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.t32 TTS g4309.t32 1118060 1118060
chr_2 g4309 g4309.t32 isoform g4309.t32 1118444 1119442
chr_2 g4309 g4309.t32 exon g4309.t32.exon1 1118444 1119184
chr_2 g4309 g4309.t32 cds g4309.t32.CDS1 1118444 1119184
chr_2 g4309 g4309.t32 exon g4309.t32.exon2 1119236 1119442
chr_2 g4309 g4309.t32 cds g4309.t32.CDS2 1119236 1119442
chr_2 g4309 g4309.t32 TSS g4309.t32 1120395 1120395

Sequences

>g4309.t32 Gene=g4309 Length=948
ATGTCAAAGATCGGTATCAATGGTTTTGGACGTATTGGACGTTTGGTCCTCCGTGCTGCT
TTGGACAAGGGAGCTCAAGTTGTTGCTGTTAACGATCCATTCATCAATGTTGACTATATG
GTTTACATGTTCAAATATGACTCAACCCACGGTCGCTTCAAGGGAGAGGTCAAGGCTGAA
GGCGGTTTCTTAGTCATCAATGGACAAGCTGGCGCTGAATACATTGTTGAATCAACTGGT
GTTTTCACTACTATTGAAAAGGCATCAGCTCACTTTGAAGGCGGTGCAAAGAAAGTCATT
ATCTCAGCTCCATCAGCTGATGCACCAATGTTCGTTTGCGGTGTCAACTTGGATGCATAC
GATCCATCAATGAAGGTCGTCTCGAACGCTTCATGCACAACCAACTGCTTGGCTCCATTA
GCTAAAGTTGTCCACGATAACTTCGAAATCATTGAGGGATTGATGACCACTGTTCATGCA
ACCACAGCTACACAAAAGACCGTCGATGGCCCATCAGGCAAATTGTGGCGTGATGGACGT
GGTGCTGCTCAAAATATCATTCCAGCAGCTACTGGAGCAGCTAAGGCTGTCGGAAAAGTT
ATTCCAGCTTTGAATGGAAAATTGACTGGTATGGCTTTCCGTGTTCCAACTGCTGATGTT
TCAGTCGTTGATTTGACTGTTCGCCTCGCTAAGCCAGCTCCTTATGCCGAAATCAAGAAG
AAGGTTAAGGAAGCCGCTGAAGGTCCAATGAAGGGAATTTTGGATTACACTGAAGATGAA
GTTGTCTCAACTGATTTCACCAGTGACACACACTCATCTGTCTTTGATGCCGCCGCTGGT
ATTCCATTGAATGACCACTTCGTTAAGCTCATCTCATGGTACGATAACGAATACGGTTAC
TCCAACCGCGTTGTCGATCTCATCAAGTACATGCAAAGCAAGGATTAA

>g4309.t32 Gene=g4309 Length=315
MSKIGINGFGRIGRLVLRAALDKGAQVVAVNDPFINVDYMVYMFKYDSTHGRFKGEVKAE
GGFLVINGQAGAEYIVESTGVFTTIEKASAHFEGGAKKVIISAPSADAPMFVCGVNLDAY
DPSMKVVSNASCTTNCLAPLAKVVHDNFEIIEGLMTTVHATTATQKTVDGPSGKLWRDGR
GAAQNIIPAATGAAKAVGKVIPALNGKLTGMAFRVPTADVSVVDLTVRLAKPAPYAEIKK
KVKEAAEGPMKGILDYTEDEVVSTDFTSDTHSSVFDAAAGIPLNDHFVKLISWYDNEYGY
SNRVVDLIKYMQSKD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g4309.t32 Gene3D G3DSA:3.40.50.720 - 3 308 2.1E-138
13 g4309.t32 Gene3D G3DSA:3.30.360.10 Dihydrodipicolinate Reductase; domain 2 130 296 2.1E-138
3 g4309.t32 PANTHER PTHR10836:SF103 GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 2 3 315 8.9E-172
4 g4309.t32 PANTHER PTHR10836 GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE 3 315 8.9E-172
14 g4309.t32 PIRSF PIRSF000149 GAPDH 1 315 6.0E-111
8 g4309.t32 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 91 104 2.7E-48
6 g4309.t32 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 126 144 2.7E-48
5 g4309.t32 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 153 169 2.7E-48
7 g4309.t32 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 210 227 2.7E-48
9 g4309.t32 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 250 265 2.7E-48
2 g4309.t32 Pfam PF00044 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain 3 69 2.5E-22
1 g4309.t32 Pfam PF02800 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain 137 294 2.3E-66
15 g4309.t32 ProSitePatterns PS00071 Glyceraldehyde 3-phosphate dehydrogenase active site. 130 137 -
16 g4309.t32 SMART SM00846 gp_dh_n_7 2 132 1.2E-80
10 g4309.t32 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 3 152 1.34E-65
11 g4309.t32 SUPERFAMILY SSF55347 Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain 131 294 1.43E-80
17 g4309.t32 TIGRFAM TIGR01534 GAPDH-I: glyceraldehyde-3-phosphate dehydrogenase, type I 3 306 2.4E-115

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:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor MF
GO:0006006 glucose metabolic process BP
GO:0051287 NAD binding MF
GO:0055114 NA NA

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