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.t28 isoform g4309.t28 1118057 1120395
chr_2 g4309 g4309.t28 exon g4309.t28.exon1 1118057 1119111
chr_2 g4309 g4309.t28 TTS g4309.t28 1118060 1118060
chr_2 g4309 g4309.t28 cds g4309.t28.CDS1 1118444 1119111
chr_2 g4309 g4309.t28 exon g4309.t28.exon2 1119204 1119483
chr_2 g4309 g4309.t28 cds g4309.t28.CDS2 1119204 1119243
chr_2 g4309 g4309.t28 exon g4309.t28.exon3 1120354 1120395
chr_2 g4309 g4309.t28 TSS g4309.t28 1120395 1120395

Sequences

>g4309.t28 Gene=g4309 Length=1377
ATTCTGCATCGAGCTGCGGTCTTGAACAGACATAAACTAAAAACTTAATCGTATTCAGCA
AAGCTAAAGCAAACTAATCAAAAATGTCAAAGATCGGTATCAATGGTTTTGGACGTATTG
GACGTTTGGTCCTCCGTGCTGCTTTGGACAAGGGAGCTCAAGTTGTTGCTGTTAACGATC
CATTCATCAATGTTGACTATATGGTTTACATGTTCAAATATGACTCAACCCACGGTCGCT
TCAAGGGAGAGGTCAAGGCTGAAGGCGGTTTCTTAGTCATCAATGGACAAAAGATTACAG
TTTTCCAAGAACGTGATCCAAAGCGGTGCAAAGAAAGTCATTATCTCAGCTCCATCAGCT
GATGCACCAATGTTCGTTTGCGGTGTCAACTTGGATGCATACGATCCATCAATGAAGGTC
GTCTCGAACGCTTCATGCACAACCAACTGCTTGGCTCCATTAGCTAAAGTTGTCCACGAT
AACTTCGAAATCATTGAGGGATTGATGACCACTGTTCATGCAACCACAGCTACACAAAAG
ACCGTCGATGGCCCATCAGGCAAATTGTGGCGTGATGGACGTGGTGCTGCTCAAAATATC
ATTCCAGCAGCTACTGGAGCAGCTAAGGCTGTCGGAAAAGTTATTCCAGCTTTGAATGGA
AAATTGACTGGTATGGCTTTCCGTGTTCCAACTGCTGATGTTTCAGTCGTTGATTTGACT
GTTCGCCTCGCTAAGCCAGCTCCTTATGCCGAAATCAAGAAGAAGGTTAAGGAAGCCGCT
GAAGGTCCAATGAAGGGAATTTTGGATTACACTGAAGATGAAGTTGTCTCAACTGATTTC
ACCAGTGACACACACTCATCTGTCTTTGATGCCGCCGCTGGTATTCCATTGAATGACCAC
TTCGTTAAGCTCATCTCATGGTACGATAACGAATACGGTTACTCCAACCGCGTTGTCGAT
CTCATCAAGTACATGCAAAGCAAGGATTAAATCAATTGTTACTAAATGATTCCAGTCCTT
CAATTTAAAAAATGAGAAGCATCACAACATCTGCATGCAGATTCTTTTAAATAATTAAAA
AGTGATTGGTGACACACACGTATGAATTTTAATAATTATTACTACCATAATACATATTAT
AATGCTGCTAGATTGAAAAGTGAAATAGTTTGTGAATTATTATTGGTTAAAGTTGAAAAT
ATGAAAATAGGTCAAAAAATAGGTTCCTTTACCCTATATCAGCAAAAATAATATTCAATA
TTATTATTCAAACAACAACACACTTAAATCTGATGTCATCAATTTATCTAGATTGTAAGG
CATAATAATTTTTAAGGAAATAAAATACATCGTTCTGTGAAGCAGTTACAAAAGAAA

>g4309.t28 Gene=g4309 Length=235
MDKRLQFSKNVIQSGAKKVIISAPSADAPMFVCGVNLDAYDPSMKVVSNASCTTNCLAPL
AKVVHDNFEIIEGLMTTVHATTATQKTVDGPSGKLWRDGRGAAQNIIPAATGAAKAVGKV
IPALNGKLTGMAFRVPTADVSVVDLTVRLAKPAPYAEIKKKVKEAAEGPMKGILDYTEDE
VVSTDFTSDTHSSVFDAAAGIPLNDHFVKLISWYDNEYGYSNRVVDLIKYMQSKD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g4309.t28 Gene3D G3DSA:3.30.360.10 Dihydrodipicolinate Reductase; domain 2 50 216 4.4E-87
2 g4309.t28 PANTHER PTHR10836 GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE 10 234 3.1E-130
7 g4309.t28 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 11 24 9.1E-47
6 g4309.t28 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 46 64 9.1E-47
5 g4309.t28 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 73 89 9.1E-47
3 g4309.t28 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 130 147 9.1E-47
4 g4309.t28 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 170 185 9.1E-47
1 g4309.t28 Pfam PF02800 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain 57 214 1.0E-66
11 g4309.t28 ProSitePatterns PS00071 Glyceraldehyde 3-phosphate dehydrogenase active site. 50 57 -
10 g4309.t28 SMART SM00846 gp_dh_n_7 3 52 0.0012
8 g4309.t28 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 10 68 2.37E-20
9 g4309.t28 SUPERFAMILY SSF55347 Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain 51 214 6.24E-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