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.t25 TSS g4841.t25 5203197 5203197
chr_2 g4841 g4841.t25 isoform g4841.t25 5203286 5204882
chr_2 g4841 g4841.t25 exon g4841.t25.exon1 5203286 5203403
chr_2 g4841 g4841.t25 cds g4841.t25.CDS1 5203286 5203403
chr_2 g4841 g4841.t25 exon g4841.t25.exon2 5203466 5204462
chr_2 g4841 g4841.t25 cds g4841.t25.CDS2 5203466 5204462
chr_2 g4841 g4841.t25 exon g4841.t25.exon3 5204587 5204697
chr_2 g4841 g4841.t25 cds g4841.t25.CDS3 5204587 5204593
chr_2 g4841 g4841.t25 exon g4841.t25.exon4 5204757 5204882
chr_2 g4841 g4841.t25 TTS g4841.t25 5205040 5205040

Sequences

>g4841.t25 Gene=g4841 Length=1352
ATGGTTTTGGATATTGAGTTCTTCCGTGGTGATAAGGGAAATGACGTGAATAAAGTCCGA
ACTAATCAGGAAAAGAGATTTAAAGATCTGAAGTTAGTAGAAACAGTGATTGAACAAGAT
GCGGAATGGAGACAACGAAGATTTAAAGGCGATCTCTTCAATAAATTGAAAAATTTATGT
AGCAAAGAAATTGGAGAACGTATGAAAAAGAAAGAAGCCGCTGGTAATGAAGATGATCCA
GTTTCAGACGAATTAGTAGCAAAACTTGAAGAACTCAAGATTGATGACTTAAAACCCTTA
ACAATCGCTCAAATTAAAAAAGTACGTACTTTTATCGATGAAGCAATTGTCGAAAATGAG
AAGAAAATACTCGAGACTGAGTCGACTCGAAATAATGCTTTAAGAGAAGTCGGTAATTGG
CTCCACGAGTCTGTTCCTGTTAGCAATGACGAAGATGAGAACGGAATTGAAAGAACATGG
GGTGATTGTGAAATAAAGAAGAAATATTCTCATGTTGATTTAATTCATATGATTGATGGA
ATGAATGGTGAGAAGGGAGCAGTAGTTAGTGGAAATCGTGGATATTTTTTAACCGGAGCA
GCCGTTTTTCTCGAGCAAGCACTTATTCAGCATGCACTTCATATTCTTTTCAACAAAGGC
TATACACCACTTTACACTCCATTCTTTATGCGAAAGGATGTTATGCAGGAAGTAGCACAA
TTGTCTCAATTTGATGAAGAATTATACAAGGTTGTTGGAAAAAATCAAGACAAAGCTGAT
GAAAATGATGAGAAATATTTAATTGCAACTTCAGAACAGCCAATTGCAGCTTATCATCGT
GATGAATGGATTCCAGAAGCTTCATTGCCCATAAAATATGCTGGCTTATCAACTTGTTTT
CGTCAAGAAGTTGGAAGTCACGGTCGCGATACACGTGGCATCTTTCGTGTACATCAGTTT
GAAAAGATTGAACAATTTGTGCTGACATCACCTCACGACAACAAATCATGGGAAATGATG
GATGAAATGATTGGAAACGCTGAGGAGTTTTGTCAATCATTAGGAATTCCTTATCGCATT
GTCAACATTGTTTCAGGCGCACTTAATCATGCAGCAAGATGAATGCAAATATTGATTATG
TGCATATGCTAAATGCAACTATGTGTGCAACTACAAGAGTTATTTGCGCAATTCTTGAAA
CTCATCAAACTGAGACTGGTATTAAGGTTCCAGAAGTATTGCAGAAATACATGCCTGAAA
AATATAAACTTGAAATTCCATTTGTTAAACCAGCTCCAATTGAAGAAGAAGAAAAGAAAA
AGGCAAAGAAGGGCAAAAAAGAAGCAGCATAA

>g4841.t25 Gene=g4841 Length=373
MVLDIEFFRGDKGNDVNKVRTNQEKRFKDLKLVETVIEQDAEWRQRRFKGDLFNKLKNLC
SKEIGERMKKKEAAGNEDDPVSDELVAKLEELKIDDLKPLTIAQIKKVRTFIDEAIVENE
KKILETESTRNNALREVGNWLHESVPVSNDEDENGIERTWGDCEIKKKYSHVDLIHMIDG
MNGEKGAVVSGNRGYFLTGAAVFLEQALIQHALHILFNKGYTPLYTPFFMRKDVMQEVAQ
LSQFDEELYKVVGKNQDKADENDEKYLIATSEQPIAAYHRDEWIPEASLPIKYAGLSTCF
RQEVGSHGRDTRGIFRVHQFEKIEQFVLTSPHDNKSWEMMDEMIGNAEEFCQSLGIPYRI
VNIVSGALNHAAR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g4841.t25 Gene3D G3DSA:1.10.287.40 - 1 138 0.0000000
9 g4841.t25 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 139 373 0.0000000
3 g4841.t25 PANTHER PTHR11778 SERYL-TRNA SYNTHETASE 1 372 0.0000000
12 g4841.t25 PIRSF PIRSF001529 Ser-tRNA_ligase 2 101 0.0000000
13 g4841.t25 PIRSF PIRSF001529 Ser-tRNA_ligase 82 373 0.0000000
6 g4841.t25 PRINTS PR00981 Seryl-tRNA synthetase signature 303 315 0.0000000
5 g4841.t25 PRINTS PR00981 Seryl-tRNA synthetase signature 315 328 0.0000000
4 g4841.t25 PRINTS PR00981 Seryl-tRNA synthetase signature 357 370 0.0000000
2 g4841.t25 Pfam PF02403 Seryl-tRNA synthetase N-terminal domain 2 93 0.0000000
1 g4841.t25 Pfam PF00587 tRNA synthetase class II core domain (G, H, P, S and T) 260 363 0.0000000
11 g4841.t25 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 204 373 14.1350000
8 g4841.t25 SUPERFAMILY SSF46589 tRNA-binding arm 3 146 0.0000006
7 g4841.t25 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 167 372 0.0000000

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