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.t4 TSS g2530.t4 18488703 18488703
chr_3 g2530 g2530.t4 isoform g2530.t4 18488758 18490609
chr_3 g2530 g2530.t4 exon g2530.t4.exon1 18488758 18488791
chr_3 g2530 g2530.t4 cds g2530.t4.CDS1 18488758 18488791
chr_3 g2530 g2530.t4 exon g2530.t4.exon2 18488967 18489927
chr_3 g2530 g2530.t4 cds g2530.t4.CDS2 18488967 18489927
chr_3 g2530 g2530.t4 exon g2530.t4.exon3 18489984 18490609
chr_3 g2530 g2530.t4 cds g2530.t4.CDS3 18489984 18490005
chr_3 g2530 g2530.t4 TTS g2530.t4 18491463 18491463

Sequences

>g2530.t4 Gene=g2530 Length=1621
ATGGCTACAGAAGCTCTAGAAAAACTGTCGCTAAGTGAACTATATACATCTGAGAAACGT
GGTAGTGATGAGACGGGAGATGGAAGTGAGAAAAAACCATTTAAGACAATTTTGCAGGCG
ATGAGACATGCAGGGAAGGAACCATTTCCAACTATTTATTCTGATGCAAAAGATGAGAAA
TCTGAAAGTTTATATGAGCCAGCGGCTAAATCACAATTAAAGAAAGTAAAGAAACAATGG
CTTACAGAGTTACAAAAAATGGCAGAAAAGTCAAAACGTGATGAAGAAGAAGCTGCTCAA
AGAGAGAAAAATTTAGAAGAAGCAAAGTTGATCAAAATTGCAGAAGATCCATCCTGGCCT
GTTGCTAAACAAATAAGAATTAATGAAGGATTGCAAAATCGTGGCATTCGAGTTAAAATA
TATGGTTGGATTCATCGTCTTAGACGTCAAGGAAAGGGTTTGATGTTTGCAACATTACGT
GATGGCTATGGCTATTTGCAATGTGTTTTAAGCGACTTGCTATGTCAAACTTATGAAGGA
TTATTACTTTCAACTGAATCATCCGTGCTTTTCTTTGGCACTTTGAAAGAAGTTCCTGAG
GGAAAAACTGCACCAGATCAGCATGAATTGCATGTTGATTATTATGAAGTAGTAGGTCAT
TCACCAGCTGGTGGTGCTGATAATTTATTGAACGAATTTGCAAATCCAGATGTAATGCTT
GACAATCGACATATGATGATTCGTGGTGAAAACACATCAAAAATATTAAAAATGCGCAGT
GTAGTGACTCAAGCTTTTCGTAGTCACTTTTATGACAATGGTTACACAGAAGTTTGTCCG
CCAACTCTTGTTCAAACACAAGTCGAAGGAGGCTCAACACTCTTCAAATTTGATTATTTT
GGTGAAGAGGCATATTTAACTCAAAGTTCACAATTATATCTTGAGACATGTATGCCATCA
CTTGGAGACGTTTTCTGCATTGCACAAAGTTATCGAGCGTGCTTTCATCACGTTTGATGA
TTTATTAAATTCAATGGAACATTTGATTTGTGATGTAGTTGATCGTGTTCTAAAGTCACC
ATATGCTCAACTGGTGAAAGATTTAAATCCTGATTTCAAGCCACCAAAAAGACCTTTCCG
TCGAATGGATTATGCTGAAGCGATTGAATGGTTGAAAACAAATAATGTAACAAAAGAGGA
TGGTTCATTTTACGAATTTGGCGAAGACATTCCTGAAGCACCTGAACGAAAAATGACCGA
TACAATTAATGAACCAATTATGCTCTGCCGATTTCCAGCTGGAATTAAAGCCTTTTATAT
GGCTCGTTGTCCTGAAAATGAAGAATTAACTGAAAGTGTTGATGTTTTACTGCCAGGTGT
TGGAGAAATTATCGGAGGTTCAATGCGTGAGGCTAACAATGAAAAATTATTAGCCGCATA
CAAAAAAGAAGGAATTGATCCAACACCATATTATTGGTACACTGATCAACGTGTTTATGG
AACAACTCCTCATGGTGGTTATGGTCTTGGATTAGAACGATTTTTATGCTGGCTTTTGAA
TCGATATCATATCAGAGAAGTTTGTCTCTATCCTCGTTTCTTACAACGTTGCAGACCTTA
A

>g2530.t4 Gene=g2530 Length=338
MATEALEKLSLSELYTSEKRGSDETGDGSEKKPFKTILQAMRHAGKEPFPTIYSDAKDEK
SESLYEPAAKSQLKKVKKQWLTELQKMAEKSKRDEEEAAQREKNLEEAKLIKIAEDPSWP
VAKQIRINEGLQNRGIRVKIYGWIHRLRRQGKGLMFATLRDGYGYLQCVLSDLLCQTYEG
LLLSTESSVLFFGTLKEVPEGKTAPDQHELHVDYYEVVGHSPAGGADNLLNEFANPDVML
DNRHMMIRGENTSKILKMRSVVTQAFRSHFYDNGYTEVCPPTLVQTQVEGGSTLFKFDYF
GEEAYLTQSSQLYLETCMPSLGDVFCIAQSYRACFHHV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g2530.t4 CDD cd04323 AsnRS_cyto_like_N 137 220 5.4318E-38
14 g2530.t4 Coils Coil Coil 70 108 -
11 g2530.t4 Gene3D G3DSA:1.10.10.1430 - 10 87 8.5E-32
13 g2530.t4 Gene3D G3DSA:2.40.50.140 - 107 223 3.2E-26
12 g2530.t4 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 229 334 2.9E-29
7 g2530.t4 MobiDBLite mobidb-lite consensus disorder prediction 1 34 -
8 g2530.t4 MobiDBLite mobidb-lite consensus disorder prediction 13 31 -
10 g2530.t4 MobiDBLite mobidb-lite consensus disorder prediction 48 71 -
9 g2530.t4 MobiDBLite mobidb-lite consensus disorder prediction 52 71 -
3 g2530.t4 PANTHER PTHR22594 ASPARTYL/LYSYL-TRNA SYNTHETASE 43 333 3.0E-116
4 g2530.t4 PANTHER PTHR22594:SF16 ASPARAGINE–TRNA LIGASE, CYTOPLASMIC 43 333 3.0E-116
1 g2530.t4 Pfam PF01336 OB-fold nucleic acid binding domain 138 217 4.3E-11
2 g2530.t4 Pfam PF00152 tRNA synthetases class II (D, K and N) 237 333 1.1E-29
6 g2530.t4 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 103 222 8.08E-21
5 g2530.t4 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 235 333 5.39E-25

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.

Raw TPM values