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.t5 TSS g2530.t5 18488703 18488703
chr_3 g2530 g2530.t5 isoform g2530.t5 18489019 18490766
chr_3 g2530 g2530.t5 exon g2530.t5.exon1 18489019 18490766
chr_3 g2530 g2530.t5 cds g2530.t5.CDS1 18489053 18490609
chr_3 g2530 g2530.t5 TTS g2530.t5 18491463 18491463

Sequences

>g2530.t5 Gene=g2530 Length=1748
TGAGAAAAAACCATTTAAGACAATTTTGCAGGCGATGAGACATGCAGGGAAGGAACCATT
TCCAACTATTTATTCTGATGCAAAAGATGAGAAATCTGAAAGTTTATATGAGCCAGCGGC
TAAATCACAATTAAAGAAAGTAAAGAAACAATGGCTTACAGAGTTACAAAAAATGGCAGA
AAAGTCAAAACGTGATGAAGAAGAAGCTGCTCAAAGAGAGAAAAATTTAGAAGAAGCAAA
GTTGATCAAAATTGCAGAAGATCCATCCTGGCCTGTTGCTAAACAAATAAGAATTAATGA
AGGATTGCAAAATCGTGGCATTCGAGTTAAAATATATGGTTGGATTCATCGTCTTAGACG
TCAAGGAAAGGGTTTGATGTTTGCAACATTACGTGATGGCTATGGCTATTTGCAATGTGT
TTTAAGCGACTTGCTATGTCAAACTTATGAAGGATTATTACTTTCAACTGAATCATCCGT
GCTTTTCTTTGGCACTTTGAAAGAAGTTCCTGAGGGAAAAACTGCACCAGATCAGCATGA
ATTGCATGTTGATTATTATGAAGTAGTAGGTCATTCACCAGCTGGTGGTGCTGATAATTT
ATTGAACGAATTTGCAAATCCAGATGTAATGCTTGACAATCGACATATGATGATTCGTGG
TGAAAACACATCAAAAATATTAAAAATGCGCAGTGTAGTGACTCAAGCTTTTCGTAGTCA
CTTTTATGACAATGGTTACACAGAAGTTTGTCCGCCAACTCTTGTTCAAACACAAGTCGA
AGGAGGCTCAACACTCTTCAAATTTGATTATTTTGGTGAAGAGGCATATTTAACTCAAAG
TTCACAATTATATCTTGAGACATGTATGCCATCACTTGGAGACGTTTTCTGCATTGCACA
AAGTTATCGAGCAGAGCAATCTCGAACAAGAAGACATTTGGCTGAATATAGTCATGTCGA
AGCAGAGCGTGCTTTCATCACGTTTGATGATTTATTAAATTCAATGGAACATTTGATTTG
TGATGTAGTTGATCGTGTTCTAAAGTCACCATATGCTCAACTGGTGAAAGATTTAAATCC
TGATTTCAAGCCACCAAAAAGACCTTTCCGTCGAATGGATTATGCTGAAGCGATTGAATG
GTTGAAAACAAATAATGTAACAAAAGAGGATGGTTCATTTTACGAATTTGGCGAAGACAT
TCCTGAAGCACCTGAACGAAAAATGACCGATACAATTAATGAACCAATTATGCTCTGCCG
ATTTCCAGCTGGAATTAAAGCCTTTTATATGGCTCGTTGTCCTGAAAATGAAGAATTAAC
TGAAAGTGTTGATGTTTTACTGCCAGGTGTTGGAGAAATTATCGGAGGTTCAATGCGTGA
GGCTAACAATGAAAAATTATTAGCCGCATACAAAAAAGAAGGAATTGATCCAACACCATA
TTATTGGTACACTGATCAACGTGTTTATGGAACAACTCCTCATGGTGGTTATGGTCTTGG
ATTAGAACGATTTTTATGCTGGCTTTTGAATCGATATCATATCAGAGAAGTTTGTCTCTA
TCCTCGTTTCTTACAACGTTGCAGACCTTAAATTATTTATATTCGTTTTGAATTGCATTT
ATAATGAGAAATTTCTTAATCTTTATCTCTCACTTTTGCTTACTAAAACATTACTTAAAA
GATGTTTCATTTTAATAAGTTTAAAATAAATTTTTTTATTATAGCTTTTGCAATTCAAAA
ACAATTTT

>g2530.t5 Gene=g2530 Length=518
MRHAGKEPFPTIYSDAKDEKSESLYEPAAKSQLKKVKKQWLTELQKMAEKSKRDEEEAAQ
REKNLEEAKLIKIAEDPSWPVAKQIRINEGLQNRGIRVKIYGWIHRLRRQGKGLMFATLR
DGYGYLQCVLSDLLCQTYEGLLLSTESSVLFFGTLKEVPEGKTAPDQHELHVDYYEVVGH
SPAGGADNLLNEFANPDVMLDNRHMMIRGENTSKILKMRSVVTQAFRSHFYDNGYTEVCP
PTLVQTQVEGGSTLFKFDYFGEEAYLTQSSQLYLETCMPSLGDVFCIAQSYRAEQSRTRR
HLAEYSHVEAERAFITFDDLLNSMEHLICDVVDRVLKSPYAQLVKDLNPDFKPPKRPFRR
MDYAEAIEWLKTNNVTKEDGSFYEFGEDIPEAPERKMTDTINEPIMLCRFPAGIKAFYMA
RCPENEELTESVDVLLPGVGEIIGGSMREANNEKLLAAYKKEGIDPTPYYWYTDQRVYGT
TPHGGYGLGLERFLCWLLNRYHIREVCLYPRFLQRCRP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g2530.t5 CDD cd04323 AsnRS_cyto_like_N 97 180 9.2539E-37
15 g2530.t5 CDD cd00776 AsxRS_core 194 512 6.38048E-146
14 g2530.t5 Coils Coil Coil 30 68 -
11 g2530.t5 Gene3D G3DSA:1.10.10.1430 - 1 47 9.8E-11
13 g2530.t5 Gene3D G3DSA:2.40.50.140 - 68 183 7.2E-26
12 g2530.t5 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 188 518 3.1E-107
17 g2530.t5 MobiDBLite mobidb-lite consensus disorder prediction 1 31 -
3 g2530.t5 PANTHER PTHR22594 ASPARTYL/LYSYL-TRNA SYNTHETASE 11 518 4.2E-257
4 g2530.t5 PANTHER PTHR22594:SF16 ASPARAGINE–TRNA LIGASE, CYTOPLASMIC 11 518 4.2E-257
7 g2530.t5 PRINTS PR01042 Aspartyl-tRNA synthetase signature 266 278 7.1E-14
6 g2530.t5 PRINTS PR01042 Aspartyl-tRNA synthetase signature 282 295 7.1E-14
8 g2530.t5 PRINTS PR01042 Aspartyl-tRNA synthetase signature 433 449 7.1E-14
5 g2530.t5 PRINTS PR01042 Aspartyl-tRNA synthetase signature 473 487 7.1E-14
1 g2530.t5 Pfam PF01336 OB-fold nucleic acid binding domain 98 177 8.6E-11
2 g2530.t5 Pfam PF00152 tRNA synthetases class II (D, K and N) 197 511 2.7E-100
19 g2530.t5 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 216 510 14.807
10 g2530.t5 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 63 182 1.81E-20
9 g2530.t5 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 195 512 1.37E-86
18 g2530.t5 TIGRFAM TIGR00457 asnS: asparagine–tRNA ligase 89 517 5.5E-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