General information for g12975.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Serine–tRNA ligase, mitochondrial.
Parent gene
- The parent gene g12975 is located on chr_1: 27284250..27285028 (- 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_1 | g12975 | g12975.t1 | TTS | g12975.t1 | 27282782 | 27282782 |
| chr_1 | g12975 | g12975.t1 | isoform | g12975.t1 | 27282888 | 27284250 |
| chr_1 | g12975 | g12975.t1 | exon | g12975.t1.exon1 | 27282888 | 27283676 |
| chr_1 | g12975 | g12975.t1 | cds | g12975.t1.CDS1 | 27282888 | 27283676 |
| chr_1 | g12975 | g12975.t1 | exon | g12975.t1.exon2 | 27283732 | 27284250 |
| chr_1 | g12975 | g12975.t1 | cds | g12975.t1.CDS2 | 27283732 | 27284250 |
| chr_1 | g12975 | g12975.t1 | TSS | g12975.t1 | 27284298 | 27284298 |
Sequences
>g12975.t1 Gene=g12975 Length=1308
ATGAACTGTATAAGACAATTAAGACTTTTAAGAACTTATAATACATCGTATTATTTGAGA
AATAAAGCTGCCAGCAAATGTCAAGATAAGATAGAAGAACGTCAACATAAATTTCAATTA
TCAGAACCGATTCTAAATGAAAAATATTTGCTTGATCCAAAAAATGCTGCGAAAATAAGT
GAAAACTCTTTAATGAGGAAAGGAATTGGTGATATATATTTAGTGCATGAAATAAATAAT
AAATTGAAAGATGAATCATTAAATCCTGACGAAAGACGAGACCTTGAAAGTCAATTAAAA
AATGAGTTGAAGAAAATTCCAAATGATACACATCCAGCAGTAAGAAACTATGGCGAAGAA
CCGAAAGTAGTAGCATTATTCAATAAAGAACCAGAGTTTAAACATAAAGTATATGAATTT
TCAGAAATATGCAGAAAATTAAATATTCTTAGGACTGATCATTTAGGAAACTTTGCAGGA
CATAAAAGCTACTACTTAATGAACGATTTAGCAGAGTTGGAGCAAGCACTTATCAGATAT
ACTCTCTCAGAAATTCTTCAACATGGCTTTAACTTAATTTCGGTTCCTGACATTCTACCA
GCTGAAGTGATAAAATCTTGTGGCATGCAAACTGATGGTGATAGAACACAAGTTTATCGT
TTACTACCTTCAAATCTTTGTCTCTCTGGTACTTCTGAAATGGCACTAGCTGGATATTTT
GCTGGATCAAAGCTCTCACAGAAAGAATTGCCAATTAAAGTTACTGCAGTTAGTCGATGT
TTTAGAGCTGAAACATCAGGAACAACTGAAGAGAGAGGCATTTATCGTGTTCATCAATTT
ACAAAAGTAGAAATGTTTTCAGTATGTAGTCCAGCACAATCGGAAGATATTTTAAATGAG
TTTAAAGAAATTGAAATTGCTCTATTCAATAAACTTGGATTGCATTTTAAATTGCTTGAC
ATGCCACCTCATGAACTCGGTGCACCTGCTTATCGAAAATATGATATAGAAACTTTTATG
CCAGGTAGAAAAATATGGGGTGAAATTTCAAGTTGTAGCAACTGTACAGATTATCAATCG
AGAAGACTAAATATAACAATAGATGAAAGTGCTGAATTTGCACATACAGTTAATGGTACG
GCATGTGCAATACCTAGAATGTTGATTGCAATTATAGAAAGCTTTCAAAATGAAAAAGGT
TTTATCGAAATTCCAAAAGTACTTCAACCTTATATGAAGAAAGATAAAATTGTCAAACAA
AAAGTAATTCCAGAATTGAAGCTAATTAAACATGCAATAAAGAGCTAA
>g12975.t1 Gene=g12975 Length=435
MNCIRQLRLLRTYNTSYYLRNKAASKCQDKIEERQHKFQLSEPILNEKYLLDPKNAAKIS
ENSLMRKGIGDIYLVHEINNKLKDESLNPDERRDLESQLKNELKKIPNDTHPAVRNYGEE
PKVVALFNKEPEFKHKVYEFSEICRKLNILRTDHLGNFAGHKSYYLMNDLAELEQALIRY
TLSEILQHGFNLISVPDILPAEVIKSCGMQTDGDRTQVYRLLPSNLCLSGTSEMALAGYF
AGSKLSQKELPIKVTAVSRCFRAETSGTTEERGIYRVHQFTKVEMFSVCSPAQSEDILNE
FKEIEIALFNKLGLHFKLLDMPPHELGAPAYRKYDIETFMPGRKIWGEISSCSNCTDYQS
RRLNITIDESAEFAHTVNGTACAIPRMLIAIIESFQNEKGFIEIPKVLQPYMKKDKIVKQ
KVIPELKLIKHAIKS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g12975.t1 | Gene3D | G3DSA:3.30.930.10 | Bira Bifunctional Protein; Domain 2 | 101 | 425 | 0.0 |
| 2 | g12975.t1 | PANTHER | PTHR11778 | SERYL-TRNA SYNTHETASE | 25 | 415 | 0.0 |
| 3 | g12975.t1 | PANTHER | PTHR11778:SF7 | SERINE–TRNA LIGASE, CYTOPLASMIC-RELATED | 25 | 415 | 0.0 |
| 9 | g12975.t1 | PIRSF | PIRSF001529 | Ser-tRNA_ligase | 8 | 421 | 0.0 |
| 4 | g12975.t1 | PRINTS | PR00981 | Seryl-tRNA synthetase signature | 275 | 288 | 0.0 |
| 5 | g12975.t1 | PRINTS | PR00981 | Seryl-tRNA synthetase signature | 332 | 348 | 0.0 |
| 6 | g12975.t1 | PRINTS | PR00981 | Seryl-tRNA synthetase signature | 350 | 366 | 0.0 |
| 1 | g12975.t1 | Pfam | PF00587 | tRNA synthetase class II core domain (G, H, P, S and T) | 225 | 394 | 0.0 |
| 10 | g12975.t1 | ProSiteProfiles | PS50862 | Aminoacyl-transfer RNA synthetases class-II family profile. | 172 | 410 | 16.3 |
| 7 | g12975.t1 | SUPERFAMILY | SSF55681 | Class II aaRS and biotin synthetases | 126 | 418 | 0.0 |
| 11 | g12975.t1 | TIGRFAM | TIGR00414 | serS: serine–tRNA ligase | 21 | 412 | 0.0 |
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.
