Gene loci information

Transcript annotation

  • This transcript has been annotated as Serine–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_2 g4841 g4841.t37 TSS g4841.t37 5203877 5203877
chr_2 g4841 g4841.t37 isoform g4841.t37 5203985 5204882
chr_2 g4841 g4841.t37 exon g4841.t37.exon1 5203985 5204520
chr_2 g4841 g4841.t37 cds g4841.t37.CDS1 5204035 5204520
chr_2 g4841 g4841.t37 exon g4841.t37.exon2 5204686 5204882
chr_2 g4841 g4841.t37 cds g4841.t37.CDS2 5204686 5204721
chr_2 g4841 g4841.t37 TTS g4841.t37 5205040 5205040

Sequences

>g4841.t37 Gene=g4841 Length=733
TTCATATTCTTTTCAACAAAGGCTATACACCACTTTACACTCCATTCTTTATGCGAAAGG
ATGTTATGCAGGAAGTAGCACAATTGTCTCAATTTGATGAAGAATTATACAAGGTTGTTG
GAAAAAATCAAGACAAAGCTGATGAAAATGATGAGAAATATTTAATTGCAACTTCAGAAC
AGCCAATTGCAGCTTATCATCGTGATGAATGGATTCCAGAAGCTTCATTGCCCATAAAAT
ATGCTGGCTTATCAACTTGTTTTCGTCAAGAAGTTGGAAGTCACGGTCGCGATACACGTG
GCATCTTTCGTGTACATCAGTTTGAAAAGATTGAACAATTTGTGCTGACATCACCTCACG
ACAACAAATCATGGGAAATGATGGATGAAATGATTGGAAACGCTGAGGAGTTTTGTCAAT
CATTAGGAATTCCTTATCGCATTGTCAACATTGTTTCAGGCGCACTTAATCATGCAGCGT
CAAAGAAACTTGATTTAGAAGCTTGGTTCTGTGGATCAGGCGCTTTTAGAGAACTCACTG
GTATTAAGGTGAGTGACAAATTGAACTGTTAGTATTTACTGAATTTAAATATGATTATCC
ATTTTAGGTTCCAGAAGTATTGCAGAAATACATGCCTGAAAAATATAAACTTGAAATTCC
ATTTGTTAAACCAGCTCCAATTGAAGAAGAAGAAAAGAAAAAGGCAAAGAAGGGCAAAAA
AGAAGCAGCATAA

>g4841.t37 Gene=g4841 Length=173
MRKDVMQEVAQLSQFDEELYKVVGKNQDKADENDEKYLIATSEQPIAAYHRDEWIPEASL
PIKYAGLSTCFRQEVGSHGRDTRGIFRVHQFEKIEQFVLTSPHDNKSWEMMDEMIGNAEE
FCQSLGIPYRIVNIVSGALNHAASKKLDLEAWFCGSGAFRELTGIKVSDKLNC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g4841.t37 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 1 169 0.000
2 g4841.t37 PANTHER PTHR11778 SERYL-TRNA SYNTHETASE 1 163 0.000
6 g4841.t37 PRINTS PR00981 Seryl-tRNA synthetase signature 74 86 0.000
3 g4841.t37 PRINTS PR00981 Seryl-tRNA synthetase signature 86 99 0.000
4 g4841.t37 PRINTS PR00981 Seryl-tRNA synthetase signature 128 141 0.000
5 g4841.t37 PRINTS PR00981 Seryl-tRNA synthetase signature 145 161 0.000
1 g4841.t37 Pfam PF00587 tRNA synthetase class II core domain (G, H, P, S and T) 31 167 0.000
9 g4841.t37 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 1 164 12.117
7 g4841.t37 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 1 165 0.000

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:0004828 serine-tRNA ligase activity MF
GO:0006418 tRNA aminoacylation for protein translation BP
GO:0000166 nucleotide binding MF
GO:0004812 aminoacyl-tRNA ligase activity MF
GO:0006434 seryl-tRNA aminoacylation BP

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