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.t2 isoform g4309.t2 1113005 1120395
chr_2 g4309 g4309.t2 exon g4309.t2.exon1 1113005 1113011
chr_2 g4309 g4309.t2 exon g4309.t2.exon2 1118100 1119483
chr_2 g4309 g4309.t2 cds g4309.t2.CDS1 1118444 1119442
chr_2 g4309 g4309.t2 exon g4309.t2.exon3 1120354 1120395
chr_2 g4309 g4309.t2 TSS g4309.t2 1120395 1120395
chr_2 g4309 g4309.t2 TTS g4309.t2 NA NA

Sequences

>g4309.t2 Gene=g4309 Length=1433
ATTCTGCATCGAGCTGCGGTCTTGAACAGACATAAACTAAAAACTTAATCGTATTCAGCA
AAGCTAAAGCAAACTAATCAAAAATGTCAAAGATCGGTATCAATGGTTTTGGACGTATTG
GACGTTTGGTCCTCCGTGCTGCTTTGGACAAGGGAGCTCAAGTTGTTGCTGTTAACGATC
CATTCATCAATGTTGACTATATGGTTTACATGTTCAAATATGACTCAACCCACGGTCGCT
TCAAGGGAGAGGTCAAGGCTGAAGGCGGTTTCTTAGTCATCAATGGACAAAAGATTACAG
TTTTCCAAGAACGTGATCCAAAGAATATTGCATGGGGAAAGGCTGGCGCTGAATACATTG
TTGAATCAACTGGTGTTTTCACTACTATTGAAAAGGCATCAGCTCACTTTGAAGGCGGTG
CAAAGAAAGTCATTATCTCAGCTCCATCAGCTGATGCACCAATGTTCGTTTGCGGTGTCA
ACTTGGATGCATACGATCCATCAATGAAGGTCGTCTCGAACGCTTCATGCACAACCAACT
GCTTGGCTCCATTAGCTAAAGTTGTCCACGATAACTTCGAAATCATTGAGGGATTGATGA
CCACTGTTCATGCAACCACAGCTACACAAAAGACCGTCGATGGCCCATCAGGCAAATTGT
GGCGTGATGGACGTGGTGCTGCTCAAAATATCATTCCAGCAGCTACTGGAGCAGCTAAGG
CTGTCGGAAAAGTTATTCCAGCTTTGAATGGAAAATTGACTGGTATGGCTTTCCGTGTTC
CAACTGCTGATGTTTCAGTCGTTGATTTGACTGTTCGCCTCGCTAAGCCAGCTCCTTATG
CCGAAATCAAGAAGAAGGTTAAGGAAGCCGCTGAAGGTCCAATGAAGGGAATTTTGGATT
ACACTGAAGATGAAGTTGTCTCAACTGATTTCACCAGTGACACACACTCATCTGTCTTTG
ATGCCGCCGCTGGTATTCCATTGAATGACCACTTCGTTAAGCTCATCTCATGGTACGATA
ACGAATACGGTTACTCCAACCGCGTTGTCGATCTCATCAAGTACATGCAAAGCAAGGATT
AAATCAATTGTTACTAAATGATTCCAGTCCTTCAATTTAAAAAATGAGAAGCATCACAAC
ATCTGCATGCAGATTCTTTTAAATAATTAAAAAGTGATTGGTGACACACACGTATGAATT
TTAATAATTATTACTACCATAATACATATTATAATGCTGCTAGATTGAAAAGTGAAATAG
TTTGTGAATTATTATTGGTTAAAGTTGAAAATATGAAAATAGGTCAAAAAATAGGTTCCT
TTACCCTATATCAGCAAAAATAATATTCAATATTATTATTCAAACAACAACACACTTAAA
TCTGATGTCATCAATTTATCTAGATTGTAAGGCATAATAATTTTTAGAAATAA

>g4309.t2 Gene=g4309 Length=332
MSKIGINGFGRIGRLVLRAALDKGAQVVAVNDPFINVDYMVYMFKYDSTHGRFKGEVKAE
GGFLVINGQKITVFQERDPKNIAWGKAGAEYIVESTGVFTTIEKASAHFEGGAKKVIISA
PSADAPMFVCGVNLDAYDPSMKVVSNASCTTNCLAPLAKVVHDNFEIIEGLMTTVHATTA
TQKTVDGPSGKLWRDGRGAAQNIIPAATGAAKAVGKVIPALNGKLTGMAFRVPTADVSVV
DLTVRLAKPAPYAEIKKKVKEAAEGPMKGILDYTEDEVVSTDFTSDTHSSVFDAAAGIPL
NDHFVKLISWYDNEYGYSNRVVDLIKYMQSKD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g4309.t2 Gene3D G3DSA:3.40.50.720 - 3 326 2.9E-155
13 g4309.t2 Gene3D G3DSA:3.30.360.10 Dihydrodipicolinate Reductase; domain 2 148 313 2.9E-155
3 g4309.t2 PANTHER PTHR10836:SF103 GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 2 3 332 4.9E-187
4 g4309.t2 PANTHER PTHR10836 GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE 3 332 4.9E-187
14 g4309.t2 PIRSF PIRSF000149 GAPDH 1 332 4.4E-124
8 g4309.t2 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 108 121 3.3E-48
6 g4309.t2 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 143 161 3.3E-48
5 g4309.t2 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 170 186 3.3E-48
7 g4309.t2 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 227 244 3.3E-48
9 g4309.t2 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 267 282 3.3E-48
2 g4309.t2 Pfam PF00044 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain 3 101 2.6E-37
1 g4309.t2 Pfam PF02800 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain 154 311 2.7E-66
15 g4309.t2 ProSitePatterns PS00071 Glyceraldehyde 3-phosphate dehydrogenase active site. 147 154 -
16 g4309.t2 SMART SM00846 gp_dh_n_7 2 149 1.5E-96
10 g4309.t2 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 3 169 1.83E-76
11 g4309.t2 SUPERFAMILY SSF55347 Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain 148 311 1.65E-80
17 g4309.t2 TIGRFAM TIGR01534 GAPDH-I: glyceraldehyde-3-phosphate dehydrogenase, type I 3 323 1.1E-127

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