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.t22 isoform g4309.t22 1118057 1120395
chr_2 g4309 g4309.t22 exon g4309.t22.exon1 1118057 1119123
chr_2 g4309 g4309.t22 TTS g4309.t22 1118060 1118060
chr_2 g4309 g4309.t22 cds g4309.t22.CDS1 1118444 1119123
chr_2 g4309 g4309.t22 exon g4309.t22.exon2 1119214 1119483
chr_2 g4309 g4309.t22 cds g4309.t22.CDS2 1119214 1119442
chr_2 g4309 g4309.t22 exon g4309.t22.exon3 1120354 1120395
chr_2 g4309 g4309.t22 TSS g4309.t22 1120395 1120395

Sequences

>g4309.t22 Gene=g4309 Length=1379
ATTCTGCATCGAGCTGCGGTCTTGAACAGACATAAACTAAAAACTTAATCGTATTCAGCA
AAGCTAAAGCAAACTAATCAAAAATGTCAAAGATCGGTATCAATGGTTTTGGACGTATTG
GACGTTTGGTCCTCCGTGCTGCTTTGGACAAGGGAGCTCAAGTTGTTGCTGTTAACGATC
CATTCATCAATGTTGACTATATGGTTTACATGTTCAAATATGACTCAACCCACGGTCGCT
TCAAGGGAGAGGTCAAGGCTGAAGGCGGTTTCTTAGTCATCAATGGACAAAAGATTACAG
TTTTCCAAGAACCTCACTTTGAAGGCGGTGCAAAGAAAGTCATTATCTCAGCTCCATCAG
CTGATGCACCAATGTTCGTTTGCGGTGTCAACTTGGATGCATACGATCCATCAATGAAGG
TCGTCTCGAACGCTTCATGCACAACCAACTGCTTGGCTCCATTAGCTAAAGTTGTCCACG
ATAACTTCGAAATCATTGAGGGATTGATGACCACTGTTCATGCAACCACAGCTACACAAA
AGACCGTCGATGGCCCATCAGGCAAATTGTGGCGTGATGGACGTGGTGCTGCTCAAAATA
TCATTCCAGCAGCTACTGGAGCAGCTAAGGCTGTCGGAAAAGTTATTCCAGCTTTGAATG
GAAAATTGACTGGTATGGCTTTCCGTGTTCCAACTGCTGATGTTTCAGTCGTTGATTTGA
CTGTTCGCCTCGCTAAGCCAGCTCCTTATGCCGAAATCAAGAAGAAGGTTAAGGAAGCCG
CTGAAGGTCCAATGAAGGGAATTTTGGATTACACTGAAGATGAAGTTGTCTCAACTGATT
TCACCAGTGACACACACTCATCTGTCTTTGATGCCGCCGCTGGTATTCCATTGAATGACC
ACTTCGTTAAGCTCATCTCATGGTACGATAACGAATACGGTTACTCCAACCGCGTTGTCG
ATCTCATCAAGTACATGCAAAGCAAGGATTAAATCAATTGTTACTAAATGATTCCAGTCC
TTCAATTTAAAAAATGAGAAGCATCACAACATCTGCATGCAGATTCTTTTAAATAATTAA
AAAGTGATTGGTGACACACACGTATGAATTTTAATAATTATTACTACCATAATACATATT
ATAATGCTGCTAGATTGAAAAGTGAAATAGTTTGTGAATTATTATTGGTTAAAGTTGAAA
ATATGAAAATAGGTCAAAAAATAGGTTCCTTTACCCTATATCAGCAAAAATAATATTCAA
TATTATTATTCAAACAACAACACACTTAAATCTGATGTCATCAATTTATCTAGATTGTAA
GGCATAATAATTTTTAAGGAAATAAAATACATCGTTCTGTGAAGCAGTTACAAAAGAAA

>g4309.t22 Gene=g4309 Length=302
MSKIGINGFGRIGRLVLRAALDKGAQVVAVNDPFINVDYMVYMFKYDSTHGRFKGEVKAE
GGFLVINGQKITVFQEPHFEGGAKKVIISAPSADAPMFVCGVNLDAYDPSMKVVSNASCT
TNCLAPLAKVVHDNFEIIEGLMTTVHATTATQKTVDGPSGKLWRDGRGAAQNIIPAATGA
AKAVGKVIPALNGKLTGMAFRVPTADVSVVDLTVRLAKPAPYAEIKKKVKEAAEGPMKGI
LDYTEDEVVSTDFTSDTHSSVFDAAAGIPLNDHFVKLISWYDNEYGYSNRVVDLIKYMQS
KD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g4309.t22 Gene3D G3DSA:3.40.50.720 - 1 77 1.2E-32
15 g4309.t22 Gene3D G3DSA:3.30.360.10 Dihydrodipicolinate Reductase; domain 2 117 283 9.3E-87
4 g4309.t22 PANTHER PTHR10836:SF103 GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 2 3 75 5.1E-164
6 g4309.t22 PANTHER PTHR10836 GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE 3 75 5.1E-164
3 g4309.t22 PANTHER PTHR10836:SF103 GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 2 78 302 5.1E-164
5 g4309.t22 PANTHER PTHR10836 GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE 78 302 5.1E-164
16 g4309.t22 PIRSF PIRSF000149 GAPDH 1 81 1.6E-22
17 g4309.t22 PIRSF PIRSF000149 GAPDH 75 302 8.3E-85
9 g4309.t22 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 78 91 2.3E-48
11 g4309.t22 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 113 131 2.3E-48
10 g4309.t22 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 140 156 2.3E-48
8 g4309.t22 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 197 214 2.3E-48
7 g4309.t22 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 237 252 2.3E-48
2 g4309.t22 Pfam PF00044 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain 3 77 2.2E-25
1 g4309.t22 Pfam PF02800 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain 124 281 2.1E-66
18 g4309.t22 ProSitePatterns PS00071 Glyceraldehyde 3-phosphate dehydrogenase active site. 117 124 -
19 g4309.t22 SMART SM00846 gp_dh_n_7 2 119 8.1E-69
12 g4309.t22 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 3 139 2.2E-58
13 g4309.t22 SUPERFAMILY SSF55347 Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain 118 281 1.28E-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