| 11 | g2530.t3 | Gene3D | G3DSA:1.10.10.1430 | - | 10 | 87 | 1.3E-31 |
| 13 | g2530.t3 | Gene3D | G3DSA:2.40.50.140 | - | 108 | 223 | 5.2E-26 |
| 12 | g2530.t3 | Gene3D | G3DSA:3.30.930.10 | Bira Bifunctional Protein; Domain 2 | 228 | 431 | 1.5E-51 |
| 7 | g2530.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 34 | - |
| 8 | g2530.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 13 | 31 | - |
| 10 | g2530.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 48 | 71 | - |
| 9 | g2530.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 52 | 71 | - |
| 3 | g2530.t3 | PANTHER | PTHR22594 | ASPARTYL/LYSYL-TRNA SYNTHETASE | 43 | 431 | 2.1E-165 |
| 4 | g2530.t3 | PANTHER | PTHR22594:SF16 | ASPARAGINE–TRNA LIGASE, CYTOPLASMIC | 43 | 431 | 2.1E-165 |
| 1 | g2530.t3 | Pfam | PF01336 | OB-fold nucleic acid binding domain | 138 | 217 | 6.4E-11 |
| 2 | g2530.t3 | Pfam | PF00152 | tRNA synthetases class II (D, K and N) | 237 | 430 | 6.1E-50 |
| 6 | g2530.t3 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 103 | 222 | 1.3E-20 |
| 5 | g2530.t3 | SUPERFAMILY | SSF55681 | Class II aaRS and biotin synthetases | 235 | 430 | 1.02E-42 |
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:0006418 | tRNA aminoacylation for protein translation | BP |
| GO:0000166 | nucleotide binding | MF |
| GO:0004812 | aminoacyl-tRNA ligase activity | MF |
| GO:0003676 | nucleic acid binding | 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. There were no conditions that were differentially expressed