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.t31 isoform g4309.t31 1118057 1120395
chr_2 g4309 g4309.t31 exon g4309.t31.exon1 1118057 1118970
chr_2 g4309 g4309.t31 TTS g4309.t31 1118060 1118060
chr_2 g4309 g4309.t31 cds g4309.t31.CDS1 1118444 1118929
chr_2 g4309 g4309.t31 exon g4309.t31.exon2 1119078 1119483
chr_2 g4309 g4309.t31 exon g4309.t31.exon3 1120354 1120395
chr_2 g4309 g4309.t31 TSS g4309.t31 1120395 1120395

Sequences

>g4309.t31 Gene=g4309 Length=1362
ATTCTGCATCGAGCTGCGGTCTTGAACAGACATAAACTAAAAACTTAATCGTATTCAGCA
AAGCTAAAGCAAACTAATCAAAAATGTCAAAGATCGGTATCAATGGTTTTGGACGTATTG
GACGTTTGGTCCTCCGTGCTGCTTTGGACAAGGGAGCTCAAGTTGTTGCTGTTAACGATC
CATTCATCAATGTTGACTATATGGTTTACATGTTCAAATATGACTCAACCCACGGTCGCT
TCAAGGGAGAGGTCAAGGCTGAAGGCGGTTTCTTAGTCATCAATGGACAAAAGATTACAG
TTTTCCAAGAACGTGATCCAAAGAATATTGCATGGGGAAAGGCTGGCGCTGAATACATTG
TTGAATCAACTGGTGTTTTCACTACTATTGAAAAGGCATCAGCTCACTTTGAAGGCGGTG
CAAAGAAAGTCATTATCTCAGCTCCATCCTAAAGTTGTCCACGATAACTTCGAAATCATT
GAGGGATTGATGACCACTGTTCATGCAACCACAGCTACACAAAAGACCGTCGATGGCCCA
TCAGGCAAATTGTGGCGTGATGGACGTGGTGCTGCTCAAAATATCATTCCAGCAGCTACT
GGAGCAGCTAAGGCTGTCGGAAAAGTTATTCCAGCTTTGAATGGAAAATTGACTGGTATG
GCTTTCCGTGTTCCAACTGCTGATGTTTCAGTCGTTGATTTGACTGTTCGCCTCGCTAAG
CCAGCTCCTTATGCCGAAATCAAGAAGAAGGTTAAGGAAGCCGCTGAAGGTCCAATGAAG
GGAATTTTGGATTACACTGAAGATGAAGTTGTCTCAACTGATTTCACCAGTGACACACAC
TCATCTGTCTTTGATGCCGCCGCTGGTATTCCATTGAATGACCACTTCGTTAAGCTCATC
TCATGGTACGATAACGAATACGGTTACTCCAACCGCGTTGTCGATCTCATCAAGTACATG
CAAAGCAAGGATTAAATCAATTGTTACTAAATGATTCCAGTCCTTCAATTTAAAAAATGA
GAAGCATCACAACATCTGCATGCAGATTCTTTTAAATAATTAAAAAGTGATTGGTGACAC
ACACGTATGAATTTTAATAATTATTACTACCATAATACATATTATAATGCTGCTAGATTG
AAAAGTGAAATAGTTTGTGAATTATTATTGGTTAAAGTTGAAAATATGAAAATAGGTCAA
AAAATAGGTTCCTTTACCCTATATCAGCAAAAATAATATTCAATATTATTATTCAAACAA
CAACACACTTAAATCTGATGTCATCAATTTATCTAGATTGTAAGGCATAATAATTTTTAA
GGAAATAAAATACATCGTTCTGTGAAGCAGTTACAAAAGAAA

>g4309.t31 Gene=g4309 Length=161
MTTVHATTATQKTVDGPSGKLWRDGRGAAQNIIPAATGAAKAVGKVIPALNGKLTGMAFR
VPTADVSVVDLTVRLAKPAPYAEIKKKVKEAAEGPMKGILDYTEDEVVSTDFTSDTHSSV
FDAAAGIPLNDHFVKLISWYDNEYGYSNRVVDLIKYMQSKD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g4309.t31 Gene3D G3DSA:3.30.360.10 Dihydrodipicolinate Reductase; domain 2 1 142 0
7 g4309.t31 Gene3D G3DSA:3.40.50.720 - 143 154 0
2 g4309.t31 PANTHER PTHR10836:SF103 GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 2 1 161 0
3 g4309.t31 PANTHER PTHR10836 GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE 1 161 0
5 g4309.t31 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 56 73 0
4 g4309.t31 PRINTS PR00078 Glyceraldehyde-3-phosphate dehydrogenase signature 96 111 0
1 g4309.t31 Pfam PF02800 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain 1 140 0
6 g4309.t31 SUPERFAMILY SSF55347 Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain 1 140 0

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: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