Gene loci information

Transcript annotation

  • This transcript has been annotated as Asparagine–tRNA ligase, cytoplasmic.

Parent gene

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.t1 TSS g2530.t1 18488703 18488703
chr_3 g2530 g2530.t1 isoform g2530.t1 18488758 18490609
chr_3 g2530 g2530.t1 exon g2530.t1.exon1 18488758 18488791
chr_3 g2530 g2530.t1 cds g2530.t1.CDS1 18488758 18488791
chr_3 g2530 g2530.t1 exon g2530.t1.exon2 18488967 18490609
chr_3 g2530 g2530.t1 cds g2530.t1.CDS2 18488967 18490609
chr_3 g2530 g2530.t1 TTS g2530.t1 18491463 18491463

Sequences

>g2530.t1 Gene=g2530 Length=1677
ATGGCTACAGAAGCTCTAGAAAAACTGTCGCTAAGTGAACTATATACATCTGAGAAACGT
GGTAGTGATGAGACGGGAGATGGAAGTGAGAAAAAACCATTTAAGACAATTTTGCAGGCG
ATGAGACATGCAGGGAAGGAACCATTTCCAACTATTTATTCTGATGCAAAAGATGAGAAA
TCTGAAAGTTTATATGAGCCAGCGGCTAAATCACAATTAAAGAAAGTAAAGAAACAATGG
CTTACAGAGTTACAAAAAATGGCAGAAAAGTCAAAACGTGATGAAGAAGAAGCTGCTCAA
AGAGAGAAAAATTTAGAAGAAGCAAAGTTGATCAAAATTGCAGAAGATCCATCCTGGCCT
GTTGCTAAACAAATAAGAATTAATGAAGGATTGCAAAATCGTGGCATTCGAGTTAAAATA
TATGGTTGGATTCATCGTCTTAGACGTCAAGGAAAGGGTTTGATGTTTGCAACATTACGT
GATGGCTATGGCTATTTGCAATGTGTTTTAAGCGACTTGCTATGTCAAACTTATGAAGGA
TTATTACTTTCAACTGAATCATCCGTGCTTTTCTTTGGCACTTTGAAAGAAGTTCCTGAG
GGAAAAACTGCACCAGATCAGCATGAATTGCATGTTGATTATTATGAAGTAGTAGGTCAT
TCACCAGCTGGTGGTGCTGATAATTTATTGAACGAATTTGCAAATCCAGATGTAATGCTT
GACAATCGACATATGATGATTCGTGGTGAAAACACATCAAAAATATTAAAAATGCGCAGT
GTAGTGACTCAAGCTTTTCGTAGTCACTTTTATGACAATGGTTACACAGAAGTTTGTCCG
CCAACTCTTGTTCAAACACAAGTCGAAGGAGGCTCAACACTCTTCAAATTTGATTATTTT
GGTGAAGAGGCATATTTAACTCAAAGTTCACAATTATATCTTGAGACATGTATGCCATCA
CTTGGAGACGTTTTCTGCATTGCACAAAGTTATCGAGCAGAGCAATCTCGAACAAGAAGA
CATTTGGCTGAATATAGTCATGTCGAAGCAGAGCGTGCTTTCATCACGTTTGATGATTTA
TTAAATTCAATGGAACATTTGATTTGTGATGTAGTTGATCGTGTTCTAAAGTCACCATAT
GCTCAACTGGTGAAAGATTTAAATCCTGATTTCAAGCCACCAAAAAGACCTTTCCGTCGA
ATGGATTATGCTGAAGCGATTGAATGGTTGAAAACAAATAATGTAACAAAAGAGGATGGT
TCATTTTACGAATTTGGCGAAGACATTCCTGAAGCACCTGAACGAAAAATGACCGATACA
ATTAATGAACCAATTATGCTCTGCCGATTTCCAGCTGGAATTAAAGCCTTTTATATGGCT
CGTTGTCCTGAAAATGAAGAATTAACTGAAAGTGTTGATGTTTTACTGCCAGGTGTTGGA
GAAATTATCGGAGGTTCAATGCGTGAGGCTAACAATGAAAAATTATTAGCCGCATACAAA
AAAGAAGGAATTGATCCAACACCATATTATTGGTACACTGATCAACGTGTTTATGGAACA
ACTCCTCATGGTGGTTATGGTCTTGGATTAGAACGATTTTTATGCTGGCTTTTGAATCGA
TATCATATCAGAGAAGTTTGTCTCTATCCTCGTTTCTTACAACGTTGCAGACCTTAA

>g2530.t1 Gene=g2530 Length=558
MATEALEKLSLSELYTSEKRGSDETGDGSEKKPFKTILQAMRHAGKEPFPTIYSDAKDEK
SESLYEPAAKSQLKKVKKQWLTELQKMAEKSKRDEEEAAQREKNLEEAKLIKIAEDPSWP
VAKQIRINEGLQNRGIRVKIYGWIHRLRRQGKGLMFATLRDGYGYLQCVLSDLLCQTYEG
LLLSTESSVLFFGTLKEVPEGKTAPDQHELHVDYYEVVGHSPAGGADNLLNEFANPDVML
DNRHMMIRGENTSKILKMRSVVTQAFRSHFYDNGYTEVCPPTLVQTQVEGGSTLFKFDYF
GEEAYLTQSSQLYLETCMPSLGDVFCIAQSYRAEQSRTRRHLAEYSHVEAERAFITFDDL
LNSMEHLICDVVDRVLKSPYAQLVKDLNPDFKPPKRPFRRMDYAEAIEWLKTNNVTKEDG
SFYEFGEDIPEAPERKMTDTINEPIMLCRFPAGIKAFYMARCPENEELTESVDVLLPGVG
EIIGGSMREANNEKLLAAYKKEGIDPTPYYWYTDQRVYGTTPHGGYGLGLERFLCWLLNR
YHIREVCLYPRFLQRCRP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g2530.t1 CDD cd04323 AsnRS_cyto_like_N 137 220 1.23437E-36
15 g2530.t1 CDD cd00776 AsxRS_core 234 552 1.94948E-145
14 g2530.t1 Coils Coil Coil 70 108 -
11 g2530.t1 Gene3D G3DSA:1.10.10.1430 - 10 87 1.9E-31
13 g2530.t1 Gene3D G3DSA:2.40.50.140 - 108 223 8.1E-26
12 g2530.t1 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 228 558 3.8E-107
17 g2530.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 34 -
18 g2530.t1 MobiDBLite mobidb-lite consensus disorder prediction 13 31 -
20 g2530.t1 MobiDBLite mobidb-lite consensus disorder prediction 48 71 -
19 g2530.t1 MobiDBLite mobidb-lite consensus disorder prediction 52 71 -
3 g2530.t1 PANTHER PTHR22594 ASPARTYL/LYSYL-TRNA SYNTHETASE 44 558 1.4E-257
4 g2530.t1 PANTHER PTHR22594:SF16 ASPARAGINE–TRNA LIGASE, CYTOPLASMIC 44 558 1.4E-257
6 g2530.t1 PRINTS PR01042 Aspartyl-tRNA synthetase signature 306 318 9.2E-14
5 g2530.t1 PRINTS PR01042 Aspartyl-tRNA synthetase signature 322 335 9.2E-14
8 g2530.t1 PRINTS PR01042 Aspartyl-tRNA synthetase signature 473 489 9.2E-14
7 g2530.t1 PRINTS PR01042 Aspartyl-tRNA synthetase signature 513 527 9.2E-14
1 g2530.t1 Pfam PF01336 OB-fold nucleic acid binding domain 138 217 9.6E-11
2 g2530.t1 Pfam PF00152 tRNA synthetases class II (D, K and N) 237 551 3.4E-100
22 g2530.t1 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 256 550 14.807
10 g2530.t1 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 103 222 2.08E-20
9 g2530.t1 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 235 552 1.69E-86
21 g2530.t1 TIGRFAM TIGR00457 asnS: asparagine–tRNA ligase 129 557 7.1E-113

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:0006421 asparaginyl-tRNA aminoacylation BP
GO:0005524 ATP binding MF
GO:0006418 tRNA aminoacylation for protein translation BP
GO:0000166 nucleotide binding MF
GO:0004816 asparagine-tRNA ligase activity MF
GO:0004812 aminoacyl-tRNA ligase activity MF
GO:0003676 nucleic acid binding MF

KEGG

Orthology

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.

Raw TPM values