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.t36 TSS g4841.t36 5203877 5203877
chr_2 g4841 g4841.t36 isoform g4841.t36 5203917 5204882
chr_2 g4841 g4841.t36 exon g4841.t36.exon1 5203917 5204697
chr_2 g4841 g4841.t36 cds g4841.t36.CDS1 5204035 5204697
chr_2 g4841 g4841.t36 exon g4841.t36.exon2 5204764 5204882
chr_2 g4841 g4841.t36 cds g4841.t36.CDS2 5204764 5204880
chr_2 g4841 g4841.t36 TTS g4841.t36 5205040 5205040

Sequences

>g4841.t36 Gene=g4841 Length=900
TGGAAATCGTGGATATTTTTTAACCGGAGCAGCCGTTTTTCTCGAGCAAGCACTTATTCA
GCATGCACTTCATATTCTTTTCAACAAAGGCTATACACCACTTTACACTCCATTCTTTAT
GCGAAAGGATGTTATGCAGGAAGTAGCACAATTGTCTCAATTTGATGAAGAATTATACAA
GGTTGTTGGAAAAAATCAAGACAAAGCTGATGAAAATGATGAGAAATATTTAATTGCAAC
TTCAGAACAGCCAATTGCAGCTTATCATCGTGATGAATGGATTCCAGAAGCTTCATTGCC
CATAAAATATGCTGGCTTATCAACTTGTTTTCGTCAAGAAGTTGGAAGTCACGGTCGCGA
TACACGTGGCATCTTTCGTGTACATCAGTTTGAAAAGATTGAACAATTTGTGCTGACATC
ACCTCACGACAACAAATCATGGGAAATGATGGATGAAATGATTGGAAACGCTGAGGAGTT
TTGTCAATCATTAGGAATTCCTTATCGCATTGTCAACATTGTTTCAGGCGCACTTAATCA
TGCAGCGTCAAAGAAACTTGATTTAGAAGCTTGGTTCTGTGGATCAGGCGCTTTTAGAGA
ACTCGTTTCATGCAGCAATTGTCTCGATTATCAAGCTCGTCGTCTTCTCGTTCGTTATGG
AATGACAAAGAAGATGAATGCAAATATTGATTATGTGCATATGCTAAATGCAACTATGTG
TGCAACTACAAGAGTTATTTGCGCAATTCTTGAAACTCATCAAACTGAGACTGGTATTAA
GAAGTATTGCAGAAATACATGCCTGAAAAATATAAACTTGAAATTCCATTTGTTAAACCA
GCTCCAATTGAAGAAGAAGAAAAGAAAAAGGCAAAGAAGGGCAAAAAAGAAGCAGCATAA

>g4841.t36 Gene=g4841 Length=260
MRKDVMQEVAQLSQFDEELYKVVGKNQDKADENDEKYLIATSEQPIAAYHRDEWIPEASL
PIKYAGLSTCFRQEVGSHGRDTRGIFRVHQFEKIEQFVLTSPHDNKSWEMMDEMIGNAEE
FCQSLGIPYRIVNIVSGALNHAASKKLDLEAWFCGSGAFRELVSCSNCLDYQARRLLVRY
GMTKKMNANIDYVHMLNATMCATTRVICAILETHQTETGIKKYCRNTCLKNINLKFHLLN
QLQLKKKKRKRQRRAKKKQH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g4841.t36 Coils Coil Coil 239 259 -
9 g4841.t36 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 1 233 3.3E-95
2 g4841.t36 PANTHER PTHR11778 SERYL-TRNA SYNTHETASE 1 220 1.2E-111
7 g4841.t36 PRINTS PR00981 Seryl-tRNA synthetase signature 74 86 1.6E-30
3 g4841.t36 PRINTS PR00981 Seryl-tRNA synthetase signature 86 99 1.6E-30
4 g4841.t36 PRINTS PR00981 Seryl-tRNA synthetase signature 128 141 1.6E-30
5 g4841.t36 PRINTS PR00981 Seryl-tRNA synthetase signature 145 161 1.6E-30
6 g4841.t36 PRINTS PR00981 Seryl-tRNA synthetase signature 163 179 1.6E-30
1 g4841.t36 Pfam PF00587 tRNA synthetase class II core domain (G, H, P, S and T) 31 213 5.1E-39
11 g4841.t36 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 1 214 14.345
8 g4841.t36 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 1 221 9.66E-61

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.

Raw TPM values