Gene loci information

Transcript annotation

  • This transcript has been annotated as 6-phosphogluconate dehydrogenase, decarboxylating.

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 g3365 g3365.t4 TTS g3365.t4 24877436 24877436
chr_3 g3365 g3365.t4 isoform g3365.t4 24877527 24879318
chr_3 g3365 g3365.t4 exon g3365.t4.exon1 24877527 24878453
chr_3 g3365 g3365.t4 cds g3365.t4.CDS1 24877527 24878453
chr_3 g3365 g3365.t4 exon g3365.t4.exon2 24878524 24878810
chr_3 g3365 g3365.t4 cds g3365.t4.CDS2 24878524 24878810
chr_3 g3365 g3365.t4 exon g3365.t4.exon3 24879231 24879318
chr_3 g3365 g3365.t4 cds g3365.t4.CDS3 24879231 24879288
chr_3 g3365 g3365.t4 TSS g3365.t4 24879992 24879992

Sequences

>g3365.t4 Gene=g3365 Length=1302
AAGGGAACAAAAATAATCGGTGCAACATCAATGGAAGATATGGTTAGCAAATTGAAGACT
CCTCGACGTGTTATGCTTCTGGTCAAAGCTGGGAGTGCTGTTGATGATTTTATCAAACAA
TTAACTCCATTACTTTCACCTGGTGATATCATCATTGATGGTGGAAATTCTGAATATCAA
GATACTGCAAGACGTGTTGAAGAATGCAAAAAGAATAAATTATTGTTTGTTGGTTCAGGT
GTAAGCGGAGGTGAAGAAGGTGCACGTTATGGACCATCATTAATGCCTGGCGGTAATCCT
GAAGCTTGGCCACATATTAAAGACATTTTCCAATCAATCTGTGCACGTGCTGACAATGAA
CCTTGTTGTGAGTGGGTCGGTGAAGGCGGTAGCGGTCATTTTGTTAAAATGGTACATAAT
GGAATTGAGTATGGTGATATGCAACTAATTTGTGAAGCATATGATTTAATGAAAGCAATG
GGTATGAGTCAAAAAGAAATGGCTGATGCATTTACTGAATGGAACAAAGGCGAACTTGAT
TCTTTCCTCATTGAAATTACCAGTAGTATTCTCAATTATAAAGATAAGGAAGGATATTTG
CTTGAACGTATTCGTGACACTGCTGGTCAAAAAGGTACTGGGAAATGGACTGCAATTGCT
GCTCTTCAATACGGTGTACCCGTTACTCTAATTGGTGAAGCTGTCTTCTCTCGTTGCTTA
TCTGCTCTTAAAAGTGAACGAGTTGCTGCAAGCAAAGTACTGAATGGTCCAGACACAAAA
CCAACTGTCGCTAACAAGGCTGAATTCTTGAATCACATTAAGAATGCTCTTTATTGTGCA
AAAATTGTTTCATATGCTCAAGGTTTTATGTTGATGCGTGAGGCTGCAAAGGAAAATGGC
TGGCACTTAAATTATGGCGGTATTGCTTTGATGTGGAGAGGTGGTTGCATCATAAGAAGT
GTATTCTTAGGAAACATTAAAGAAGCATTCACTCGTAATCCACAATTATCAAATTTATTA
CTTGATGACTTTTTCAAGAATGCAATTACTAAAAATCAAAATTCCTGGCGACAAGTTGTA
TCAAATGCGACACTTTGGGGAATTCCAGTTCCAGCACTTTCAGCTGCTCTTGCCTTCTTT
GACGGCTATCGTGCTGATCGTCTTCCGGCTAATCTATTGCAAGCACAAAGAGACTTCTTT
GGTGCTCATACATATGAATTGTTAGGTCAAGAGGGCAAATTTGTTCATACAAATTGGACT
GGAACTGGTGGAAATGTTAGTGCATCATCATATAATGCATAA

>g3365.t4 Gene=g3365 Length=423
MEDMVSKLKTPRRVMLLVKAGSAVDDFIKQLTPLLSPGDIIIDGGNSEYQDTARRVEECK
KNKLLFVGSGVSGGEEGARYGPSLMPGGNPEAWPHIKDIFQSICARADNEPCCEWVGEGG
SGHFVKMVHNGIEYGDMQLICEAYDLMKAMGMSQKEMADAFTEWNKGELDSFLIEITSSI
LNYKDKEGYLLERIRDTAGQKGTGKWTAIAALQYGVPVTLIGEAVFSRCLSALKSERVAA
SKVLNGPDTKPTVANKAEFLNHIKNALYCAKIVSYAQGFMLMREAAKENGWHLNYGGIAL
MWRGGCIIRSVFLGNIKEAFTRNPQLSNLLLDDFFKNAITKNQNSWRQVVSNATLWGIPV
PALSAALAFFDGYRADRLPANLLQAQRDFFGAHTYELLGQEGKFVHTNWTGTGGNVSASS
YNA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g3365.t4 Gene3D G3DSA:3.40.50.720 - 1 123 1.2E-34
14 g3365.t4 Gene3D G3DSA:1.10.1040.10 - 124 376 6.4E-110
13 g3365.t4 Gene3D G3DSA:1.20.5.320 - 377 423 3.8E-25
3 g3365.t4 PANTHER PTHR11811:SF50 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING 2 422 8.5E-205
4 g3365.t4 PANTHER PTHR11811 6-PHOSPHOGLUCONATE DEHYDROGENASE 2 422 8.5E-205
9 g3365.t4 PRINTS PR00076 6-phosphogluconate dehydrogenase signature 10 39 3.7E-68
7 g3365.t4 PRINTS PR00076 6-phosphogluconate dehydrogenase signature 63 88 3.7E-68
8 g3365.t4 PRINTS PR00076 6-phosphogluconate dehydrogenase signature 111 139 3.7E-68
6 g3365.t4 PRINTS PR00076 6-phosphogluconate dehydrogenase signature 190 217 3.7E-68
5 g3365.t4 PRINTS PR00076 6-phosphogluconate dehydrogenase signature 298 320 3.7E-68
2 g3365.t4 Pfam PF03446 NAD binding domain of 6-phosphogluconate dehydrogenase 2 116 1.1E-30
1 g3365.t4 Pfam PF00393 6-phosphogluconate dehydrogenase, C-terminal domain 122 409 2.0E-129
15 g3365.t4 ProSitePatterns PS00461 6-phosphogluconate dehydrogenase signature. 194 206 -
16 g3365.t4 SMART SM01350 6PGD_2 122 410 1.3E-214
10 g3365.t4 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 2 119 4.82E-32
11 g3365.t4 SUPERFAMILY SSF48179 6-phosphogluconate dehydrogenase C-terminal domain-like 120 413 2.47E-129
17 g3365.t4 TIGRFAM TIGR00873 gnd: 6-phosphogluconate dehydrogenase (decarboxylating) 1 410 2.0E-196

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:0050661 NADP binding MF
GO:0006098 pentose-phosphate shunt BP
GO:0004616 phosphogluconate dehydrogenase (decarboxylating) activity MF
GO:0055114 NA NA
GO:0016491 oxidoreductase activity 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