Gene loci information

Transcript annotation

  • This transcript has been annotated as Cytoplasmic tRNA 2-thiolation protein 1.

Parent gene

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.t8 TTS g3577.t8 26523607 26523607
chr_3 g3577 g3577.t8 isoform g3577.t8 26523714 26524850
chr_3 g3577 g3577.t8 exon g3577.t8.exon1 26523714 26523899
chr_3 g3577 g3577.t8 cds g3577.t8.CDS1 26523714 26523899
chr_3 g3577 g3577.t8 exon g3577.t8.exon2 26523990 26524137
chr_3 g3577 g3577.t8 cds g3577.t8.CDS2 26523990 26524137
chr_3 g3577 g3577.t8 exon g3577.t8.exon3 26524186 26524850
chr_3 g3577 g3577.t8 cds g3577.t8.CDS3 26524186 26524397
chr_3 g3577 g3577.t8 TSS g3577.t8 26524908 26524908

Sequences

>g3577.t8 Gene=g3577 Length=999
ATGGTTTTATGTAAAGCCAACTGTGGAAATAAAGCCATTTTAAAGGTAAGTTAAATATTT
ATTACAGTGTACAGAAATCAATTTGTAACTAATTGAATTATTGTATTTAAGAGACCAAAA
ACTGGCGATGCACTTTGTAAAGAATGTTTCTTCACAGCATTTGAATGTGAAATTCATGAA
ACAATTACAAAAGGACAACTCTTTAAAAGTGGTGATAAAGTAGCAATAGGTAATATTCTT
TAAAAATCAAAGAATCAAAAAATTATCTCTATTTTCCATTTTTTAGGAGCCAGTGGTGGA
AAAGATTCAACAGTTTTAGCTTATGTACTGAAATTACTAAATGAACGATATAAATATAAT
TTGAAAATTGTTCTATTATCAATTGATGAAGGAATTACTGGATATAGAGATGATTCTCTT
GAAACTGTAAAGAAAAATAGAGATGATTATGGAATGGAGCTGAAAATTTTATCGTACGAA
GAATTATATGGTTGGACGATGGATAAGGTAGTTTCAGTGATTGGAAAAACTAATAACTGT
ACATTCTGTGGTGTCTTTAGACGACAAGCTCTCGATAGAGGAGCTAAAATGCTTGAAGTA
GACTGCGTAGCAACAGGACATAATGCAGATGACATTGCCGAGACAGTTTTGATGAACATT
CTAAGCAACGAAGATGCTATTCCTCGAGTAAAACCTCTTAAATACACATATGAAAAGGAG
ATTGTAATGTATGCTCATTTCAAAAAACTCGTATACTTTTCAACAGAATGTATATTTGCT
CCAAATGCTTATCGTGGTCATGCAAGAATGTTTCCTGTTCTTGATATATGTCAAACATGT
GGATTTGTGTCATCTTGTCAACCTTGCAAAGCTTGTGTTCTACTTGAAGGATTAAATAGA
GGATTACCAAAGCTTGGAATTGGTAAAAAATCAAAAGGAGAACGAATGATAGCACAACAA
AATCTTGAAAGAATACATCGTGTAAAAAATGACTTTTGA

>g3577.t8 Gene=g3577 Length=181
MELKILSYEELYGWTMDKVVSVIGKTNNCTFCGVFRRQALDRGAKMLEVDCVATGHNADD
IAETVLMNILSNEDAIPRVKPLKYTYEKEIVMYAHFKKLVYFSTECIFAPNAYRGHARMF
PVLDICQTCGFVSSCQPCKACVLLEGLNRGLPKLGIGKKSKGERMIAQQNLERIHRVKND
F

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g3577.t8 CDD cd01993 Alpha_ANH_like_II 1 112 0.00000
8 g3577.t8 Gene3D G3DSA:3.40.50.620 HUPs 1 160 0.00000
4 g3577.t8 PANTHER PTHR11807 ATPASES OF THE PP SUPERFAMILY-RELATED 1 120 0.00000
6 g3577.t8 PANTHER PTHR11807:SF12 CYTOPLASMIC TRNA 2-THIOLATION PROTEIN 1 1 120 0.00000
3 g3577.t8 PANTHER PTHR11807 ATPASES OF THE PP SUPERFAMILY-RELATED 124 164 0.00000
5 g3577.t8 PANTHER PTHR11807:SF12 CYTOPLASMIC TRNA 2-THIOLATION PROTEIN 1 124 164 0.00000
1 g3577.t8 Pfam PF01171 PP-loop family 35 73 0.00026
2 g3577.t8 Pfam PF16503 Zinc-ribbon 126 154 0.00000
7 g3577.t8 SUPERFAMILY SSF52402 Adenine nucleotide alpha hydrolases-like 2 120 0.00000

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

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.

Raw TPM values