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.t24 TSS g4841.t24 5203197 5203197
chr_2 g4841 g4841.t24 isoform g4841.t24 5203286 5204882
chr_2 g4841 g4841.t24 exon g4841.t24.exon1 5203286 5203403
chr_2 g4841 g4841.t24 cds g4841.t24.CDS1 5203286 5203403
chr_2 g4841 g4841.t24 exon g4841.t24.exon2 5203466 5203779
chr_2 g4841 g4841.t24 cds g4841.t24.CDS2 5203466 5203779
chr_2 g4841 g4841.t24 exon g4841.t24.exon3 5203849 5204697
chr_2 g4841 g4841.t24 cds g4841.t24.CDS3 5203849 5204697
chr_2 g4841 g4841.t24 exon g4841.t24.exon4 5204757 5204882
chr_2 g4841 g4841.t24 cds g4841.t24.CDS4 5204757 5204882
chr_2 g4841 g4841.t24 TTS g4841.t24 5205040 5205040

Sequences

>g4841.t24 Gene=g4841 Length=1407
ATGGTTTTGGATATTGAGTTCTTCCGTGGTGATAAGGGAAATGACGTGAATAAAGTCCGA
ACTAATCAGGAAAAGAGATTTAAAGATCTGAAGTTAGTAGAAACAGTGATTGAACAAGAT
GCGGAATGGAGACAACGAAGATTTAAAGGCGATCTCTTCAATAAATTGAAAAATTTATGT
AGCAAAGAAATTGGAGAACGTATGAAAAAGAAAGAAGCCGCTGGTAATGAAGATGATCCA
GTTTCAGACGAATTAGTAGCAAAACTTGAAGAACTCAAGATTGATGACTTAAAACCCTTA
ACAATCGCTCAAATTAAAAAAGTACGTACTTTTATCGATGAAGCAATTGTCGAAAATGAG
AAGAAAATACTCGAGACTGAGTCGACTCGAAATAATGCTTTAAGAGAAGTCGGTAATTGG
CTCCACGAGTCTAAATATTCTCATGTTGATTTAATTCATATGATTGATGGAATGAATGGT
GAGAAGGGAGCAGTAGTTAGTGGAAATCGTGGATATTTTTTAACCGGAGCAGCCGTTTTT
CTCGAGCAAGCACTTATTCAGCATGCACTTCATATTCTTTTCAACAAAGGCTATACACCA
CTTTACACTCCATTCTTTATGCGAAAGGATGTTATGCAGGAAGTAGCACAATTGTCTCAA
TTTGATGAAGAATTATACAAGGTTGTTGGAAAAAATCAAGACAAAGCTGATGAAAATGAT
GAGAAATATTTAATTGCAACTTCAGAACAGCCAATTGCAGCTTATCATCGTGATGAATGG
ATTCCAGAAGCTTCATTGCCCATAAAATATGCTGGCTTATCAACTTGTTTTCGTCAAGAA
GTTGGAAGTCACGGTCGCGATACACGTGGCATCTTTCGTGTACATCAGTTTGAAAAGATT
GAACAATTTGTGCTGACATCACCTCACGACAACAAATCATGGGAAATGATGGATGAAATG
ATTGGAAACGCTGAGGAGTTTTGTCAATCATTAGGAATTCCTTATCGCATTGTCAACATT
GTTTCAGGCGCACTTAATCATGCAGCGTCAAAGAAACTTGATTTAGAAGCTTGGTTCTGT
GGATCAGGCGCTTTTAGAGAACTCGTTTCATGCAGCAATTGTCTCGATTATCAAGCTCGT
CGTCTTCTCGTTCGTTATGGAATGACAAAGAAGATGAATGCAAATATTGATTATGTGCAT
ATGCTAAATGCAACTATGTGTGCAACTACAAGAGTTATTTGCGCAATTCTTGAAACTCAT
CAAACTGAGACTGGTATTAAGGTTCCAGAAGTATTGCAGAAATACATGCCTGAAAAATAT
AAACTTGAAATTCCATTTGTTAAACCAGCTCCAATTGAAGAAGAAGAAAAGAAAAAGGCA
AAGAAGGGCAAAAAAGAAGCAGCATAA

>g4841.t24 Gene=g4841 Length=468
MVLDIEFFRGDKGNDVNKVRTNQEKRFKDLKLVETVIEQDAEWRQRRFKGDLFNKLKNLC
SKEIGERMKKKEAAGNEDDPVSDELVAKLEELKIDDLKPLTIAQIKKVRTFIDEAIVENE
KKILETESTRNNALREVGNWLHESKYSHVDLIHMIDGMNGEKGAVVSGNRGYFLTGAAVF
LEQALIQHALHILFNKGYTPLYTPFFMRKDVMQEVAQLSQFDEELYKVVGKNQDKADEND
EKYLIATSEQPIAAYHRDEWIPEASLPIKYAGLSTCFRQEVGSHGRDTRGIFRVHQFEKI
EQFVLTSPHDNKSWEMMDEMIGNAEEFCQSLGIPYRIVNIVSGALNHAASKKLDLEAWFC
GSGAFRELVSCSNCLDYQARRLLVRYGMTKKMNANIDYVHMLNATMCATTRVICAILETH
QTETGIKVPEVLQKYMPEKYKLEIPFVKPAPIEEEEKKKAKKGKKEAA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g4841.t24 CDD cd00770 SerRS_core 146 436 1.36396E-174
13 g4841.t24 Coils Coil Coil 458 468 -
12 g4841.t24 Gene3D G3DSA:1.10.287.40 - 2 107 3.3E-22
11 g4841.t24 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2 116 452 1.3E-130
3 g4841.t24 PANTHER PTHR11778 SERYL-TRNA SYNTHETASE 1 447 1.1E-164
14 g4841.t24 PIRSF PIRSF001529 Ser-tRNA_ligase 2 445 2.3E-132
6 g4841.t24 PRINTS PR00981 Seryl-tRNA synthetase signature 280 292 1.9E-29
4 g4841.t24 PRINTS PR00981 Seryl-tRNA synthetase signature 292 305 1.9E-29
5 g4841.t24 PRINTS PR00981 Seryl-tRNA synthetase signature 334 347 1.9E-29
8 g4841.t24 PRINTS PR00981 Seryl-tRNA synthetase signature 351 367 1.9E-29
7 g4841.t24 PRINTS PR00981 Seryl-tRNA synthetase signature 369 385 1.9E-29
2 g4841.t24 Pfam PF02403 Seryl-tRNA synthetase N-terminal domain 2 93 1.6E-13
1 g4841.t24 Pfam PF00587 tRNA synthetase class II core domain (G, H, P, S and T) 237 419 2.5E-38
17 g4841.t24 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile. 181 429 20.272
10 g4841.t24 SUPERFAMILY SSF46589 tRNA-binding arm 3 91 3.87E-5
9 g4841.t24 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases 143 437 1.14E-77
16 g4841.t24 TIGRFAM TIGR00414 serS: serine–tRNA ligase 12 436 1.9E-117

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