General information for g1609.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Serine–tRNA synthetase-like protein Slimp.
Parent gene
- The parent gene g1609 is located on chr_3: 12103251..12104362 (- 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_3 | g1609 | g1609.t1 | TTS | g1609.t1 | 12102147 | 12102147 |
| chr_3 | g1609 | g1609.t1 | isoform | g1609.t1 | 12102167 | 12103429 |
| chr_3 | g1609 | g1609.t1 | exon | g1609.t1.exon1 | 12102167 | 12103429 |
| chr_3 | g1609 | g1609.t1 | cds | g1609.t1.CDS1 | 12102167 | 12103429 |
| chr_3 | g1609 | g1609.t1 | TSS | g1609.t1 | 12103465 | 12103465 |
Sequences
>g1609.t1 Gene=g1609 Length=1263
ATGCTACGGCGATTATTTAATTCAAGTATTTTAATCAAAAGAAATGCATCCGCTTTATAT
GTAACAGGTGACAAAGCAATGGAGAATTTTGCTGTCCTTTCGCCTTTCCTTCAGATTGAT
GAAAGAATGAGTAATTTTGAAGAAATTAAAGCAAATATTACAAAAAGAAAGATGACACTT
AATTTAGATGAATTAAAGTCGGAATATGAACTGTATGCAGATGTTGAAAAAAGAAAGAGA
GAGTTAGAGAATAGACGAGTTGAAATTGTAGCTTTAATGAAGCAAGAACCAAGTGAAGGT
TTGAAATTAGAAGGAATAAACTTAAGAGAAAATTTGAAAAAGCTGAAAGAAAACTCATAT
TATCTAGAAGACCAATTTATTCATAATTTTCTAAAAATTCCAAATTATATTCACAACAAA
ACACCGGCTAATGAGAAAGAAGTAATTTATAGTTTTCTCGATAAACCATCTGATGTGATT
GTAAATGATAAAATACACAAACTTATTGAATTTTACGATTCAACTTGTTACTACATGAAA
GGTGATGCTGCTAAATTTGATATTCAAATAGCTTTAGACGTATGTGATTATTATAAAGAA
GCTGGCTTTATCAAATTTAGCAATCCAGATTTCGTTAGAAGTATAATACCAGAAGCAGCA
GCTGTCGATTTAAGCAATATTTTTCTCTTGAAAGAGGATGCAATTGAGAACAAACTAAAC
TTACTTCATTTAACTGGAAATGGTTCAATGCTCAACTTTTTATCGTTTTTTGCTAAACTC
ACTATATTTTCAACACAATTACCTATTCAACTAATAAGCACAGGAAGAAACTACAACAGT
ATGAATCATTTTGACCATCAAGATTTATATAGTGTCGTTCAAACTACATGTTGTCAAAAT
TTTATTGCTGTAAATGATGAGAAATCCTTTGATAAAATCATCGAAGATCAAATATTACAT
TGGAAAAATATCTTTGAACGTTTTAATCAGCATTTTAGAATAATCAGTTATCCAGCAGAA
TCATTAGCAATTAGTGAATCATATAAATTGGGTCTTGAAATGTATTCGAATAGTCAAAAC
GAATATATAGAAGTGGCAAATTTCTCTTACTATAGTGACTTCATAAGCAAACGACTCTTG
TTCAATTACAAGCAAGATAAAGTAACGAAATTTCCGCATATTTATTCTGGAACAGTAATG
AATGTCATGAAATTATTGATTAATCTTGTTGAAAGCAATAGTGATCTTAAGAAATTTATT
TAA
>g1609.t1 Gene=g1609 Length=420
MLRRLFNSSILIKRNASALYVTGDKAMENFAVLSPFLQIDERMSNFEEIKANITKRKMTL
NLDELKSEYELYADVEKRKRELENRRVEIVALMKQEPSEGLKLEGINLRENLKKLKENSY
YLEDQFIHNFLKIPNYIHNKTPANEKEVIYSFLDKPSDVIVNDKIHKLIEFYDSTCYYMK
GDAAKFDIQIALDVCDYYKEAGFIKFSNPDFVRSIIPEAAAVDLSNIFLLKEDAIENKLN
LLHLTGNGSMLNFLSFFAKLTIFSTQLPIQLISTGRNYNSMNHFDHQDLYSVVQTTCCQN
FIAVNDEKSFDKIIEDQILHWKNIFERFNQHFRIISYPAESLAISESYKLGLEMYSNSQN
EYIEVANFSYYSDFISKRLLFNYKQDKVTKFPHIYSGTVMNVMKLLINLVESNSDLKKFI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g1609.t1 | Coils | Coil | Coil | 65 | 92 | - |
| 7 | g1609.t1 | Coils | Coil | Coil | 98 | 118 | - |
| 5 | g1609.t1 | Gene3D | G3DSA:3.30.930.10 | Bira Bifunctional Protein; Domain 2 | 135 | 420 | 3.5E-32 |
| 1 | g1609.t1 | PANTHER | PTHR11778:SF2 | SERINE–TRNA SYNTHETASE-LIKE PROTEIN SLIMP | 20 | 413 | 1.7E-96 |
| 2 | g1609.t1 | PANTHER | PTHR11778 | SERYL-TRNA SYNTHETASE | 20 | 413 | 1.7E-96 |
| 8 | g1609.t1 | PIRSF | PIRSF001529 | Ser-tRNA_ligase | 36 | 418 | 8.4E-14 |
| 4 | g1609.t1 | SUPERFAMILY | SSF46589 | tRNA-binding arm | 39 | 142 | 2.04E-9 |
| 3 | g1609.t1 | SUPERFAMILY | SSF55681 | Class II aaRS and biotin synthetases | 253 | 415 | 6.55E-11 |
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:0000166 | nucleotide binding | 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.
