General information for g1213.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t12 | TSS | g1213.t12 | 8797313 | 8797313 |
| chr_3 | g1213 | g1213.t12 | isoform | g1213.t12 | 8797434 | 8799190 |
| chr_3 | g1213 | g1213.t12 | exon | g1213.t12.exon1 | 8797434 | 8798691 |
| chr_3 | g1213 | g1213.t12 | cds | g1213.t12.CDS1 | 8797753 | 8798691 |
| chr_3 | g1213 | g1213.t12 | exon | g1213.t12.exon2 | 8798751 | 8798869 |
| chr_3 | g1213 | g1213.t12 | cds | g1213.t12.CDS2 | 8798751 | 8798869 |
| chr_3 | g1213 | g1213.t12 | exon | g1213.t12.exon3 | 8798944 | 8799190 |
| chr_3 | g1213 | g1213.t12 | cds | g1213.t12.CDS3 | 8798944 | 8799190 |
| chr_3 | g1213 | g1213.t12 | TTS | g1213.t12 | 8799210 | 8799210 |
Sequences
>g1213.t12 Gene=g1213 Length=1624
ATGGCAGAAGAATTGACATTTGAAAAGAAACTTGAGTTAATCAAAAGAAATCTGCAAGAG
GTTCTTGGTGAAGAAAATCTGCACAAGATTGTGAAAGAACGAGATTTAAAACTTTATTGG
GGAACTGCCACAACTGGAAAACCTCATATTGCATATTTCGTGCCAATGACAAAAATTGCA
GACTTTCTAAAAGCTGGATGTGAAGTGAGTAATTGTTTTTTCTAAGAAATTTAATGTATA
TATCATACGACAGGTTATTTCATTACTTCTCTTTAAGGTCACAATCTTGTTTGCAGACTT
ACATGCATATTTAGATAATATGAAAGCACCATGGTCACTTCTAGAAGAGAGAACAAAATA
TTATGAAGCTGTTATTAAAGCTATGCTTCAATCACTAGGTGTACCATTGGAGAAACTTAA
ATTCGTGCAAGGCACAAGTTTTGAATTGTCTCGTGAATACTCTTTAGATGTTTATAGACT
CACATCAATTGTGACTCAACATGATGCTAAAAAAGCTGGTGCTGAAGTTGTGAAACAAGT
TGAATATCCTCTTTTATCTGGATTGCTTTATCCTGGCCTTCAGGCACTCGATGAAGAATA
TTTAAAAGTTGATGCTCAATTTGGAGGTGTTGATCAAAGAAAAATTTTTACTTTTGCTGA
AAAATATCTTCCACAACTCGGTTATGCAAAGAGAATTCATCTTATGAATCCCATGGTGCC
TGGTTTAACAGGTGGCAAAATGTCTTCTTCTGAAGAGGACTCTAAAATTGATCTTCTTGA
TTCAGCTGCTAATGTTAAGAAAAAAATTAAAAGAGCATTCTGTGAACCAGGAAATATTCA
AGACAATGGACTTTTATCATTTGTAAAGCACGTTTTATTTTCAATTTTTAAAGAAGATCA
AGGATTTGAAATTAAAAGAAAGGAAGAGAATGGTGGCGATGTAACATTTATGAAATATGA
AGATTTAGAAAAGGCGTTTGCAGAAGAAAAAATTCATCCAGGCGATTTAAAAGCAGCTGT
CGAAACTTATATCAATTGGCTTTTAGATCCAATTAGGAAAATATTTGATGATCAATATCA
TCGAGATCTAACTGAAAGAGCTTATCCTACAAAGAAAGAGGTAGCTCAAAAATCTGATGA
AAATTCACCAGATAAGATGGAATTAAAAGTAGGAAAAATTATAGAAGCTACCAAACATCC
AGATGCTGACACATTATGCATAATGAAAGTTAATGTTGGAAAAGATGAAATTAGATCGAT
TGTTAGTAATTTAATGTCTTATTATAAACTCGATGAGCTAGTGAACAGAAATGTCGTTGT
ATTGACAAACATGAAATCTTCAAAAATACGCGGAGTAGAAAGCGAAGGTTTAGTGTTCAC
TGATAAATATGAGCCATTAATTCCACCATTTGATGCAAATGTTGGTGATAGAATCTTCAT
TGAAGGCTATAACAATACAACTTCTGATGTAGCTCAATTGAATCCTAAGAAGAAAGTGTG
GGACAAAATTCAGAACGAGTTGAAAACAAATTCAGATGGTGAATGTGTATGGCGAGAATT
TAGTATGATGTCGATTAATGGTGAAAAAATTACAAGCAGCCTTATTAATTGTAACGTGAA
ATAA
>g1213.t12 Gene=g1213 Length=434
MKAPWSLLEERTKYYEAVIKAMLQSLGVPLEKLKFVQGTSFELSREYSLDVYRLTSIVTQ
HDAKKAGAEVVKQVEYPLLSGLLYPGLQALDEEYLKVDAQFGGVDQRKIFTFAEKYLPQL
GYAKRIHLMNPMVPGLTGGKMSSSEEDSKIDLLDSAANVKKKIKRAFCEPGNIQDNGLLS
FVKHVLFSIFKEDQGFEIKRKEENGGDVTFMKYEDLEKAFAEEKIHPGDLKAAVETYINW
LLDPIRKIFDDQYHRDLTERAYPTKKEVAQKSDENSPDKMELKVGKIIEATKHPDADTLC
IMKVNVGKDEIRSIVSNLMSYYKLDELVNRNVVVLTNMKSSKIRGVESEGLVFTDKYEPL
IPPFDANVGDRIFIEGYNNTTSDVAQLNPKKKVWDKIQNELKTNSDGECVWREFSMMSIN
GEKITSSLINCNVK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g1213.t12 | Gene3D | G3DSA:3.40.50.620 | HUPs | 1 | 131 | 0.0000000 |
| 10 | g1213.t12 | Gene3D | G3DSA:1.10.240.10 | - | 132 | 261 | 0.0000000 |
| 12 | g1213.t12 | Gene3D | G3DSA:2.40.50.140 | - | 271 | 434 | 0.0000000 |
| 3 | g1213.t12 | PANTHER | PTHR42765 | SOLEUCYL-TRNA SYNTHETASE | 1 | 301 | 0.0000000 |
| 4 | g1213.t12 | PANTHER | PTHR42765:SF2 | TYROSINE–TRNA LIGASE | 1 | 301 | 0.0000000 |
| 6 | g1213.t12 | PRINTS | PR01040 | Tyrosyl-tRNA synthetase signature | 76 | 91 | 0.0000004 |
| 5 | g1213.t12 | PRINTS | PR01040 | Tyrosyl-tRNA synthetase signature | 93 | 115 | 0.0000004 |
| 7 | g1213.t12 | PRINTS | PR01040 | Tyrosyl-tRNA synthetase signature | 126 | 138 | 0.0000004 |
| 1 | g1213.t12 | Pfam | PF00579 | tRNA synthetases class I (W and Y) | 2 | 242 | 0.0000000 |
| 2 | g1213.t12 | Pfam | PF01588 | Putative tRNA binding domain | 282 | 354 | 0.0000000 |
| 14 | g1213.t12 | ProSiteProfiles | PS50886 | tRNA-binding domain profile. | 276 | 385 | 25.4010000 |
| 8 | g1213.t12 | SUPERFAMILY | SSF52374 | Nucleotidylyl transferase | 8 | 260 | 0.0000000 |
| 9 | g1213.t12 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 276 | 433 | 0.0000000 |
| 13 | g1213.t12 | TIGRFAM | TIGR00234 | tyrS: tyrosine–tRNA ligase | 9 | 251 | 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:0005524 | ATP binding | MF |
| GO:0006418 | tRNA aminoacylation for protein translation | BP |
| GO:0000166 | nucleotide binding | MF |
| GO:0004831 | tyrosine-tRNA ligase activity | MF |
| GO:0004812 | aminoacyl-tRNA ligase activity | MF |
| GO:0000049 | tRNA binding | MF |
| GO:0006437 | tyrosyl-tRNA aminoacylation | BP |
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. There were no conditions that were differentially expressed