General information for g4841.t26
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Serine–tRNA ligase, cytoplasmic.
Parent gene
- The parent gene g4841 is located on chr_2: 5203985..5205147 (+ strand)
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.t26 | TSS | g4841.t26 | 5203197 | 5203197 |
| chr_2 | g4841 | g4841.t26 | isoform | g4841.t26 | 5203286 | 5204882 |
| chr_2 | g4841 | g4841.t26 | exon | g4841.t26.exon1 | 5203286 | 5203403 |
| chr_2 | g4841 | g4841.t26 | cds | g4841.t26.CDS1 | 5203286 | 5203403 |
| chr_2 | g4841 | g4841.t26 | exon | g4841.t26.exon2 | 5203604 | 5204697 |
| chr_2 | g4841 | g4841.t26 | cds | g4841.t26.CDS2 | 5203604 | 5204697 |
| chr_2 | g4841 | g4841.t26 | exon | g4841.t26.exon3 | 5204757 | 5204882 |
| chr_2 | g4841 | g4841.t26 | cds | g4841.t26.CDS3 | 5204757 | 5204882 |
| chr_2 | g4841 | g4841.t26 | TTS | g4841.t26 | 5205040 | 5205040 |
Sequences
>g4841.t26 Gene=g4841 Length=1338
ATGGTTTTGGATATTGAGTTCTTCCGTGGTGATAAGGGAAATGACGTGAATAAAGTCCGA
ACTAATCAGGAAAAGAGATTTAAAGATCTGAAGTTAGTAGAAACAGTGATTGAACAAGTA
GCAAAACTTGAAGAACTCAAGATTGATGACTTAAAACCCTTAACAATCGCTCAAATTAAA
AAAGTACGTACTTTTATCGATGAAGCAATTGTCGAAAATGAGAAGAAAATACTCGAGACT
GAGTCGACTCGAAATAATGCTTTAAGAGAAGTCGGTAATTGGCTCCACGAGTCTGTTCCT
GTTAGCAATGACGAAGATGAGAACGGAATTGAAAGAACATGGGGTGATTGTGAAATAAAG
AAGAAATATTCTCATGTTGATTTAATTCATATGATTGATGGAATGAATGGTGAGAAGGGA
GCAGTAGTTAGTGGAAATCGTGGATATTTTTTAACCGGAGCAGCCGTTTTTCTCGAGCAA
GCACTTATTCAGCATGCACTTCATATTCTTTTCAACAAAGGCTATACACCACTTTACACT
CCATTCTTTATGCGAAAGGATGTTATGCAGGAAGTAGCACAATTGTCTCAATTTGATGAA
GAATTATACAAGGTTGTTGGAAAAAATCAAGACAAAGCTGATGAAAATGATGAGAAATAT
TTAATTGCAACTTCAGAACAGCCAATTGCAGCTTATCATCGTGATGAATGGATTCCAGAA
GCTTCATTGCCCATAAAATATGCTGGCTTATCAACTTGTTTTCGTCAAGAAGTTGGAAGT
CACGGTCGCGATACACGTGGCATCTTTCGTGTACATCAGTTTGAAAAGATTGAACAATTT
GTGCTGACATCACCTCACGACAACAAATCATGGGAAATGATGGATGAAATGATTGGAAAC
GCTGAGGAGTTTTGTCAATCATTAGGAATTCCTTATCGCATTGTCAACATTGTTTCAGGC
GCACTTAATCATGCAGCGTCAAAGAAACTTGATTTAGAAGCTTGGTTCTGTGGATCAGGC
GCTTTTAGAGAACTCGTTTCATGCAGCAATTGTCTCGATTATCAAGCTCGTCGTCTTCTC
GTTCGTTATGGAATGACAAAGAAGATGAATGCAAATATTGATTATGTGCATATGCTAAAT
GCAACTATGTGTGCAACTACAAGAGTTATTTGCGCAATTCTTGAAACTCATCAAACTGAG
ACTGGTATTAAGGTTCCAGAAGTATTGCAGAAATACATGCCTGAAAAATATAAACTTGAA
ATTCCATTTGTTAAACCAGCTCCAATTGAAGAAGAAGAAAAGAAAAAGGCAAAGAAGGGC
AAAAAAGAAGCAGCATAA
>g4841.t26 Gene=g4841 Length=445
MVLDIEFFRGDKGNDVNKVRTNQEKRFKDLKLVETVIEQVAKLEELKIDDLKPLTIAQIK
KVRTFIDEAIVENEKKILETESTRNNALREVGNWLHESVPVSNDEDENGIERTWGDCEIK
KKYSHVDLIHMIDGMNGEKGAVVSGNRGYFLTGAAVFLEQALIQHALHILFNKGYTPLYT
PFFMRKDVMQEVAQLSQFDEELYKVVGKNQDKADENDEKYLIATSEQPIAAYHRDEWIPE
ASLPIKYAGLSTCFRQEVGSHGRDTRGIFRVHQFEKIEQFVLTSPHDNKSWEMMDEMIGN
AEEFCQSLGIPYRIVNIVSGALNHAASKKLDLEAWFCGSGAFRELVSCSNCLDYQARRLL
VRYGMTKKMNANIDYVHMLNATMCATTRVICAILETHQTETGIKVPEVLQKYMPEKYKLE
IPFVKPAPIEEEEKKKAKKGKKEAA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g4841.t26 | CDD | cd00770 | SerRS_core | 107 | 413 | 0.000 |
| 11 | g4841.t26 | Gene3D | G3DSA:1.10.287.40 | - | 1 | 39 | 0.000 |
| 10 | g4841.t26 | Gene3D | G3DSA:1.10.287.40 | - | 40 | 92 | 0.000 |
| 9 | g4841.t26 | Gene3D | G3DSA:3.30.930.10 | Bira Bifunctional Protein; Domain 2 | 93 | 429 | 0.000 |
| 2 | g4841.t26 | PANTHER | PTHR11778 | SERYL-TRNA SYNTHETASE | 1 | 424 | 0.000 |
| 12 | g4841.t26 | PIRSF | PIRSF001529 | Ser-tRNA_ligase | 2 | 422 | 0.000 |
| 6 | g4841.t26 | PRINTS | PR00981 | Seryl-tRNA synthetase signature | 257 | 269 | 0.000 |
| 7 | g4841.t26 | PRINTS | PR00981 | Seryl-tRNA synthetase signature | 269 | 282 | 0.000 |
| 5 | g4841.t26 | PRINTS | PR00981 | Seryl-tRNA synthetase signature | 311 | 324 | 0.000 |
| 3 | g4841.t26 | PRINTS | PR00981 | Seryl-tRNA synthetase signature | 328 | 344 | 0.000 |
| 4 | g4841.t26 | PRINTS | PR00981 | Seryl-tRNA synthetase signature | 346 | 362 | 0.000 |
| 1 | g4841.t26 | Pfam | PF00587 | tRNA synthetase class II core domain (G, H, P, S and T) | 214 | 396 | 0.000 |
| 15 | g4841.t26 | ProSiteProfiles | PS50862 | Aminoacyl-transfer RNA synthetases class-II family profile. | 158 | 406 | 20.272 |
| 8 | g4841.t26 | SUPERFAMILY | SSF55681 | Class II aaRS and biotin synthetases | 121 | 414 | 0.000 |
| 14 | g4841.t26 | TIGRFAM | TIGR00414 | serS: serine–tRNA ligase | 17 | 413 | 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 transcript has been annotated with K01875 (seryl-tRNA synthetase)
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.
