General information for g1919.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cysteine–tRNA ligase, cytoplasmic.
Parent gene
- The parent gene g1919 is located on chr_3: 13863709..13864604 (+ 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 | g1919 | g1919.t2 | TSS | g1919.t2 | 13861421 | 13861421 |
| chr_3 | g1919 | g1919.t2 | isoform | g1919.t2 | 13862163 | 13863800 |
| chr_3 | g1919 | g1919.t2 | exon | g1919.t2.exon1 | 13862163 | 13863800 |
| chr_3 | g1919 | g1919.t2 | cds | g1919.t2.CDS1 | 13862171 | 13863709 |
| chr_3 | g1919 | g1919.t2 | TTS | g1919.t2 | NA | NA |
Sequences
>g1919.t2 Gene=g1919 Length=1638
ACAATGATATGAATGCACTAAATGTATTACCGCCTCATGTTCTCACACGCGTAACAGAAT
ATGTTCCTGAGATTATCACTTTTATTGAAAAGATTATTGTAAATGGTTATGGATATGAGT
CTAATGGTTCCGTATATTTTGATGTTGCTAAATTTGATGCAGCTAAACAACATCATTATG
CTAAACTTGTGCCAGAGGCTTTTGGAGATACTGCTCAATTGCAAGAAGGCGAAGGTGATT
TGAGTGGTGATAAAGGTCAGGAAAAACGGTCACCTAATGATTTTGCGTTATGGAAGAATA
GTAAAGAAGGTGAACCTGCTTGGAATTCGCCTTGGGGTCAAGGAAGACCAGGCTGGCACA
TTGAATGTTCCGCGATGGCTTCTGAAATATTCAAAGGTGATCTTGACATTCATACAGGTG
GTGTCGATTTAAAATTTCCACATCATGATAATGAAATTGCACAGAGCGAAGCTCATTTTG
ATACTAGTGGATGGGTTAAATATTTTCTTCATACTGGACATTTAACAATTAGTGGTTGCA
AAATGTCAAAATCATTGAAAAATTTCATCACAATTAAGGAAGCTCTGAAGCAACATACAG
CTACACAAATACGATTTGCATTCTTATTGCATTCATGGAAAGATACACTTGATTATAGTG
CAAATACAATGGAAATTGCTATTAGATATGAAAAAATGCTTAATGAGTTCTTCCTCAATG
TAAAGGATTTTATTCGTCAACGAAAGAGCAATGAAATGGTTAAGTTTACAGAACGCGATC
TTGAATTGAGTCGGAAGTTTTATGATACTAAAAGAGCTGTGCATGAAGCATTGTGTGACA
ATATTGATACAAAATCAGCACTTGATGCCATTCGTGAACTCATTTCATATGCAAATATTT
ATATTCGTGACATGCAAGCTAATGTAAATGTTCAATTACTCGAAGACATTGCAGTTTACA
TCACAGACTTGCTTGAGATATTTGGGGCAATTTCTCGTAGTAGTAATAAAAAATCCATCG
GTTTTCCATCTATCTCTGGTGATTCAAATGGAACTAATAAGGAAGAGATTTTATTGCCTT
ATTTATCAGCTTTAGCTGATTTTAGAAAAGTCGTTCGTGAAAATGCACTTGAAGTAAAAG
CGGTTAAAATTCTTCAATTATGTGATGAGTTACGGGATGAAATTTTACCAAATTTGAGTG
TTCGATTAGAAGATAAAGAAGGTCAATCAGTAATTAAACTCGTTGATCGTGAAGTTCTTA
TGAAAGAGAAAGAAGAGAAGAAACGACGTGAAGAGCAGAAAAAAGCAGAGCAATTAGCAA
AAGCAGAATTACAACGCCAAAAAGAGAAAGAACGTGAGGAGCAAAGAAAAATTAATCCAA
AAGATATGTTTAGAAATCAAACTGACAAGTACTCAGCATTCGATGATGAAGGTTTACCAA
CACTTGATCATGAAGGTAAAGAAATTAGCAAAGGTCAACAGAAGAAATTGAAAAAGTTAC
AACAGCAACAAGAAGTCAAGTATGCCGAATATCTCAAATCAATTTAACATTGATATTAAA
GATTAAAATAAAAAGAATTTTATTAATATTATAATTATATATAATGCATACATAATAAAT
CCTTATTTAATGGCGCTT
>g1919.t2 Gene=g1919 Length=512
MNALNVLPPHVLTRVTEYVPEIITFIEKIIVNGYGYESNGSVYFDVAKFDAAKQHHYAKL
VPEAFGDTAQLQEGEGDLSGDKGQEKRSPNDFALWKNSKEGEPAWNSPWGQGRPGWHIEC
SAMASEIFKGDLDIHTGGVDLKFPHHDNEIAQSEAHFDTSGWVKYFLHTGHLTISGCKMS
KSLKNFITIKEALKQHTATQIRFAFLLHSWKDTLDYSANTMEIAIRYEKMLNEFFLNVKD
FIRQRKSNEMVKFTERDLELSRKFYDTKRAVHEALCDNIDTKSALDAIRELISYANIYIR
DMQANVNVQLLEDIAVYITDLLEIFGAISRSSNKKSIGFPSISGDSNGTNKEEILLPYLS
ALADFRKVVRENALEVKAVKILQLCDELRDEILPNLSVRLEDKEGQSVIKLVDREVLMKE
KEEKKRREEQKKAEQLAKAELQRQKEKEREEQRKINPKDMFRNQTDKYSAFDDEGLPTLD
HEGKEISKGQQKKLKKLQQQQEVKYAEYLKSI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g1919.t2 | Coils | Coil | Coil | 411 | 454 | - |
| 9 | g1919.t2 | Gene3D | G3DSA:3.40.50.620 | HUPs | 1 | 217 | 4.5E-95 |
| 8 | g1919.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 421 | 497 | - |
| 2 | g1919.t2 | PANTHER | PTHR10890:SF3 | CYSTEINE–TRNA LIGASE, CYTOPLASMIC | 1 | 502 | 1.9E-187 |
| 3 | g1919.t2 | PANTHER | PTHR10890 | CYSTEINYL-TRNA SYNTHETASE | 1 | 502 | 1.9E-187 |
| 5 | g1919.t2 | PRINTS | PR00983 | Cysteinyl-tRNA synthetase signature | 102 | 120 | 5.8E-19 |
| 4 | g1919.t2 | PRINTS | PR00983 | Cysteinyl-tRNA synthetase signature | 133 | 154 | 5.8E-19 |
| 1 | g1919.t2 | Pfam | PF01406 | tRNA synthetases class I (C) catalytic domain | 1 | 224 | 3.5E-87 |
| 6 | g1919.t2 | SUPERFAMILY | SSF52374 | Nucleotidylyl transferase | 1 | 222 | 4.29E-54 |
| 7 | g1919.t2 | SUPERFAMILY | SSF47323 | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 257 | 407 | 4.25E-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:0006418 | tRNA aminoacylation for protein translation | BP |
| GO:0000166 | nucleotide binding | MF |
| GO:0004812 | aminoacyl-tRNA ligase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K01883 (cysteinyl-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.
