General information for g2979.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Glucose dehydrogenase.
Parent gene
- The parent gene g2979 is located on chr_3: 21705788..21706584 (+ 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 | g2979 | g2979.t1 | isoform | g2979.t1 | 21703314 | 21705921 |
| chr_3 | g2979 | g2979.t1 | exon | g2979.t1.exon1 | 21703314 | 21703404 |
| chr_3 | g2979 | g2979.t1 | cds | g2979.t1.CDS1 | 21703314 | 21703404 |
| chr_3 | g2979 | g2979.t1 | exon | g2979.t1.exon2 | 21703462 | 21703695 |
| chr_3 | g2979 | g2979.t1 | cds | g2979.t1.CDS2 | 21703462 | 21703695 |
| chr_3 | g2979 | g2979.t1 | exon | g2979.t1.exon3 | 21703755 | 21703884 |
| chr_3 | g2979 | g2979.t1 | cds | g2979.t1.CDS3 | 21703755 | 21703884 |
| chr_3 | g2979 | g2979.t1 | exon | g2979.t1.exon4 | 21703940 | 21704118 |
| chr_3 | g2979 | g2979.t1 | cds | g2979.t1.CDS4 | 21703940 | 21704118 |
| chr_3 | g2979 | g2979.t1 | exon | g2979.t1.exon5 | 21704178 | 21704279 |
| chr_3 | g2979 | g2979.t1 | cds | g2979.t1.CDS5 | 21704178 | 21704279 |
| chr_3 | g2979 | g2979.t1 | exon | g2979.t1.exon6 | 21704338 | 21704970 |
| chr_3 | g2979 | g2979.t1 | cds | g2979.t1.CDS6 | 21704338 | 21704970 |
| chr_3 | g2979 | g2979.t1 | exon | g2979.t1.exon7 | 21705029 | 21705409 |
| chr_3 | g2979 | g2979.t1 | cds | g2979.t1.CDS7 | 21705029 | 21705409 |
| chr_3 | g2979 | g2979.t1 | exon | g2979.t1.exon8 | 21705518 | 21705724 |
| chr_3 | g2979 | g2979.t1 | cds | g2979.t1.CDS8 | 21705518 | 21705724 |
| chr_3 | g2979 | g2979.t1 | exon | g2979.t1.exon9 | 21705788 | 21705921 |
| chr_3 | g2979 | g2979.t1 | cds | g2979.t1.CDS9 | 21705788 | 21705921 |
| chr_3 | g2979 | g2979.t1 | TSS | g2979.t1 | NA | NA |
| chr_3 | g2979 | g2979.t1 | TTS | g2979.t1 | NA | NA |
Sequences
>g2979.t1 Gene=g2979 Length=2091
ATGGTTGTTGGGATTGCTGCTGCTGGTTTTTCAGCAGTCAAAATTATTCCCGCGATAGGC
GGTGCAGCGTTGAAAGTGATACCAGCAATAGGTCTAGCATCTGCTGGAGCAGGAAAACTA
GCAGCAACGGTCACCACTGGTGTCAAAGCAGCTACAGCAATTATTGGCGTTGGAAAGCTT
GCCATTATACCTGTATTAATTGCTGCACTTGCTTACTATCATTATGATGTTTTCGACCCT
GAAAATCGACCTTTCAATATAAAAGAGGTCGAACATGAATATGATTTTATTGTTGTTGGA
TCGGGAGCGGGTGGTTCAGTTGTTGCAAGCCGATTATCAGAAATTGGTAATTGGAAAGTG
CTTTTGTTAGAAGCTGGCGGTCACGAGACTGAAATCTCTGATGTTCCAATACTTTCATTA
TATTTACATAAGAGTAAATTGGATTGGAAATATAGATATTTAACATTATGTAATTCATTT
CGAAGGACTCAACCGCAAAAGACAGCATGTCAAGCTATGGTTGATAAGCGATGTTGTTGG
ACACGCGGTAAAGTTTTGGGTGGTAGTACTGTATTAAATACGATGCTTTACATTCGAGGA
AATAGAAGAGATTTTGATTTGTGGGAAGCTTTAGGTAACGACGGATGGGGGTATGAAGAC
ATTCTTCCGTATTTTAAGAAATCAGAAGATCAAAGAAATCCATATTTGGCAAAAAATACT
CGATATCATTCAACAGGCGGTTACTTGACAATCCAAGACGCACCATATTTAACACCAATT
GGACCAGCATTTTTGCAAGCTGCTGAAGAGCAAGGCTATGATATTGTCGATATTAATGGT
GAACAACAAACTGGCTTTGCATTCTTTCAATTCCATCAACGACGTGCTTCGCGATGCAGT
GCAGCGAAAGCATTTTTGAGACCAGCACGATTACGTAAGAATCTTCACGTGGCACTATTT
GCACACGTTACAAGAGTAATAATGGATGAAACAACCAAAAGAGCACTTGGAGTCGAATTC
ATAAGAAATGGAAGAAAACAAGTAGTTTATGCAAAACGAGAAGTGATTTTAGCAGCTGGA
GCAATTGGAACACCACATTTATTAATGTTAAGTGGAATTGGACCAAAACAACATTTAGAA
CAACACGGTATCAAAGTTATTCATGATAGTCCTGGAGTAGGACGGAATTTACAAGATCAT
CCAGCCGCTGGTGGCCTTGTCTTTCAAATTGATCATCCAGTCGGATTGGTTATGAACAGA
TTAGTCAATATTAATTCAGCAGTTCGTTATGCAGTAACAGAAGATGGACCATTGACAAGC
AATATTGGAATTGAAGCTGTTGGATTTATTAGCACAAAATACGCAAACCAATCTGATGAT
TGGCCTGACATTGAATTTCATCTTACGAGTGCTTCAACAACATCTGATGAACAAGCAAAA
ATTGCACATGGTCTAACTGATGAATTTTACGAGTACATGTTTGCAGATGTGAAGAATAAA
GACGTTTTTGGTGTGTTTCCAATGTTATTGCGACCAAAAAGTCGAGGTTTTATGAAACTT
CAATCGAAAAATCCATTACGTTATCCTTTACTCTATCACAATTACTTCACACATCCTGAT
GACATTGCAGTACTGCGAGAAGGTGTCAAATCAGCCATTTCACTTATCGAAACACAAGCG
TTAAAGAAATTCGGTGCAAGATTTCACGATAGAAAAGTTCCTAATTGTAGACATTTAGAA
ATGTACACAGATGAATATTGGGACTGCTCAATTAGACAATACACAATGTCTATTTACCAT
TATAGTGGCACTGCGAAAATGGGAACAGCTGACGATCCGTTTGCTGTTGTCGACAATCAG
CTTCGAGTGTATGGTGTACAAGGTCTCAGAGTCATTGACGCGAGCATTATGCCGACAATT
ACGAACGGAAATATCGTAGCGCCTGTAATTATGATTGGTGAGAAAGGTGCTGACATGATA
AAAAGTCTTTGGTTACAATCAACAGATCATTTCGAAGATTACAGATTTAAGCGAAACGAT
AATACTACAATAGATTCAAATAATCAAAATGTTGACAAAGTACCGAGCTGA
>g2979.t1 Gene=g2979 Length=696
MVVGIAAAGFSAVKIIPAIGGAALKVIPAIGLASAGAGKLAATVTTGVKAATAIIGVGKL
AIIPVLIAALAYYHYDVFDPENRPFNIKEVEHEYDFIVVGSGAGGSVVASRLSEIGNWKV
LLLEAGGHETEISDVPILSLYLHKSKLDWKYRYLTLCNSFRRTQPQKTACQAMVDKRCCW
TRGKVLGGSTVLNTMLYIRGNRRDFDLWEALGNDGWGYEDILPYFKKSEDQRNPYLAKNT
RYHSTGGYLTIQDAPYLTPIGPAFLQAAEEQGYDIVDINGEQQTGFAFFQFHQRRASRCS
AAKAFLRPARLRKNLHVALFAHVTRVIMDETTKRALGVEFIRNGRKQVVYAKREVILAAG
AIGTPHLLMLSGIGPKQHLEQHGIKVIHDSPGVGRNLQDHPAAGGLVFQIDHPVGLVMNR
LVNINSAVRYAVTEDGPLTSNIGIEAVGFISTKYANQSDDWPDIEFHLTSASTTSDEQAK
IAHGLTDEFYEYMFADVKNKDVFGVFPMLLRPKSRGFMKLQSKNPLRYPLLYHNYFTHPD
DIAVLREGVKSAISLIETQALKKFGARFHDRKVPNCRHLEMYTDEYWDCSIRQYTMSIYH
YSGTAKMGTADDPFAVVDNQLRVYGVQGLRVIDASIMPTITNGNIVAPVIMIGEKGADMI
KSLWLQSTDHFEDYRFKRNDNTTIDSNNQNVDKVPS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g2979.t1 | Gene3D | G3DSA:3.50.50.60 | - | 94 | 661 | 2.4E-185 |
| 12 | g2979.t1 | Gene3D | G3DSA:3.30.560.10 | Glucose Oxidase | 133 | 599 | 2.4E-185 |
| 3 | g2979.t1 | PANTHER | PTHR11552:SF154 | FI04917P | 22 | 674 | 0.0 |
| 4 | g2979.t1 | PANTHER | PTHR11552 | GLUCOSE-METHANOL-CHOLINE GMC OXIDOREDUCTASE | 22 | 674 | 0.0 |
| 13 | g2979.t1 | PIRSF | PIRSF000137 | Alcohol_oxidase | 72 | 670 | 5.2E-161 |
| 1 | g2979.t1 | Pfam | PF00732 | GMC oxidoreductase | 94 | 402 | 3.0E-81 |
| 2 | g2979.t1 | Pfam | PF05199 | GMC oxidoreductase | 512 | 655 | 5.3E-39 |
| 10 | g2979.t1 | ProSitePatterns | PS00623 | GMC oxidoreductases signature 1. | 183 | 206 | - |
| 9 | g2979.t1 | ProSitePatterns | PS00624 | GMC oxidoreductases signature 2. | 360 | 374 | - |
| 8 | g2979.t1 | SUPERFAMILY | SSF51905 | FAD/NAD(P)-binding domain | 90 | 664 | 9.64E-86 |
| 7 | g2979.t1 | SUPERFAMILY | SSF54373 | FAD-linked reductases, C-terminal domain | 444 | 604 | 4.91E-42 |
| 6 | g2979.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 15 | 37 | - |
| 5 | g2979.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 50 | 72 | - |
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:0016614 | oxidoreductase activity, acting on CH-OH group of donors | MF |
| GO:0050660 | flavin adenine dinucleotide binding | MF |
| GO:0055114 | NA | NA |
KEGG
Orthology
- This transcript has been annotated with K00108 (choline dehydrogenase)
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