General information for g4309.t17
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Glyceraldehyde-3-phosphate dehydrogenase.
Parent gene
- The parent gene g4309 is located on chr_2: 1118444..1120395 (- strand)
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.t17 | isoform | g4309.t17 | 1118057 | 1120395 |
| chr_2 | g4309 | g4309.t17 | exon | g4309.t17.exon1 | 1118057 | 1118588 |
| chr_2 | g4309 | g4309.t17 | TTS | g4309.t17 | 1118060 | 1118060 |
| chr_2 | g4309 | g4309.t17 | cds | g4309.t17.CDS1 | 1118586 | 1118588 |
| chr_2 | g4309 | g4309.t17 | exon | g4309.t17.exon2 | 1118714 | 1119483 |
| chr_2 | g4309 | g4309.t17 | cds | g4309.t17.CDS2 | 1118714 | 1119442 |
| chr_2 | g4309 | g4309.t17 | exon | g4309.t17.exon3 | 1120354 | 1120395 |
| chr_2 | g4309 | g4309.t17 | TSS | g4309.t17 | 1120395 | 1120395 |
Sequences
>g4309.t17 Gene=g4309 Length=1344
ATTCTGCATCGAGCTGCGGTCTTGAACAGACATAAACTAAAAACTTAATCGTATTCAGCA
AAGCTAAAGCAAACTAATCAAAAATGTCAAAGATCGGTATCAATGGTTTTGGACGTATTG
GACGTTTGGTCCTCCGTGCTGCTTTGGACAAGGGAGCTCAAGTTGTTGCTGTTAACGATC
CATTCATCAATGTTGACTATATGGTTTACATGTTCAAATATGACTCAACCCACGGTCGCT
TCAAGGGAGAGGTCAAGGCTGAAGGCGGTTTCTTAGTCATCAATGGACAAAAGATTACAG
TTTTCCAAGAACGTGATCCAAAGAATATTGCATGGGGAAAGGCTGGCGCTGAATACATTG
TTGAATCAACTGGTGTTTTCACTACTATTGAAAAGGCATCAGCTCACTTTGAAGGCGGTG
CAAAGAAAGTCATTATCTCAGCTCCATCAGCTGATGCACCAATGTTCGTTTGCGGTGTCA
ACTTGGATGCATACGATCCATCAATGAAGGTCGTCTCGAACGCTTCATGCACAACCAACT
GCTTGGCTCCATTAGCTAAAGTTGTCCACGATAACTTCGAAATCATTGAGGGATTGATGA
CCACTGTTCATGCAACCACAGCTACACAAAAGACCGTCGATGGCCCATCAGGCAAATTGT
GGCGTGATGGACGTGGTGCTGCTCAAAATATCATTCCAGCAGCTACTGGAGCAGCTAAGG
CTGTCGGAAAAGTTATTCCAGCTTTGAATGGAAAATTGACTGGTATGGCTTTCCGTGTTC
CAACTGCTGATGTTTCAGTCGTTGATTTGACTTGACACACACTCATCTGTCTTTGATGCC
GCCGCTGGTATTCCATTGAATGACCACTTCGTTAAGCTCATCTCATGGTACGATAACGAA
TACGGTTACTCCAACCGCGTTGTCGATCTCATCAAGTACATGCAAAGCAAGGATTAAATC
AATTGTTACTAAATGATTCCAGTCCTTCAATTTAAAAAATGAGAAGCATCACAACATCTG
CATGCAGATTCTTTTAAATAATTAAAAAGTGATTGGTGACACACACGTATGAATTTTAAT
AATTATTACTACCATAATACATATTATAATGCTGCTAGATTGAAAAGTGAAATAGTTTGT
GAATTATTATTGGTTAAAGTTGAAAATATGAAAATAGGTCAAAAAATAGGTTCCTTTACC
CTATATCAGCAAAAATAATATTCAATATTATTATTCAAACAACAACACACTTAAATCTGA
TGTCATCAATTTATCTAGATTGTAAGGCATAATAATTTTTAAGGAAATAAAATACATCGT
TCTGTGAAGCAGTTACAAAAGAAA
>g4309.t17 Gene=g4309 Length=243
MSKIGINGFGRIGRLVLRAALDKGAQVVAVNDPFINVDYMVYMFKYDSTHGRFKGEVKAE
GGFLVINGQKITVFQERDPKNIAWGKAGAEYIVESTGVFTTIEKASAHFEGGAKKVIISA
PSADAPMFVCGVNLDAYDPSMKVVSNASCTTNCLAPLAKVVHDNFEIIEGLMTTVHATTA
TQKTVDGPSGKLWRDGRGAAQNIIPAATGAAKAVGKVIPALNGKLTGMAFRVPTADVSVV
DLT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g4309.t17 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 169 | 2.0E-76 |
| 3 | g4309.t17 | PANTHER | PTHR10836:SF103 | GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 2 | 3 | 243 | 6.3E-136 |
| 4 | g4309.t17 | PANTHER | PTHR10836 | GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE | 3 | 243 | 6.3E-136 |
| 8 | g4309.t17 | PRINTS | PR00078 | Glyceraldehyde-3-phosphate dehydrogenase signature | 108 | 121 | 1.1E-38 |
| 6 | g4309.t17 | PRINTS | PR00078 | Glyceraldehyde-3-phosphate dehydrogenase signature | 143 | 161 | 1.1E-38 |
| 5 | g4309.t17 | PRINTS | PR00078 | Glyceraldehyde-3-phosphate dehydrogenase signature | 170 | 186 | 1.1E-38 |
| 7 | g4309.t17 | PRINTS | PR00078 | Glyceraldehyde-3-phosphate dehydrogenase signature | 227 | 243 | 1.1E-38 |
| 2 | g4309.t17 | Pfam | PF00044 | Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain | 3 | 101 | 1.4E-37 |
| 1 | g4309.t17 | Pfam | PF02800 | Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain | 154 | 243 | 3.9E-40 |
| 12 | g4309.t17 | ProSitePatterns | PS00071 | Glyceraldehyde 3-phosphate dehydrogenase active site. | 147 | 154 | - |
| 11 | g4309.t17 | SMART | SM00846 | gp_dh_n_7 | 2 | 149 | 1.5E-96 |
| 9 | g4309.t17 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 3 | 169 | 7.62E-77 |
| 10 | g4309.t17 | SUPERFAMILY | SSF55347 | Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 148 | 243 | 8.51E-49 |
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.
