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.t31 TSS g4841.t31 5203197 5203197
chr_2 g4841 g4841.t31 isoform g4841.t31 5203484 5204882
chr_2 g4841 g4841.t31 exon g4841.t31.exon1 5203484 5204701
chr_2 g4841 g4841.t31 cds g4841.t31.CDS1 5203549 5204701
chr_2 g4841 g4841.t31 exon g4841.t31.exon2 5204757 5204882
chr_2 g4841 g4841.t31 cds g4841.t31.CDS2 5204757 5204788
chr_2 g4841 g4841.t31 TTS g4841.t31 5205040 5205040

Sequences

>g4841.t31 Gene=g4841 Length=1344
GAAGATTTAAAGGCGATCTCTTCAATAAATTGAAAAATTTATGTAGCAAAGAAATTGGAG
AACGTATGAAAAAGAAAGAAGCCGCTGGTAATGAAGATGATCCAGTTTCAGACGAATTAG
TAGCAAAACTTGAAGAACTCAAGATTGATGACTTAAAACCCTTAACAATCGCTCAAATTA
AAAAAGTACGTACTTTTATCGATGAAGCAATTGTCGAAAATGAGAAGAAAATACTCGAGA
CTGAGTCGACTCGAAATAATGCTTTAAGAGAAGTCGGTAATTGGCTCCACGAGTCTGTTC
CTGTTAGCAATGACGAAGATGAGAACGGAATTGAAAGAACATGGGGTGATTGTGAAATAA
AGAAGAAATATTCTCATGTTGATTTAATTCATATGATTGATGGAATGAATGGTGAGAAGG
GAGCAGTAGTTAGTGGAAATCGTGGATATTTTTTAACCGGAGCAGCCGTTTTTCTCGAGC
AAGCACTTATTCAGCATGCACTTCATATTCTTTTCAACAAAGGCTATACACCACTTTACA
CTCCATTCTTTATGCGAAAGGATGTTATGCAGGAAGTAGCACAATTGTCTCAATTTGATG
AAGAATTATACAAGGTTGTTGGAAAAAATCAAGACAAAGCTGATGAAAATGATGAGAAAT
ATTTAATTGCAACTTCAGAACAGCCAATTGCAGCTTATCATCGTGATGAATGGATTCCAG
AAGCTTCATTGCCCATAAAATATGCTGGCTTATCAACTTGTTTTCGTCAAGAAGTTGGAA
GTCACGGTCGCGATACACGTGGCATCTTTCGTGTACATCAGTTTGAAAAGATTGAACAAT
TTGTGCTGACATCACCTCACGACAACAAATCATGGGAAATGATGGATGAAATGATTGGAA
ACGCTGAGGAGTTTTGTCAATCATTAGGAATTCCTTATCGCATTGTCAACATTGTTTCAG
GCGCACTTAATCATGCAGCGTCAAAGAAACTTGATTTAGAAGCTTGGTTCTGTGGATCAG
GCGCTTTTAGAGAACTCGTTTCATGCAGCAATTGTCTCGATTATCAAGCTCGTCGTCTTC
TCGTTCGTTATGGAATGACAAAGAAGATGAATGCAAATATTGATTATGTGCATATGCTAA
ATGCAACTATGTGTGCAACTACAAGAGTTATTTGCGCAATTCTTGAAACTCATCAAACTG
AGACTGGTATTAAGGTGAGTTCCAGAAGTATTGCAGAAATACATGCCTGAAAAATATAAA
CTTGAAATTCCATTTGTTAAACCAGCTCCAATTGAAGAAGAAGAAAAGAAAAAGGCAAAG
AAGGGCAAAAAAGAAGCAGCATAA

>g4841.t31 Gene=g4841 Length=394
MKKKEAAGNEDDPVSDELVAKLEELKIDDLKPLTIAQIKKVRTFIDEAIVENEKKILETE
STRNNALREVGNWLHESVPVSNDEDENGIERTWGDCEIKKKYSHVDLIHMIDGMNGEKGA
VVSGNRGYFLTGAAVFLEQALIQHALHILFNKGYTPLYTPFFMRKDVMQEVAQLSQFDEE
LYKVVGKNQDKADENDEKYLIATSEQPIAAYHRDEWIPEASLPIKYAGLSTCFRQEVGSH
GRDTRGIFRVHQFEKIEQFVLTSPHDNKSWEMMDEMIGNAEEFCQSLGIPYRIVNIVSGA
LNHAASKKLDLEAWFCGSGAFRELVSCSNCLDYQARRLLVRYGMTKKMNANIDYVHMLNA
TMCATTRVICAILETHQTETGIKVSSRSIAEIHA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g4841.t31 CDD cd00770 SerRS_core 86 384 0.000
10 g4841.t31 Gene3D G3DSA:1.10.287.40 - 1 71 0.000
9 g4841.t31 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 72 387 0.000
2 g4841.t31 PANTHER PTHR11778 SERYL-TRNA SYNTHETASE 13 384 0.000
11 g4841.t31 PIRSF PIRSF001529 Ser-tRNA_ligase 3 388 0.000
6 g4841.t31 PRINTS PR00981 Seryl-tRNA synthetase signature 236 248 0.000
3 g4841.t31 PRINTS PR00981 Seryl-tRNA synthetase signature 248 261 0.000
5 g4841.t31 PRINTS PR00981 Seryl-tRNA synthetase signature 290 303 0.000
4 g4841.t31 PRINTS PR00981 Seryl-tRNA synthetase signature 307 323 0.000
7 g4841.t31 PRINTS PR00981 Seryl-tRNA synthetase signature 325 341 0.000
1 g4841.t31 Pfam PF00587 tRNA synthetase class II core domain (G, H, P, S and T) 193 375 0.000
14 g4841.t31 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 137 391 18.317
8 g4841.t31 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 100 384 0.000
13 g4841.t31 TIGRFAM TIGR00414 serS: serine–tRNA ligase 35 381 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

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. There were no conditions that were differentially expressed