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.t18 isoform g4309.t18 1118057 1120395
chr_2 g4309 g4309.t18 exon g4309.t18.exon1 1118057 1119084
chr_2 g4309 g4309.t18 TTS g4309.t18 1118060 1118060
chr_2 g4309 g4309.t18 cds g4309.t18.CDS1 1118444 1119084
chr_2 g4309 g4309.t18 exon g4309.t18.exon2 1119259 1119483
chr_2 g4309 g4309.t18 cds g4309.t18.CDS2 1119259 1119442
chr_2 g4309 g4309.t18 exon g4309.t18.exon3 1120354 1120395
chr_2 g4309 g4309.t18 TSS g4309.t18 1120395 1120395

Sequences

>g4309.t18 Gene=g4309 Length=1295
ATTCTGCATCGAGCTGCGGTCTTGAACAGACATAAACTAAAAACTTAATCGTATTCAGCA
AAGCTAAAGCAAACTAATCAAAAATGTCAAAGATCGGTATCAATGGTTTTGGACGTATTG
GACGTTTGGTCCTCCGTGCTGCTTTGGACAAGGGAGCTCAAGTTGTTGCTGTTAACGATC
CATTCATCAATGTTGACTATATGGTTTACATGTTCAAATATGACTCAACCCACGGTCGCT
TCAAGGGAGAGGTCAAGGCTGAAGGCGCTCCATCAGCTGATGCACCAATGTTCGTTTGCG
GTGTCAACTTGGATGCATACGATCCATCAATGAAGGTCGTCTCGAACGCTTCATGCACAA
CCAACTGCTTGGCTCCATTAGCTAAAGTTGTCCACGATAACTTCGAAATCATTGAGGGAT
TGATGACCACTGTTCATGCAACCACAGCTACACAAAAGACCGTCGATGGCCCATCAGGCA
AATTGTGGCGTGATGGACGTGGTGCTGCTCAAAATATCATTCCAGCAGCTACTGGAGCAG
CTAAGGCTGTCGGAAAAGTTATTCCAGCTTTGAATGGAAAATTGACTGGTATGGCTTTCC
GTGTTCCAACTGCTGATGTTTCAGTCGTTGATTTGACTGTTCGCCTCGCTAAGCCAGCTC
CTTATGCCGAAATCAAGAAGAAGGTTAAGGAAGCCGCTGAAGGTCCAATGAAGGGAATTT
TGGATTACACTGAAGATGAAGTTGTCTCAACTGATTTCACCAGTGACACACACTCATCTG
TCTTTGATGCCGCCGCTGGTATTCCATTGAATGACCACTTCGTTAAGCTCATCTCATGGT
ACGATAACGAATACGGTTACTCCAACCGCGTTGTCGATCTCATCAAGTACATGCAAAGCA
AGGATTAAATCAATTGTTACTAAATGATTCCAGTCCTTCAATTTAAAAAATGAGAAGCAT
CACAACATCTGCATGCAGATTCTTTTAAATAATTAAAAAGTGATTGGTGACACACACGTA
TGAATTTTAATAATTATTACTACCATAATACATATTATAATGCTGCTAGATTGAAAAGTG
AAATAGTTTGTGAATTATTATTGGTTAAAGTTGAAAATATGAAAATAGGTCAAAAAATAG
GTTCCTTTACCCTATATCAGCAAAAATAATATTCAATATTATTATTCAAACAACAACACA
CTTAAATCTGATGTCATCAATTTATCTAGATTGTAAGGCATAATAATTTTTAAGGAAATA
AAATACATCGTTCTGTGAAGCAGTTACAAAAGAAA

>g4309.t18 Gene=g4309 Length=274
MSKIGINGFGRIGRLVLRAALDKGAQVVAVNDPFINVDYMVYMFKYDSTHGRFKGEVKAE
GAPSADAPMFVCGVNLDAYDPSMKVVSNASCTTNCLAPLAKVVHDNFEIIEGLMTTVHAT
TATQKTVDGPSGKLWRDGRGAAQNIIPAATGAAKAVGKVIPALNGKLTGMAFRVPTADVS
VVDLTVRLAKPAPYAEIKKKVKEAAEGPMKGILDYTEDEVVSTDFTSDTHSSVFDAAAGI
PLNDHFVKLISWYDNEYGYSNRVVDLIKYMQSKD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g4309.t18 Gene3D G3DSA:3.40.50.720 - 1 62 1.2E-26
14 g4309.t18 Gene3D G3DSA:3.30.360.10 Dihydrodipicolinate Reductase; domain 2 89 255 7.1E-87
3 g4309.t18 PANTHER PTHR10836:SF103 GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 2 3 61 1.7E-151
5 g4309.t18 PANTHER PTHR10836 GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE 3 61 1.7E-151
4 g4309.t18 PANTHER PTHR10836:SF103 GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 2 62 274 1.7E-151
6 g4309.t18 PANTHER PTHR10836 GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE 62 274 1.7E-151
8 g4309.t18 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 20 33 7.0E-6
7 g4309.t18 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 209 224 7.0E-6
2 g4309.t18 Pfam PF00044 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain 3 61 1.5E-20
1 g4309.t18 Pfam PF02800 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain 96 253 1.6E-66
12 g4309.t18 ProSitePatterns PS00071 Glyceraldehyde 3-phosphate dehydrogenase active site. 89 96 -
11 g4309.t18 SMART SM00846 gp_dh_n_7 2 91 1.2E-39
9 g4309.t18 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 3 111 1.63E-42
10 g4309.t18 SUPERFAMILY SSF55347 Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain 90 253 9.67E-81

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