General information for g11929.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as D-3-phosphoglycerate dehydrogenase.
Parent gene
- The parent gene g11929 is located on chr_1: 19346541..19353281 (- 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_1 | g11929 | g11929.t4 | isoform | g11929.t4 | 19345841 | 19347422 |
| chr_1 | g11929 | g11929.t4 | TTS | g11929.t4 | 19345841 | 19345841 |
| chr_1 | g11929 | g11929.t4 | exon | g11929.t4.exon1 | 19345841 | 19346480 |
| chr_1 | g11929 | g11929.t4 | cds | g11929.t4.CDS1 | 19346125 | 19346480 |
| chr_1 | g11929 | g11929.t4 | exon | g11929.t4.exon2 | 19346541 | 19346893 |
| chr_1 | g11929 | g11929.t4 | cds | g11929.t4.CDS2 | 19346541 | 19346893 |
| chr_1 | g11929 | g11929.t4 | exon | g11929.t4.exon3 | 19346974 | 19347131 |
| chr_1 | g11929 | g11929.t4 | cds | g11929.t4.CDS3 | 19346974 | 19347131 |
| chr_1 | g11929 | g11929.t4 | exon | g11929.t4.exon4 | 19347235 | 19347422 |
| chr_1 | g11929 | g11929.t4 | cds | g11929.t4.CDS4 | 19347235 | 19347369 |
| chr_1 | g11929 | g11929.t4 | TSS | g11929.t4 | 19347424 | 19347424 |
Sequences
>g11929.t4 Gene=g11929 Length=1339
TCGTTATTGCAACTTTCATCAGTCAAGTACATTTTAAGTTATTTCATTATAAAATGCCGG
TTGATATCAAAACAGTTTTAGTATGTGATGCTGTTGATCAGTCATGCATCGATTTACTTA
AATCAAATGAAATTTCTGTCGATTATAAGCTTAAACTACCAAAAGAAGAGCTCTTACGTG
AAGTCAAGAACTACGACGCCGTTATTGTTCGTTCAGATACAAAAATTACAGCAGACGTCA
TCGCTTCAGGTGTAGAAGAAAAATTGCGAGTAATCGGACGAGCTGGTGTGGGCGTTGATA
ACATTGATATTGATGCAGCTACAAAACATAATGTCATTGTACTCAACACTCCAGGCGGAA
ATTCAATTGCTGCGACTGAACTGACTTGTTTACTACTTGCGGCACTGGGTCGACCAGTTT
GCGCTGCTAATGCAAGCATGAAAGAAGGTCGATGGGATCGAAAAATATATTCAGGAACAG
AATTGTATGGAAAAACACTTGCAATTTTAGGATTAGGCAGAATTGGTCGAGAAGTTGGCT
TTAGAATGAAAGCATGGGGAATGAAAATAATTGGCTATGATCCCATCACTACTCATGAAC
AAGCTGCAGAATATGGCATTGAAAAAATGGAACTTGATGAAATTTGGCCACTTGCCGATT
ATATTACATTGCATGTTCCATTGATTCCATCAACTAAAAATTTAATATCTTCCGATTCAT
TGAGCAAATGCAAAAATGGCGTAAAAGTCGTAAATGTCGCTCGTGGAGGGGTAATAGATG
AGGAAGCAATTTTCAAGGCACTAGAAAGCGGAAAATGTGGTGGTGCTGCATTTGATGTTT
ACGAAGAAGAACCACCAAAAAAAGAAATTACAAAAAAGCTGATTGCTCATCCAAAAGTTG
TCGCAACACCTCACTTAGGAGCAAGCACAAAAGAAGCTCAAATCAAAGTTGCTGTTGAAG
TTTCCGAGCAGTTTATTGCATTGACTGGAAAATCTAAAGAATTTACGCAATATAATGGCG
TTGTTAATCGTGAAATTTTAAAAACTTATTTTTGAAAATGATTTTCTAAATTATTAAATT
CTTAAAATTAAAGTCTGTCATTGACACAAATTCGCATACAATAAATCATTTATTATCGCG
GAAAACTGCGTAAAAAATAAAAAAAAAGTAAAGTCATAAAACCACACATACACAGTTTTC
AAATCAAAGCTCATAAATTTTATGTTCACAATTTATTTTGCTCTTCTTCTAAATAAATAT
TCCATCATAATGTGAATTGAATACAATATGTACATTTTCTGATGCTTTCCAAATAAAGAA
TGAAAGAAAAAAATAGAAA
>g11929.t4 Gene=g11929 Length=333
MPVDIKTVLVCDAVDQSCIDLLKSNEISVDYKLKLPKEELLREVKNYDAVIVRSDTKITA
DVIASGVEEKLRVIGRAGVGVDNIDIDAATKHNVIVLNTPGGNSIAATELTCLLLAALGR
PVCAANASMKEGRWDRKIYSGTELYGKTLAILGLGRIGREVGFRMKAWGMKIIGYDPITT
HEQAAEYGIEKMELDEIWPLADYITLHVPLIPSTKNLISSDSLSKCKNGVKVVNVARGGV
IDEEAIFKALESGKCGGAAFDVYEEEPPKKEITKKLIAHPKVVATPHLGASTKEAQIKVA
VEVSEQFIALTGKSKEFTQYNGVVNREILKTYF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g11929.t4 | CDD | cd12173 | PGDH_4 | 8 | 313 | 1.38271E-161 |
| 9 | g11929.t4 | Gene3D | G3DSA:3.40.50.720 | - | 8 | 300 | 2.0E-114 |
| 8 | g11929.t4 | Gene3D | G3DSA:3.40.50.720 | - | 99 | 291 | 2.0E-114 |
| 3 | g11929.t4 | PANTHER | PTHR42938:SF5 | D-3-PHOSPHOGLYCERATE DEHYDROGENASE | 3 | 329 | 3.4E-133 |
| 4 | g11929.t4 | PANTHER | PTHR42938 | FORMATE DEHYDROGENASE 1 | 3 | 329 | 3.4E-133 |
| 2 | g11929.t4 | Pfam | PF00389 | D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain | 8 | 310 | 4.7E-35 |
| 1 | g11929.t4 | Pfam | PF02826 | D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain | 114 | 289 | 2.7E-56 |
| 7 | g11929.t4 | ProSitePatterns | PS00065 | D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. | 149 | 176 | - |
| 6 | g11929.t4 | SUPERFAMILY | SSF52283 | Formate/glycerate dehydrogenase catalytic domain-like | 7 | 139 | 3.97E-31 |
| 5 | g11929.t4 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 107 | 289 | 2.97E-51 |
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:0051287 | NAD binding | MF |
| GO:0055114 | NA | NA |
KEGG
Orthology
- This transcript has been annotated with K00058 (D-3-phosphoglycerate dehydrogenase / 2-oxoglutarate reductase)
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