Gene loci information

Transcript annotation

  • This transcript has been annotated as D-3-phosphoglycerate dehydrogenase.

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 g11929 g11929.t6 TTS g11929.t6 19345841 19345841
chr_1 g11929 g11929.t6 isoform g11929.t6 19346125 19347422
chr_1 g11929 g11929.t6 exon g11929.t6.exon1 19346125 19346180
chr_1 g11929 g11929.t6 cds g11929.t6.CDS1 19346139 19346180
chr_1 g11929 g11929.t6 exon g11929.t6.exon2 19346284 19346480
chr_1 g11929 g11929.t6 cds g11929.t6.CDS2 19346284 19346480
chr_1 g11929 g11929.t6 exon g11929.t6.exon3 19346541 19346893
chr_1 g11929 g11929.t6 cds g11929.t6.CDS3 19346541 19346893
chr_1 g11929 g11929.t6 exon g11929.t6.exon4 19346974 19347131
chr_1 g11929 g11929.t6 cds g11929.t6.CDS4 19346974 19347131
chr_1 g11929 g11929.t6 exon g11929.t6.exon5 19347235 19347422
chr_1 g11929 g11929.t6 cds g11929.t6.CDS5 19347235 19347369
chr_1 g11929 g11929.t6 TSS g11929.t6 19347424 19347424

Sequences

>g11929.t6 Gene=g11929 Length=952
TCGTTATTGCAACTTTCATCAGTCAAGTACATTTTAAGTTATTTCATTATAAAATGCCGG
TTGATATCAAAACAGTTTTAGTATGTGATGCTGTTGATCAGTCATGCATCGATTTACTTA
AATCAAATGAAATTTCTGTCGATTATAAGCTTAAACTACCAAAAGAAGAGCTCTTACGTG
AAGTCAAGAACTACGACGCCGTTATTGTTCGTTCAGATACAAAAATTACAGCAGACGTCA
TCGCTTCAGGTGTAGAAGAAAAATTGCGAGTAATCGGACGAGCTGGTGTGGGCGTTGATA
ACATTGATATTGATGCAGCTACAAAACATAATGTCATTGTACTCAACACTCCAGGCGGAA
ATTCAATTGCTGCGACTGAACTGACTTGTTTACTACTTGCGGCACTGGGTCGACCAGTTT
GCGCTGCTAATGCAAGCATGAAAGAAGGTCGATGGGATCGAAAAATATATTCAGGAACAG
AATTGTATGGAAAAACACTTGCAATTTTAGGATTAGGCAGAATTGGTCGAGAAGTTGGCT
TTAGAATGAAAGCATGGGGAATGAAAATAATTGGCTATGATCCCATCACTACTCATGAAC
AAGCTGCAGAATATGGCATTGAAAAAATGGAACTTGATGAAATTTGGCCACTTGCCGATT
ATATTACATTGCATGTTCCATTGATTCCATCAACTAAAAATTTAATATCTTCCGATTCAT
TGAGCAAATGCAAAAATGGCGTAAAAGTCGTAAATGTCGCTCGTGGAGGGGTAATAGATG
AGGAAGCAATTTTCAAGGCACTAGAAAGCGGAAAATGTGGTGGTGCTGCATTTGATGTTT
ACGAAGAAGAACCACCAAAAAAAGAAATTACAAAAAAGCTGATTGCTCATCCAAAAAATT
TACGCAATATAATGGCGTTGTTAATCGTGAAATTTTAAAAACTTATTTTTGA

>g11929.t6 Gene=g11929 Length=294
MPVDIKTVLVCDAVDQSCIDLLKSNEISVDYKLKLPKEELLREVKNYDAVIVRSDTKITA
DVIASGVEEKLRVIGRAGVGVDNIDIDAATKHNVIVLNTPGGNSIAATELTCLLLAALGR
PVCAANASMKEGRWDRKIYSGTELYGKTLAILGLGRIGREVGFRMKAWGMKIIGYDPITT
HEQAAEYGIEKMELDEIWPLADYITLHVPLIPSTKNLISSDSLSKCKNGVKVVNVARGGV
IDEEAIFKALESGKCGGAAFDVYEEEPPKKEITKKLIAHPKNLRNIMALLIVKF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g11929.t6 CDD cd12173 PGDH_4 8 280 8.93222E-142
9 g11929.t6 Gene3D G3DSA:3.40.50.720 - 8 98 1.2E-103
8 g11929.t6 Gene3D G3DSA:3.40.50.720 - 99 281 1.2E-103
3 g11929.t6 PANTHER PTHR42938:SF5 D-3-PHOSPHOGLYCERATE DEHYDROGENASE 3 281 7.5E-117
4 g11929.t6 PANTHER PTHR42938 FORMATE DEHYDROGENASE 1 3 281 7.5E-117
2 g11929.t6 Pfam PF00389 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain 8 113 2.6E-31
1 g11929.t6 Pfam PF02826 D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain 114 281 1.2E-51
7 g11929.t6 ProSitePatterns PS00065 D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. 149 176 -
6 g11929.t6 SUPERFAMILY SSF52283 Formate/glycerate dehydrogenase catalytic domain-like 7 139 3.02E-31
5 g11929.t6 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 107 269 2.82E-47

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:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor MF
GO:0051287 NAD binding MF
GO:0055114 NA NA

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. There were no conditions that were differentially expressed