Gene loci information

Transcript annotation

  • This transcript has been annotated as Dihydropyrimidine dehydrogenase [NADP(+)].

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_1 g9693 g9693.t4 isoform g9693.t4 4720386 4721613
chr_1 g9693 g9693.t4 exon g9693.t4.exon1 4720386 4720851
chr_1 g9693 g9693.t4 cds g9693.t4.CDS1 4720500 4720851
chr_1 g9693 g9693.t4 exon g9693.t4.exon2 4721053 4721198
chr_1 g9693 g9693.t4 cds g9693.t4.CDS2 4721053 4721198
chr_1 g9693 g9693.t4 exon g9693.t4.exon3 4721256 4721367
chr_1 g9693 g9693.t4 cds g9693.t4.CDS3 4721256 4721367
chr_1 g9693 g9693.t4 exon g9693.t4.exon4 4721474 4721613
chr_1 g9693 g9693.t4 cds g9693.t4.CDS4 4721474 4721613
chr_1 g9693 g9693.t4 TTS g9693.t4 4721695 4721695
chr_1 g9693 g9693.t4 TSS g9693.t4 NA NA

Sequences

>g9693.t4 Gene=g9693 Length=864
AATATTGGACTTGATAAAAGAACGACTTATGGTGGTGTCAGTGGAAATGCAACACGTCCA
GTTGCTTTAAGATCTGTTTCAGCTGTTGGTAATGCACTACCAAATTATCCAATTATGGCC
ACAGGTGGAATCGATTCAGCTGATGTTGCTTATCAATTTCTTCAATGTGGTGCTTCAGTT
ATGCAAATTTGTTCTGCTGTGCAGAATCAAGATTTTAGTGTAATACAAGATTATATTACT
GGTCTAAAAGCATTACTTTATTTGAGAGCAAATCCACCACCAGAAAATGTTCGTTGGGAT
GGTCAATCACCGCCAACTCAAAAACTACAAAAGGGAAAAGCTGTCGTTAGCTTAAAAGAT
GACGATGGAAAACCTTTGGTCAATTTTGGTGAATATTTGAAGAAGAAAGAAGCAAAAATG
GAAAAGATTATTGAAGAAAAAGGACCGCTATATGATCCACAAGATGAACATTTGAAGGAA
GTAAAAATTGAAACAATGAATGGAGTTAATAAAGTAGCAAAAGTCAGTGACATCATTGGA
AAAGCTTTACCAAGAATTGGTGCTTATAAAAAATTGGATAATTCCAAACAAGTTGTTGCA
TTGATCGACGATGATCTCTGCATTAACTGTGGAAAATGTTACATGACTTGCGCTGACTCT
GGCTATCAAGCAATAGAATTTGATGCAAAAACTCATTTGCCTCATGTTACTGATGATTGC
ACTGGATGCAATTTATGCTTAAGTGTTTGTCCAATTATTGATTGTATCACAATGGTACCA
AAAACAATTCCTCATGTTATCAAACGTGGTTTTCAGTCTGAAACAAACAAAACATTGATT
CATGCTTTGAGTCCATCTCAATAA

>g9693.t4 Gene=g9693 Length=249
MATGGIDSADVAYQFLQCGASVMQICSAVQNQDFSVIQDYITGLKALLYLRANPPPENVR
WDGQSPPTQKLQKGKAVVSLKDDDGKPLVNFGEYLKKKEAKMEKIIEEKGPLYDPQDEHL
KEVKIETMNGVNKVAKVSDIIGKALPRIGAYKKLDNSKQVVALIDDDLCINCGKCYMTCA
DSGYQAIEFDAKTHLPHVTDDCTGCNLCLSVCPIIDCITMVPKTIPHVIKRGFQSETNKT
LIHALSPSQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g9693.t4 Gene3D G3DSA:3.20.20.70 Aldolase class I 1 53 4.9E-14
8 g9693.t4 Gene3D G3DSA:3.30.70.20 - 128 241 4.4E-35
3 g9693.t4 PANTHER PTHR43073:SF2 DIHYDROPYRIMIDINE DEHYDROGENASE [NADP(+)] 1 235 3.7E-88
4 g9693.t4 PANTHER PTHR43073 DIHYDROPYRIMIDINE DEHYDROGENASE [NADP(+)] 1 235 3.7E-88
2 g9693.t4 Pfam PF01180 Dihydroorotate dehydrogenase 2 48 1.1E-5
1 g9693.t4 Pfam PF14697 4Fe-4S dicluster domain 162 220 1.6E-24
7 g9693.t4 ProSitePatterns PS00198 4Fe-4S ferredoxin-type iron-sulfur binding region signature. 202 213 -
10 g9693.t4 ProSiteProfiles PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. 160 192 8.424
11 g9693.t4 ProSiteProfiles PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. 193 223 9.331
5 g9693.t4 SUPERFAMILY SSF51395 FMN-linked oxidoreductases 2 50 2.73E-8
6 g9693.t4 SUPERFAMILY SSF54862 4Fe-4S ferredoxins 129 228 9.3E-25

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:0016627 oxidoreductase activity, acting on the CH-CH group of donors MF
GO:0003824 catalytic activity MF
GO:0055114 NA NA
GO:0005737 cytoplasm CC

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