General information for g2408.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic.
Parent gene
- The parent gene g2408 is located on chr_3: 17726090..17727100 (- 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_3 | g2408 | g2408.t1 | TTS | g2408.t1 | 17725761 | 17725761 |
| chr_3 | g2408 | g2408.t1 | isoform | g2408.t1 | 17725882 | 17727100 |
| chr_3 | g2408 | g2408.t1 | exon | g2408.t1.exon1 | 17725882 | 17726037 |
| chr_3 | g2408 | g2408.t1 | cds | g2408.t1.CDS1 | 17725882 | 17726037 |
| chr_3 | g2408 | g2408.t1 | exon | g2408.t1.exon2 | 17726091 | 17726887 |
| chr_3 | g2408 | g2408.t1 | cds | g2408.t1.CDS2 | 17726091 | 17726887 |
| chr_3 | g2408 | g2408.t1 | exon | g2408.t1.exon3 | 17726945 | 17727003 |
| chr_3 | g2408 | g2408.t1 | cds | g2408.t1.CDS3 | 17726945 | 17727003 |
| chr_3 | g2408 | g2408.t1 | exon | g2408.t1.exon4 | 17727060 | 17727100 |
| chr_3 | g2408 | g2408.t1 | cds | g2408.t1.CDS4 | 17727060 | 17727100 |
| chr_3 | g2408 | g2408.t1 | TSS | g2408.t1 | 17727190 | 17727190 |
Sequences
>g2408.t1 Gene=g2408 Length=1053
ATGTCTAAGTTAAGAGTAAGCATTATTGGATCAGGCAATTGGGGATCAGCTATCGCAAAA
ATAGTTGGAAAGAATGTTGAAAAATTATCACAATTTGAAAATCGTGTGAATATGTATGTT
TATGAAGAAATGGTCAATGGAAAGAAACTATCTGAAATAATTAATGAAACACACGAAAAT
GTCAAGTATCTTCCTAATCACAAACTTCCAACAACAATAATAGCCGTTCCTGATCTTTTG
AAAGCTGTTGAAGATGCTGATATTTTGATCTTTGTAATTCCACATCAATTTGTCAAGAAT
GTTGGAAATCAACTCGCAGGAAAGATCAAAAATACTGCAATTGCTCTTTCTCTTATTAAA
GGATTTGATATCGCTGAAGGAGGTGGAATTGAATTGATTTCAAATGTCATTACAAAACAT
CTTCAAATACCTTGTTCAGTACTTATGGGCGCGAATCTTGCAAATGAAGTTGCTGATGAA
AAATTCTGTGAAACAACGATTGGTTGTCATAATCCAAAAACTTCGTTAATTTTAAAAGAA
TTAATACAAACTCCAAATTTCCGTGTGGTAACAACTGAAGATGTTGAGACTGTTGAAGTG
TGTGGTGCATTGAAAAATATCGTTGCATGTGGAGCTGGCTTTAGCGACGGTTTAGATCTC
GGTGACAACACTAAAGCAGCAATCATTCGTTTGGGACTAATGGAAATGATTAAATTTGTA
GAAGTGTTTTATGATAAGAATCATAAATTGTCAACATTCTTTGAGTCATGTGGGATTGCT
GATTTAGTGACAACATGCTATGGTGGACGAAATAGAAAATGCAGTGAAGCATTTGTAAGA
ACTGGCAGAAATTTTGATGAATTAGAAAAAGAAATGTTAAATGGTCAAAGATTACAGGGT
CCAGAGACAGCAGCTGAAGTCTATCACATGTTAAAATGTAAAAATATGGAAGAAAAATTT
CCACTTTTTAGAGCTATTCATCGTATTTGCATCGGTGAGATAAAACCAAAAGATTTGATC
GACTGTATTCGTCAGCATCCGGAACACATGTGA
>g2408.t1 Gene=g2408 Length=350
MSKLRVSIIGSGNWGSAIAKIVGKNVEKLSQFENRVNMYVYEEMVNGKKLSEIINETHEN
VKYLPNHKLPTTIIAVPDLLKAVEDADILIFVIPHQFVKNVGNQLAGKIKNTAIALSLIK
GFDIAEGGGIELISNVITKHLQIPCSVLMGANLANEVADEKFCETTIGCHNPKTSLILKE
LIQTPNFRVVTTEDVETVEVCGALKNIVACGAGFSDGLDLGDNTKAAIIRLGLMEMIKFV
EVFYDKNHKLSTFFESCGIADLVTTCYGGRNRKCSEAFVRTGRNFDELEKEMLNGQRLQG
PETAAEVYHMLKCKNMEEKFPLFRAIHRICIGEIKPKDLIDCIRQHPEHM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g2408.t1 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 191 | 9.0E-78 |
| 14 | g2408.t1 | Gene3D | G3DSA:1.10.1040.10 | - | 194 | 350 | 8.4E-69 |
| 3 | g2408.t1 | PANTHER | PTHR11728:SF8 | GLYCEROL-3-PHOSPHATE DEHYDROGENASE [NAD(+)]-RELATED | 2 | 348 | 1.4E-156 |
| 4 | g2408.t1 | PANTHER | PTHR11728 | GLYCEROL-3-PHOSPHATE DEHYDROGENASE | 2 | 348 | 1.4E-156 |
| 15 | g2408.t1 | PIRSF | PIRSF000114 | Glycerol-3-P_dh | 1 | 350 | 4.4E-96 |
| 8 | g2408.t1 | PRINTS | PR00077 | NAD-dependent glycerol-3-phosphate dehydrogenase signature | 8 | 25 | 9.2E-81 |
| 10 | g2408.t1 | PRINTS | PR00077 | NAD-dependent glycerol-3-phosphate dehydrogenase signature | 70 | 97 | 9.2E-81 |
| 5 | g2408.t1 | PRINTS | PR00077 | NAD-dependent glycerol-3-phosphate dehydrogenase signature | 147 | 167 | 9.2E-81 |
| 9 | g2408.t1 | PRINTS | PR00077 | NAD-dependent glycerol-3-phosphate dehydrogenase signature | 187 | 211 | 9.2E-81 |
| 7 | g2408.t1 | PRINTS | PR00077 | NAD-dependent glycerol-3-phosphate dehydrogenase signature | 212 | 236 | 9.2E-81 |
| 6 | g2408.t1 | PRINTS | PR00077 | NAD-dependent glycerol-3-phosphate dehydrogenase signature | 255 | 272 | 9.2E-81 |
| 1 | g2408.t1 | Pfam | PF01210 | NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus | 6 | 173 | 9.6E-51 |
| 2 | g2408.t1 | Pfam | PF07479 | NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus | 194 | 340 | 9.6E-47 |
| 16 | g2408.t1 | ProSitePatterns | PS00957 | NAD-dependent glycerol-3-phosphate dehydrogenase signature. | 202 | 223 | - |
| 11 | g2408.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 2 | 194 | 8.78E-40 |
| 12 | g2408.t1 | SUPERFAMILY | SSF48179 | 6-phosphogluconate dehydrogenase C-terminal domain-like | 193 | 348 | 1.0E-45 |
| 17 | g2408.t1 | TIGRFAM | TIGR03376 | glycerol3P_DH: glycerol-3-phosphate dehydrogenase (NAD(+)) | 5 | 343 | 1.6E-147 |
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:0016616 | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | MF |
| GO:0046168 | glycerol-3-phosphate catabolic process | BP |
| GO:0051287 | NAD binding | MF |
| GO:0055114 | NA | NA |
| GO:0042803 | protein homodimerization activity | MF |
| GO:0004367 | glycerol-3-phosphate dehydrogenase [NAD+] activity | MF |
| GO:0006072 | glycerol-3-phosphate metabolic process | BP |
| GO:0009331 | glycerol-3-phosphate dehydrogenase complex | CC |
| GO:0005975 | carbohydrate metabolic process | BP |
| GO:0016491 | oxidoreductase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K00006 (glycerol-3-phosphate dehydrogenase (NAD+))
Pathway
- This transcript belongs to the following pathways
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. There were no conditions that were differentially expressed