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.t25 isoform g4309.t25 1118057 1120395
chr_2 g4309 g4309.t25 exon g4309.t25.exon1 1118057 1118784
chr_2 g4309 g4309.t25 TTS g4309.t25 1118060 1118060
chr_2 g4309 g4309.t25 cds g4309.t25.CDS1 1118779 1118784
chr_2 g4309 g4309.t25 exon g4309.t25.exon2 1118891 1119483
chr_2 g4309 g4309.t25 cds g4309.t25.CDS2 1118891 1119442
chr_2 g4309 g4309.t25 exon g4309.t25.exon3 1120354 1120395
chr_2 g4309 g4309.t25 TSS g4309.t25 1120395 1120395

Sequences

>g4309.t25 Gene=g4309 Length=1363
ATTCTGCATCGAGCTGCGGTCTTGAACAGACATAAACTAAAAACTTAATCGTATTCAGCA
AAGCTAAAGCAAACTAATCAAAAATGTCAAAGATCGGTATCAATGGTTTTGGACGTATTG
GACGTTTGGTCCTCCGTGCTGCTTTGGACAAGGGAGCTCAAGTTGTTGCTGTTAACGATC
CATTCATCAATGTTGACTATATGGTTTACATGTTCAAATATGACTCAACCCACGGTCGCT
TCAAGGGAGAGGTCAAGGCTGAAGGCGGTTTCTTAGTCATCAATGGACAAAAGATTACAG
TTTTCCAAGAACGTGATCCAAAGAATATTGCATGGGGAAAGGCTGGCGCTGAATACATTG
TTGAATCAACTGGTGTTTTCACTACTATTGAAAAGGCATCAGCTCACTTTGAAGGCGGTG
CAAAGAAAGTCATTATCTCAGCTCCATCAGCTGATGCACCAATGTTCGTTTGCGGTGTCA
ACTTGGATGCATACGATCCATCAATGAAGGTCGTCTCGAACGCTTCATGCACAACCAACT
GCTTGGCTCCATTAGCTAAAGTTGTCCACGATAACTTCGAAATCATTGAGGGATTGATGA
CCACTGTTCATGCAACCACAGCTACACAAAAGACCCTTTGAATGGAAAATTGACTGGTAT
GGCTTTCCGTGTTCCAACTGCTGATGTTTCAGTCGTTGATTTGACTGTTCGCCTCGCTAA
GCCAGCTCCTTATGCCGAAATCAAGAAGAAGGTTAAGGAAGCCGCTGAAGGTCCAATGAA
GGGAATTTTGGATTACACTGAAGATGAAGTTGTCTCAACTGATTTCACCAGTGACACACA
CTCATCTGTCTTTGATGCCGCCGCTGGTATTCCATTGAATGACCACTTCGTTAAGCTCAT
CTCATGGTACGATAACGAATACGGTTACTCCAACCGCGTTGTCGATCTCATCAAGTACAT
GCAAAGCAAGGATTAAATCAATTGTTACTAAATGATTCCAGTCCTTCAATTTAAAAAATG
AGAAGCATCACAACATCTGCATGCAGATTCTTTTAAATAATTAAAAAGTGATTGGTGACA
CACACGTATGAATTTTAATAATTATTACTACCATAATACATATTATAATGCTGCTAGATT
GAAAAGTGAAATAGTTTGTGAATTATTATTGGTTAAAGTTGAAAATATGAAAATAGGTCA
AAAAATAGGTTCCTTTACCCTATATCAGCAAAAATAATATTCAATATTATTATTCAAACA
ACAACACACTTAAATCTGATGTCATCAATTTATCTAGATTGTAAGGCATAATAATTTTTA
AGGAAATAAAATACATCGTTCTGTGAAGCAGTTACAAAAGAAA

>g4309.t25 Gene=g4309 Length=185
MSKIGINGFGRIGRLVLRAALDKGAQVVAVNDPFINVDYMVYMFKYDSTHGRFKGEVKAE
GGFLVINGQKITVFQERDPKNIAWGKAGAEYIVESTGVFTTIEKASAHFEGGAKKVIISA
PSADAPMFVCGVNLDAYDPSMKVVSNASCTTNCLAPLAKVVHDNFEIIEGLMTTVHATTA
TQKTL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g4309.t25 Gene3D G3DSA:3.40.50.720 - 3 147 9.4E-86
12 g4309.t25 Gene3D G3DSA:3.30.360.10 Dihydrodipicolinate Reductase; domain 2 148 185 9.4E-86
3 g4309.t25 PANTHER PTHR10836:SF76 GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE-RELATED 2 184 1.1E-96
4 g4309.t25 PANTHER PTHR10836 GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE 2 184 1.1E-96
7 g4309.t25 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 108 121 2.3E-25
5 g4309.t25 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 143 161 2.3E-25
6 g4309.t25 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 170 185 2.3E-25
2 g4309.t25 Pfam PF00044 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain 3 101 6.9E-38
1 g4309.t25 Pfam PF02800 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain 154 185 5.3E-9
10 g4309.t25 ProSitePatterns PS00071 Glyceraldehyde 3-phosphate dehydrogenase active site. 147 154 -
9 g4309.t25 SMART SM00846 gp_dh_n_7 2 149 1.5E-96
8 g4309.t25 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 3 169 7.35E-77

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