General information for g3577.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cytoplasmic tRNA 2-thiolation protein 1.
Parent gene
- The parent gene g3577 is located on chr_3: 26523714..26524850 (- 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 | g3577 | g3577.t2 | TTS | g3577.t2 | 26514860 | 26514860 |
| chr_3 | g3577 | g3577.t2 | isoform | g3577.t2 | 26515079 | 26524850 |
| chr_3 | g3577 | g3577.t2 | exon | g3577.t2.exon1 | 26515079 | 26515133 |
| chr_3 | g3577 | g3577.t2 | exon | g3577.t2.exon2 | 26523634 | 26524564 |
| chr_3 | g3577 | g3577.t2 | cds | g3577.t2.CDS1 | 26523714 | 26524564 |
| chr_3 | g3577 | g3577.t2 | exon | g3577.t2.exon3 | 26524622 | 26524739 |
| chr_3 | g3577 | g3577.t2 | cds | g3577.t2.CDS2 | 26524622 | 26524739 |
| chr_3 | g3577 | g3577.t2 | exon | g3577.t2.exon4 | 26524806 | 26524850 |
| chr_3 | g3577 | g3577.t2 | cds | g3577.t2.CDS3 | 26524806 | 26524850 |
| chr_3 | g3577 | g3577.t2 | TSS | g3577.t2 | 26524908 | 26524908 |
Sequences
>g3577.t2 Gene=g3577 Length=1149
ATGGTTTTATGTAAAGCCAACTGTGGAAATAAAGCCATTTTAAAGAGACCAAAAACTGGC
GATGCACTTTGTAAAGAATGTTTCTTCACAGCATTTGAATGTGAAATTCATGAAACAATT
ACAAAAGGACAACTCTTTAAAAGTGGTGATAAAGTAGCAATAGGAGCCAGTGGTGGAAAA
GATTCAACAGTTTTAGCTTATGTACTGAAATTACTAAATGAACGATATAAATATAATTTG
AAAATTGTTCTATTATCAATTGATGAAGGAATTACTGGATATAGAGATGATTCTCTTGAA
ACTGTAAAGAAAAATAGAGATGATTATGGAATGGAGCTGAAAATTTTATCGTACGAAGAA
TTATATGGTTGGACGATGGATAAGGTAGTTTCAGTGATTGGAAAAACTAATAACTGTACA
TTCTGTGGTGTCTTTAGACGACAAGCTCTCGATAGAGGAGCTAAAATGCTTGAAGTAGAC
TGCGTAGCAACAGGACATAATGCAGATGACATTGCCGAGACAGTTTTGATGAACATTCTA
AGAGGAGATATGGTTAGATTGAGACGATGTACAAAGATCAAAACTCACAGCAACGAAGAT
GCTATTCCTCGAGTAAAACCTCTTAAATACACATATGAAAAGGAGATTGTAATGTATGCT
CATTTCAAAAAACTCGTATACTTTTCAACAGAATGTATATTTGCTCCAAATGCTTATCGT
GGTCATGCAAGAATGTTTCTGAAAGATTTAGAGAAAATTAGACCTTCAGTAATAATGGAT
ATTATACATTCTGGAGAACAAATTCAATTTAAAGAGAACATAAAAAAGCCTGTTCTTGAT
ATATGTCAAACATGTGGATTTGTGTCATCTTGTCAACCTTGCAAAGCTTGTGTTCTACTT
GAAGGATTAAATAGAGGATTACCAAAGCTTGGAATTGGTAAAAAATCAAAAGGAGAACGA
ATGATAGCACAACAAAATCTTGAAAGAATACATCGTGTAAAAAATGACTTTTGATTCAAA
CGCTATAACGAACTTCAAATATTTAATAAATTCAATGCTAAAATTTTTTAAAATGAATCT
TTTGACTCAATAAAAATTATCTATCTATCTATCTATCTATCCTTTATATCATTGACGGTT
AACATTACT
>g3577.t2 Gene=g3577 Length=337
MVLCKANCGNKAILKRPKTGDALCKECFFTAFECEIHETITKGQLFKSGDKVAIGASGGK
DSTVLAYVLKLLNERYKYNLKIVLLSIDEGITGYRDDSLETVKKNRDDYGMELKILSYEE
LYGWTMDKVVSVIGKTNNCTFCGVFRRQALDRGAKMLEVDCVATGHNADDIAETVLMNIL
RGDMVRLRRCTKIKTHSNEDAIPRVKPLKYTYEKEIVMYAHFKKLVYFSTECIFAPNAYR
GHARMFLKDLEKIRPSVIMDIIHSGEQIQFKENIKKPVLDICQTCGFVSSCQPCKACVLL
EGLNRGLPKLGIGKKSKGERMIAQQNLERIHRVKNDF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g3577.t2 | CDD | cd01993 | Alpha_ANH_like_II | 51 | 238 | 3.515E-87 |
| 7 | g3577.t2 | Gene3D | G3DSA:3.40.50.620 | HUPs | 4 | 315 | 1.1E-83 |
| 5 | g3577.t2 | Hamap | MF_03053 | Cytoplasmic tRNA 2-thiolation protein 1 [CTU1]. | 2 | 315 | 50.505295 |
| 3 | g3577.t2 | PANTHER | PTHR11807 | ATPASES OF THE PP SUPERFAMILY-RELATED | 1 | 320 | 4.2E-152 |
| 4 | g3577.t2 | PANTHER | PTHR11807:SF12 | CYTOPLASMIC TRNA 2-THIOLATION PROTEIN 1 | 1 | 320 | 4.2E-152 |
| 8 | g3577.t2 | PIRSF | PIRSF004976 | ATPase_YdaO | 1 | 312 | 1.5E-111 |
| 1 | g3577.t2 | Pfam | PF01171 | PP-loop family | 51 | 229 | 2.4E-17 |
| 2 | g3577.t2 | Pfam | PF16503 | Zinc-ribbon | 282 | 310 | 2.8E-12 |
| 10 | g3577.t2 | ProSitePatterns | PS01263 | Uncharacterized protein family UPF0021 signature. | 24 | 61 | - |
| 6 | g3577.t2 | SUPERFAMILY | SSF52402 | Adenine nucleotide alpha hydrolases-like | 37 | 272 | 5.51E-53 |
| 11 | g3577.t2 | TIGRFAM | TIGR00269 | TIGR00269: TIGR00269 family protein | 202 | 302 | 1.1E-19 |
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:0002098 | tRNA wobble uridine modification | BP |
| GO:0034227 | tRNA thio-modification | BP |
| GO:0000049 | tRNA binding | MF |
| GO:0008033 | tRNA processing | BP |
KEGG
Orthology
- This transcript has been annotated with K14168 (cytoplasmic tRNA 2-thiolation protein 1 [EC:2.7.7.-])
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. There were no conditions that were differentially expressed