General information for g1213.t14
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Tyrosine–tRNA ligase, cytoplasmic.
Parent gene
- The parent gene g1213 is located on chr_3: 8799190..8800645 (+ 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 | g1213 | g1213.t14 | TSS | g1213.t14 | 8797313 | 8797313 |
| chr_3 | g1213 | g1213.t14 | isoform | g1213.t14 | 8798261 | 8799190 |
| chr_3 | g1213 | g1213.t14 | exon | g1213.t14.exon1 | 8798261 | 8798881 |
| chr_3 | g1213 | g1213.t14 | cds | g1213.t14.CDS1 | 8798383 | 8798724 |
| chr_3 | g1213 | g1213.t14 | exon | g1213.t14.exon2 | 8798944 | 8799190 |
| chr_3 | g1213 | g1213.t14 | TTS | g1213.t14 | 8799210 | 8799210 |
Sequences
>g1213.t14 Gene=g1213 Length=868
CAGGAAATATTCAAGACAATGGACTTTTATCATTTGTAAAGCACGTTTTATTTTCAATTT
TTAAAGAAGATCAAGGATTTGAAATTAAAAGAAAGGAAGAGAATGGTGGCGATGTAACAT
TTATGAAATATGAAGATTTAGAAAAGGCGTTTGCAGAAGAAAAAATTCATCCAGGCGATT
TAAAAGCAGCTGTCGAAACTTATATCAATTGGCTTTTAGATCCAATTAGGAAAATATTTG
ATGATCAATATCATCGAGATCTAACTGAAAGAGCTTATCCTACAAAGAAAGAGGTAGCTC
AAAAATCTGATGAAAATTCACCAGATAAGATGGAATTAAAAGTAGGAAAAATTATAGAAG
CTACCAAACATCCAGATGCTGACACATTATGCATAATGAAAGTTAATGTTGGAAAAGATG
AAATTAGATCGGTAAATGATTGCGTCATATATGAAACGATTTAAAAATTACAACTCTTTT
TATATTGTAGATTGTTAGTAATTTAATGTCTTATTATAAACTCGATGAGCTAGTGAACAG
AAATGTCGTTGTATTGACAAACATGAAATCTTCAAAAATACGCGGAGTAGAAAGCGAAGG
TTTAGTGTTGTGTGCATTCAACACTGATAAATATGAGCCATTAATTCCACCATTTGATGC
AAATGTTGGTGATAGAATCTTCATTGAAGGCTATAACAATACAACTTCTGATGTAGCTCA
ATTGAATCCTAAGAAGAAAGTGTGGGACAAAATTCAGAACGAGTTGAAAACAAATTCAGA
TGGTGAATGTGTATGGCGAGAATTTAGTATGATGTCGATTAATGGTGAAAAAATTACAAG
CAGCCTTATTAATTGTAACGTGAAATAA
>g1213.t14 Gene=g1213 Length=113
MKYEDLEKAFAEEKIHPGDLKAAVETYINWLLDPIRKIFDDQYHRDLTERAYPTKKEVAQ
KSDENSPDKMELKVGKIIEATKHPDADTLCIMKVNVGKDEIRSVNDCVIYETI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g1213.t14 | Gene3D | G3DSA:1.10.240.10 | - | 1 | 53 | 0.0000000 |
| 4 | g1213.t14 | Gene3D | G3DSA:2.40.50.140 | - | 61 | 106 | 0.0000000 |
| 1 | g1213.t14 | Pfam | PF01588 | Putative tRNA binding domain | 72 | 104 | 0.0000007 |
| 5 | g1213.t14 | ProSiteProfiles | PS50886 | tRNA-binding domain profile. | 66 | 113 | 14.0140000 |
| 2 | g1213.t14 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 66 | 104 | 0.0000000 |
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:0000049 | tRNA binding | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
