Gene loci information

Transcript annotation

  • This transcript has been annotated as Glyceraldehyde-3-phosphate 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_2 g4309 g4309.t34 TTS g4309.t34 1118060 1118060
chr_2 g4309 g4309.t34 isoform g4309.t34 1118444 1120395
chr_2 g4309 g4309.t34 exon g4309.t34.exon1 1118444 1118638
chr_2 g4309 g4309.t34 cds g4309.t34.CDS1 1118619 1118638
chr_2 g4309 g4309.t34 exon g4309.t34.exon2 1118710 1119483
chr_2 g4309 g4309.t34 cds g4309.t34.CDS2 1118710 1119442
chr_2 g4309 g4309.t34 exon g4309.t34.exon3 1120354 1120395
chr_2 g4309 g4309.t34 TSS g4309.t34 1120395 1120395

Sequences

>g4309.t34 Gene=g4309 Length=1011
ATTCTGCATCGAGCTGCGGTCTTGAACAGACATAAACTAAAAACTTAATCGTATTCAGCA
AAGCTAAAGCAAACTAATCAAAAATGTCAAAGATCGGTATCAATGGTTTTGGACGTATTG
GACGTTTGGTCCTCCGTGCTGCTTTGGACAAGGGAGCTCAAGTTGTTGCTGTTAACGATC
CATTCATCAATGTTGACTATATGGTTTACATGTTCAAATATGACTCAACCCACGGTCGCT
TCAAGGGAGAGGTCAAGGCTGAAGGCGGTTTCTTAGTCATCAATGGACAAAAGATTACAG
TTTTCCAAGAACGTGATCCAAAGAATATTGCATGGGGAAAGGCTGGCGCTGAATACATTG
TTGAATCAACTGGTGTTTTCACTACTATTGAAAAGGCATCAGCTCACTTTGAAGGCGGTG
CAAAGAAAGTCATTATCTCAGCTCCATCAGCTGATGCACCAATGTTCGTTTGCGGTGTCA
ACTTGGATGCATACGATCCATCAATGAAGGTCGTCTCGAACGCTTCATGCACAACCAACT
GCTTGGCTCCATTAGCTAAAGTTGTCCACGATAACTTCGAAATCATTGAGGGATTGATGA
CCACTGTTCATGCAACCACAGCTACACAAAAGACCGTCGATGGCCCATCAGGCAAATTGT
GGCGTGATGGACGTGGTGCTGCTCAAAATATCATTCCAGCAGCTACTGGAGCAGCTAAGG
CTGTCGGAAAAGTTATTCCAGCTTTGAATGGAAAATTGACTGGTATGGCTTTCCGTGTTC
CAACTGCTGATGTTTCAGTCGTTGATTTGACTGTTCGGAATTTTGGATTACACTGAAGAT
GAAGTTGTCTCAACTGATTTCACCAGTGACACACACTCATCTGTCTTTGATGCCGCCGCT
GGTATTCCATTGAATGACCACTTCGTTAAGCTCATCTCATGGTACGATAACGAATACGGT
TACTCCAACCGCGTTGTCGATCTCATCAAGTACATGCAAAGCAAGGATTAA

>g4309.t34 Gene=g4309 Length=250
MSKIGINGFGRIGRLVLRAALDKGAQVVAVNDPFINVDYMVYMFKYDSTHGRFKGEVKAE
GGFLVINGQKITVFQERDPKNIAWGKAGAEYIVESTGVFTTIEKASAHFEGGAKKVIISA
PSADAPMFVCGVNLDAYDPSMKVVSNASCTTNCLAPLAKVVHDNFEIIEGLMTTVHATTA
TQKTVDGPSGKLWRDGRGAAQNIIPAATGAAKAVGKVIPALNGKLTGMAFRVPTADVSVV
DLTVRNFGLH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g4309.t34 Gene3D G3DSA:3.40.50.720 - 1 169 2.1E-76
3 g4309.t34 PANTHER PTHR10836:SF103 GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 2 3 245 5.4E-137
4 g4309.t34 PANTHER PTHR10836 GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE 3 245 5.4E-137
8 g4309.t34 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 108 121 4.9E-39
6 g4309.t34 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 143 161 4.9E-39
5 g4309.t34 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 170 186 4.9E-39
7 g4309.t34 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 227 244 4.9E-39
2 g4309.t34 Pfam PF00044 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain 3 101 1.5E-37
1 g4309.t34 Pfam PF02800 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain 154 245 3.9E-41
12 g4309.t34 ProSitePatterns PS00071 Glyceraldehyde 3-phosphate dehydrogenase active site. 147 154 -
11 g4309.t34 SMART SM00846 gp_dh_n_7 2 149 1.5E-96
9 g4309.t34 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 3 169 7.76E-77
10 g4309.t34 SUPERFAMILY SSF55347 Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain 148 245 1.44E-49

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:0016620 oxidoreductase activity, acting on the aldehyde or oxo 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.

Raw TPM values