General information for g16542.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g16542 is located on chr_4: 9873958..9875372 (+ 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_4 | g16542 | g16542.t3 | TSS | g16542.t3 | 9873735 | 9873735 |
| chr_4 | g16542 | g16542.t3 | isoform | g16542.t3 | 9873958 | 9874678 |
| chr_4 | g16542 | g16542.t3 | exon | g16542.t3.exon1 | 9873958 | 9874678 |
| chr_4 | g16542 | g16542.t3 | cds | g16542.t3.CDS1 | 9874311 | 9874586 |
| chr_4 | g16542 | g16542.t3 | TTS | g16542.t3 | NA | NA |
Sequences
>g16542.t3 Gene=g16542 Length=721
CATTAATAAACATAACAGTCGATGGTGGAACAAATCGTTGGCTTAATTTCCTTAAAAATA
ACAATCTCGAAAATAAGCTGAAACATCCAACATTAATCACTGGTGATCTCGATTCATGTC
ATGCTGAAAGTTTAAAATTTTTTACTCAAACCAAAGTCATTCAAACTGTCGATCAGGATG
AGACTGATTTTACAAAATGTCTTAGAGTTCTTGAACCTTTCATAAATGAACTTAAACTTG
ATCATACTGTAGTGATTTGTGAAAATTCTGGTCGACTTGATCACATTATTGCAAATATTA
ATACTTTGTATAAAAATCAACTTAAATCGAATGAAATCTCAAGGCCTGTTTTTATGTTAT
CATCGACTAGCATTTCATTTTTATTACCAGAAGGTAAAAGTGAAATTCACATTCCTGAAT
GCGCAAAGAAATTATGGTGTGCACTTATGCCAATTGCTGGACCGACAACTGTTAGCACAG
AAGGATTAAAATGGAATATGAAAAATTTTGAAATGAAATTTGGTGGATTAGTCAGTACAA
GTAATAAATATGATGGAATATCAGATTTTGTAAAAGTTGAATGTAATTTGCCAATCCTTT
GGTCAATGGGAATTTGTGATGAAATTTAAAACTAAGTTTATTGGAAAATTAAAAATTCGT
ACTTAAATTGTTGTTAAATTTTATTGTAGTTTATTAATGAAAATCAAAGAAATAAAACTT
T
>g16542.t3 Gene=g16542 Length=91
MLSSTSISFLLPEGKSEIHIPECAKKLWCALMPIAGPTTVSTEGLKWNMKNFEMKFGGLV
STSNKYDGISDFVKVECNLPILWSMGICDEI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g16542.t3 | Gene3D | G3DSA:2.60.120.320 | - | 1 | 88 | 0 |
| 2 | g16542.t3 | PANTHER | PTHR13622:SF8 | THIAMIN PYROPHOSPHOKINASE 1 | 2 | 87 | 0 |
| 3 | g16542.t3 | PANTHER | PTHR13622 | THIAMIN PYROPHOSPHOKINASE | 2 | 87 | 0 |
| 1 | g16542.t3 | Pfam | PF04265 | Thiamin pyrophosphokinase, vitamin B1 binding domain | 16 | 81 | 0 |
| 5 | g16542.t3 | SMART | SM00983 | TPK_B1_binding_a_2_a | 14 | 81 | 0 |
| 4 | g16542.t3 | SUPERFAMILY | SSF63862 | Thiamin pyrophosphokinase, substrate-binding domain | 6 | 88 | 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:0030975 | thiamine binding | MF |
| GO:0009229 | thiamine diphosphate biosynthetic process | 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.
