Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Thiamin pyrophosphokinase 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_4 g16542 g16542.t2 TSS g16542.t2 9873735 9873735
chr_4 g16542 g16542.t2 isoform g16542.t2 9873768 9875372
chr_4 g16542 g16542.t2 exon g16542.t2.exon1 9873768 9873900
chr_4 g16542 g16542.t2 cds g16542.t2.CDS1 9873768 9873900
chr_4 g16542 g16542.t2 exon g16542.t2.exon2 9873958 9874678
chr_4 g16542 g16542.t2 cds g16542.t2.CDS2 9873958 9874586
chr_4 g16542 g16542.t2 exon g16542.t2.exon3 9875314 9875372
chr_4 g16542 g16542.t2 TTS g16542.t2 NA NA

Sequences

>g16542.t2 Gene=g16542 Length=913
ATGAACAAATTTTTTCCAAGTAAAATCATCACCAAGAAAGAGGTTTTAGAGTCAAATTTG
AATTATGCCTTGATCATTCTTAATCGACCAATTCAAATAAAAAGAGAACTCATCGAAACA
CTTTGGAATAATTCATTAATAAACATAACAGTCGATGGTGGAACAAATCGTTGGCTTAAT
TTCCTTAAAAATAACAATCTCGAAAATAAGCTGAAACATCCAACATTAATCACTGGTGAT
CTCGATTCATGTCATGCTGAAAGTTTAAAATTTTTTACTCAAACCAAAGTCATTCAAACT
GTCGATCAGGATGAGACTGATTTTACAAAATGTCTTAGAGTTCTTGAACCTTTCATAAAT
GAACTTAAACTTGATCATACTGTAGTGATTTGTGAAAATTCTGGTCGACTTGATCACATT
ATTGCAAATATTAATACTTTGTATAAAAATCAACTTAAATCGAATGAAATCTCAAGGCCT
GTTTTTATGTTATCATCGACTAGCATTTCATTTTTATTACCAGAAGGTAAAAGTGAAATT
CACATTCCTGAATGCGCAAAGAAATTATGGTGTGCACTTATGCCAATTGCTGGACCGACA
ACTGTTAGCACAGAAGGATTAAAATGGAATATGAAAAATTTTGAAATGAAATTTGGTGGA
TTAGTCAGTACAAGTAATAAATATGATGGAATATCAGATTTTGTAAAAGTTGAATGTAAT
TTGCCAATCCTTTGGTCAATGGGAATTTGTGATGAAATTTAAAACTAAGTTTATTGGAAA
ATTAAAAATTCGTACTTAAATTGTTGTTAAATTTTATTGTAGTTTATTAATGAAAATCAA
AGAAATAAAACTTTTGTGCAGAAATTATTGCAAAAATTGCAAAAGTAATGAAAGTAAAAA
TTGCAAGTCTCAT

>g16542.t2 Gene=g16542 Length=253
MNKFFPSKIITKKEVLESNLNYALIILNRPIQIKRELIETLWNNSLINITVDGGTNRWLN
FLKNNNLENKLKHPTLITGDLDSCHAESLKFFTQTKVIQTVDQDETDFTKCLRVLEPFIN
ELKLDHTVVICENSGRLDHIIANINTLYKNQLKSNEISRPVFMLSSTSISFLLPEGKSEI
HIPECAKKLWCALMPIAGPTTVSTEGLKWNMKNFEMKFGGLVSTSNKYDGISDFVKVECN
LPILWSMGICDEI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g16542.t2 CDD cd07995 TPK 23 238 0
8 g16542.t2 Gene3D G3DSA:3.40.50.10240 Thiamin pyrophosphokinase 22 166 0
9 g16542.t2 Gene3D G3DSA:2.60.120.320 - 167 247 0
3 g16542.t2 PANTHER PTHR13622:SF8 THIAMIN PYROPHOSPHOKINASE 1 18 249 0
4 g16542.t2 PANTHER PTHR13622 THIAMIN PYROPHOSPHOKINASE 18 249 0
2 g16542.t2 Pfam PF04263 Thiamin pyrophosphokinase, catalytic domain 39 153 0
1 g16542.t2 Pfam PF04265 Thiamin pyrophosphokinase, vitamin B1 binding domain 179 243 0
7 g16542.t2 SMART SM00983 TPK_B1_binding_a_2_a 176 243 0
5 g16542.t2 SUPERFAMILY SSF63999 Thiamin pyrophosphokinase, catalytic domain 21 150 0
6 g16542.t2 SUPERFAMILY SSF63862 Thiamin pyrophosphokinase, substrate-binding domain 168 250 0
10 g16542.t2 TIGRFAM TIGR01378 thi_PPkinase: thiamine pyrophosphokinase 24 247 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:0005524 ATP binding MF
GO:0004788 thiamine diphosphokinase activity MF
GO:0009229 thiamine diphosphate biosynthetic process BP
GO:0006772 thiamine metabolic process BP

KEGG

Orthology

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.

Raw TPM values