General information for g3577.t5
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.t5 | TTS | g3577.t5 | 26523607 | 26523607 |
| chr_3 | g3577 | g3577.t5 | isoform | g3577.t5 | 26523714 | 26524850 |
| chr_3 | g3577 | g3577.t5 | exon | g3577.t5.exon1 | 26523714 | 26524564 |
| chr_3 | g3577 | g3577.t5 | cds | g3577.t5.CDS1 | 26523714 | 26524397 |
| chr_3 | g3577 | g3577.t5 | exon | g3577.t5.exon2 | 26524622 | 26524737 |
| chr_3 | g3577 | g3577.t5 | exon | g3577.t5.exon3 | 26524806 | 26524850 |
| chr_3 | g3577 | g3577.t5 | TSS | g3577.t5 | 26524908 | 26524908 |
Sequences
>g3577.t5 Gene=g3577 Length=1012
ATGGTTTTATGTAAAGCCAACTGTGGAAATAAAGCCATTTTAAAGACCAAAAACTGGCGA
TGCACTTTGTAAAGAATGTTTCTTCACAGCATTTGAATGTGAAATTCATGAAACAATTAC
AAAAGGACAACTCTTTAAAAGTGGTGATAAAGTAGCAATAGGAGCCAGTGGTGGAAAAGA
TTCAACAGTTTTAGCTTATGTACTGAAATTACTAAATGAACGATATAAATATAATTTGAA
AATTGTTCTATTATCAATTGATGAAGGAATTACTGGATATAGAGATGATTCTCTTGAAAC
TGTAAAGAAAAATAGAGATGATTATGGAATGGAGCTGAAAATTTTATCGTACGAAGAATT
ATATGGTTGGACGATGGATAAGGTAGTTTCAGTGATTGGAAAAACTAATAACTGTACATT
CTGTGGTGTCTTTAGACGACAAGCTCTCGATAGAGGAGCTAAAATGCTTGAAGTAGACTG
CGTAGCAACAGGACATAATGCAGATGACATTGCCGAGACAGTTTTGATGAACATTCTAAG
AGGAGATATGGTTAGATTGAGACGATGTACAAAGATCAAAACTCACAGCAACGAAGATGC
TATTCCTCGAGTAAAACCTCTTAAATACACATATGAAAAGGAGATTGTAATGTATGCTCA
TTTCAAAAAACTCGTATACTTTTCAACAGAATGTATATTTGCTCCAAATGCTTATCGTGG
TCATGCAAGAATGTTTCTGAAAGATTTAGAGAAAATTAGACCTTCAGTAATAATGGATAT
TATACATTCTGGAGAACAAATTCAATTTAAAGAGAACATAAAAAAGCCTGTTCTTGATAT
ATGTCAAACATGTGGATTTGTGTCATCTTGTCAACCTTGCAAAGCTTGTGTTCTACTTGA
AGGATTAAATAGAGGATTACCAAAGCTTGGAATTGGTAAAAAATCAAAAGGAGAACGAAT
GATAGCACAACAAAATCTTGAAAGAATACATCGTGTAAAAAATGACTTTTGA
>g3577.t5 Gene=g3577 Length=227
MELKILSYEELYGWTMDKVVSVIGKTNNCTFCGVFRRQALDRGAKMLEVDCVATGHNADD
IAETVLMNILRGDMVRLRRCTKIKTHSNEDAIPRVKPLKYTYEKEIVMYAHFKKLVYFST
ECIFAPNAYRGHARMFLKDLEKIRPSVIMDIIHSGEQIQFKENIKKPVLDICQTCGFVSS
CQPCKACVLLEGLNRGLPKLGIGKKSKGERMIAQQNLERIHRVKNDF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g3577.t5 | CDD | cd01993 | Alpha_ANH_like_II | 1 | 128 | 0 |
| 6 | g3577.t5 | Gene3D | G3DSA:3.40.50.620 | HUPs | 1 | 205 | 0 |
| 3 | g3577.t5 | PANTHER | PTHR11807 | ATPASES OF THE PP SUPERFAMILY-RELATED | 1 | 210 | 0 |
| 4 | g3577.t5 | PANTHER | PTHR11807:SF12 | CYTOPLASMIC TRNA 2-THIOLATION PROTEIN 1 | 1 | 210 | 0 |
| 8 | g3577.t5 | PIRSF | PIRSF004976 | ATPase_YdaO | 1 | 202 | 0 |
| 1 | g3577.t5 | Pfam | PF01171 | PP-loop family | 35 | 119 | 0 |
| 2 | g3577.t5 | Pfam | PF16503 | Zinc-ribbon | 172 | 200 | 0 |
| 5 | g3577.t5 | SUPERFAMILY | SSF52402 | Adenine nucleotide alpha hydrolases-like | 3 | 162 | 0 |
| 7 | g3577.t5 | TIGRFAM | TIGR00269 | TIGR00269: TIGR00269 family protein | 92 | 192 | 0 |
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 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.
