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.t20 isoform g4309.t20 1118057 1120395
chr_2 g4309 g4309.t20 exon g4309.t20.exon1 1118057 1119123
chr_2 g4309 g4309.t20 TTS g4309.t20 1118060 1118060
chr_2 g4309 g4309.t20 cds g4309.t20.CDS1 1118444 1119123
chr_2 g4309 g4309.t20 exon g4309.t20.exon2 1119259 1119483
chr_2 g4309 g4309.t20 cds g4309.t20.CDS2 1119259 1119442
chr_2 g4309 g4309.t20 exon g4309.t20.exon3 1120354 1120395
chr_2 g4309 g4309.t20 TSS g4309.t20 1120395 1120395

Sequences

>g4309.t20 Gene=g4309 Length=1334
ATTCTGCATCGAGCTGCGGTCTTGAACAGACATAAACTAAAAACTTAATCGTATTCAGCA
AAGCTAAAGCAAACTAATCAAAAATGTCAAAGATCGGTATCAATGGTTTTGGACGTATTG
GACGTTTGGTCCTCCGTGCTGCTTTGGACAAGGGAGCTCAAGTTGTTGCTGTTAACGATC
CATTCATCAATGTTGACTATATGGTTTACATGTTCAAATATGACTCAACCCACGGTCGCT
TCAAGGGAGAGGTCAAGGCTGAAGGCGCTCACTTTGAAGGCGGTGCAAAGAAAGTCATTA
TCTCAGCTCCATCAGCTGATGCACCAATGTTCGTTTGCGGTGTCAACTTGGATGCATACG
ATCCATCAATGAAGGTCGTCTCGAACGCTTCATGCACAACCAACTGCTTGGCTCCATTAG
CTAAAGTTGTCCACGATAACTTCGAAATCATTGAGGGATTGATGACCACTGTTCATGCAA
CCACAGCTACACAAAAGACCGTCGATGGCCCATCAGGCAAATTGTGGCGTGATGGACGTG
GTGCTGCTCAAAATATCATTCCAGCAGCTACTGGAGCAGCTAAGGCTGTCGGAAAAGTTA
TTCCAGCTTTGAATGGAAAATTGACTGGTATGGCTTTCCGTGTTCCAACTGCTGATGTTT
CAGTCGTTGATTTGACTGTTCGCCTCGCTAAGCCAGCTCCTTATGCCGAAATCAAGAAGA
AGGTTAAGGAAGCCGCTGAAGGTCCAATGAAGGGAATTTTGGATTACACTGAAGATGAAG
TTGTCTCAACTGATTTCACCAGTGACACACACTCATCTGTCTTTGATGCCGCCGCTGGTA
TTCCATTGAATGACCACTTCGTTAAGCTCATCTCATGGTACGATAACGAATACGGTTACT
CCAACCGCGTTGTCGATCTCATCAAGTACATGCAAAGCAAGGATTAAATCAATTGTTACT
AAATGATTCCAGTCCTTCAATTTAAAAAATGAGAAGCATCACAACATCTGCATGCAGATT
CTTTTAAATAATTAAAAAGTGATTGGTGACACACACGTATGAATTTTAATAATTATTACT
ACCATAATACATATTATAATGCTGCTAGATTGAAAAGTGAAATAGTTTGTGAATTATTAT
TGGTTAAAGTTGAAAATATGAAAATAGGTCAAAAAATAGGTTCCTTTACCCTATATCAGC
AAAAATAATATTCAATATTATTATTCAAACAACAACACACTTAAATCTGATGTCATCAAT
TTATCTAGATTGTAAGGCATAATAATTTTTAAGGAAATAAAATACATCGTTCTGTGAAGC
AGTTACAAAAGAAA

>g4309.t20 Gene=g4309 Length=287
MSKIGINGFGRIGRLVLRAALDKGAQVVAVNDPFINVDYMVYMFKYDSTHGRFKGEVKAE
GAHFEGGAKKVIISAPSADAPMFVCGVNLDAYDPSMKVVSNASCTTNCLAPLAKVVHDNF
EIIEGLMTTVHATTATQKTVDGPSGKLWRDGRGAAQNIIPAATGAAKAVGKVIPALNGKL
TGMAFRVPTADVSVVDLTVRLAKPAPYAEIKKKVKEAAEGPMKGILDYTEDEVVSTDFTS
DTHSSVFDAAAGIPLNDHFVKLISWYDNEYGYSNRVVDLIKYMQSKD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g4309.t20 Gene3D G3DSA:3.40.50.720 - 1 60 1.3E-26
14 g4309.t20 Gene3D G3DSA:3.40.50.720 - 61 280 3.5E-106
16 g4309.t20 Gene3D G3DSA:3.30.360.10 Dihydrodipicolinate Reductase; domain 2 102 268 3.5E-106
4 g4309.t20 PANTHER PTHR10836:SF103 GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 2 3 61 7.3E-158
6 g4309.t20 PANTHER PTHR10836 GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE 3 61 7.3E-158
3 g4309.t20 PANTHER PTHR10836:SF103 GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 2 61 287 7.3E-158
5 g4309.t20 PANTHER PTHR10836 GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE 61 287 7.3E-158
18 g4309.t20 PIRSF PIRSF000149 GAPDH 1 63 1.4E-19
17 g4309.t20 PIRSF PIRSF000149 GAPDH 58 287 5.6E-85
11 g4309.t20 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 63 76 1.8E-48
8 g4309.t20 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 98 116 1.8E-48
7 g4309.t20 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 125 141 1.8E-48
10 g4309.t20 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 182 199 1.8E-48
9 g4309.t20 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 222 237 1.8E-48
2 g4309.t20 Pfam PF00044 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain 3 74 2.0E-21
1 g4309.t20 Pfam PF02800 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain 109 266 1.8E-66
19 g4309.t20 ProSitePatterns PS00071 Glyceraldehyde 3-phosphate dehydrogenase active site. 102 109 -
20 g4309.t20 SMART SM00846 gp_dh_n_7 2 104 6.6E-55
12 g4309.t20 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 3 124 4.85E-51
13 g4309.t20 SUPERFAMILY SSF55347 Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain 103 266 1.12E-80

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