General information for g11929.t3
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.t3 | isoform | g11929.t3 | 19345841 | 19346890 |
| chr_1 | g11929 | g11929.t3 | TTS | g11929.t3 | 19345841 | 19345841 |
| chr_1 | g11929 | g11929.t3 | exon | g11929.t3.exon1 | 19345841 | 19346480 |
| chr_1 | g11929 | g11929.t3 | cds | g11929.t3.CDS1 | 19346125 | 19346480 |
| chr_1 | g11929 | g11929.t3 | exon | g11929.t3.exon2 | 19346541 | 19346890 |
| chr_1 | g11929 | g11929.t3 | cds | g11929.t3.CDS2 | 19346541 | 19346802 |
| chr_1 | g11929 | g11929.t3 | TSS | g11929.t3 | 19347424 | 19347424 |
Sequences
>g11929.t3 Gene=g11929 Length=990
TCCAGGCGGAAATTCAATTGCTGCGACTGAACTGACTTGTTTACTACTTGCGGCACTGGG
TCGACCAGTTTGCGCTGCTAATGCAAGCATGAAAGAAGGTCGATGGGATCGAAAAATATA
TTCAGGAACAGAATTGTATGGAAAAACACTTGCAATTTTAGGATTAGGCAGAATTGGTCG
AGAAGTTGGCTTTAGAATGAAAGCATGGGGAATGAAAATAATTGGCTATGATCCCATCAC
TACTCATGAACAAGCTGCAGAATATGGCATTGAAAAAATGGAACTTGATGAAATTTGGCC
ACTTGCCGATTATATTACATTGCATGTTCCATTGATTCCATCAACTAAAAATTTAATATC
TTCCGATTCATTGAGCAAATGCAAAAATGGCGTAAAAGTCGTAAATGTCGCTCGTGGAGG
GGTAATAGATGAGGAAGCAATTTTCAAGGCACTAGAAAGCGGAAAATGTGGTGGTGCTGC
ATTTGATGTTTACGAAGAAGAACCACCAAAAAAAGAAATTACAAAAAAGCTGATTGCTCA
TCCAAAAGTTGTCGCAACACCTCACTTAGGAGCAAGCACAAAAGAAGCTCAAATCAAAGT
TGCTGTTGAAGTTTCCGAGCAGTTTATTGCATTGACTGGAAAATCTAAAGAATTTACGCA
ATATAATGGCGTTGTTAATCGTGAAATTTTAAAAACTTATTTTTGAAAATGATTTTCTAA
ATTATTAAATTCTTAAAATTAAAGTCTGTCATTGACACAAATTCGCATACAATAAATCAT
TTATTATCGCGGAAAACTGCGTAAAAAATAAAAAAAAAGTAAAGTCATAAAACCACACAT
ACACAGTTTTCAAATCAAAGCTCATAAATTTTATGTTCACAATTTATTTTGCTCTTCTTC
TAAATAAATATTCCATCATAATGTGAATTGAATACAATATGTACATTTTCTGATGCTTTC
CAAATAAAGAATGAAAGAAAAAAATAGAAA
>g11929.t3 Gene=g11929 Length=205
MKEGRWDRKIYSGTELYGKTLAILGLGRIGREVGFRMKAWGMKIIGYDPITTHEQAAEYG
IEKMELDEIWPLADYITLHVPLIPSTKNLISSDSLSKCKNGVKVVNVARGGVIDEEAIFK
ALESGKCGGAAFDVYEEEPPKKEITKKLIAHPKVVATPHLGASTKEAQIKVAVEVSEQFI
ALTGKSKEFTQYNGVVNREILKTYF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11929.t3 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 163 | 2.1E-58 |
| 2 | g11929.t3 | PANTHER | PTHR42938:SF5 | D-3-PHOSPHOGLYCERATE DEHYDROGENASE | 1 | 201 | 1.8E-86 |
| 3 | g11929.t3 | PANTHER | PTHR42938 | FORMATE DEHYDROGENASE 1 | 1 | 201 | 1.8E-86 |
| 1 | g11929.t3 | Pfam | PF02826 | D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain | 1 | 161 | 4.0E-54 |
| 5 | g11929.t3 | ProSitePatterns | PS00065 | D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. | 21 | 48 | - |
| 4 | g11929.t3 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 2 | 161 | 1.2E-47 |
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: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. There were no conditions that were differentially expressed