General information for g1842.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Glucose dehydrogenase.
Parent gene
- The parent gene g1842 is located on chr_3: 13262350..13264715 (- 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 | g1842 | g1842.t1 | isoform | g1842.t1 | 13262350 | 13264715 |
| chr_3 | g1842 | g1842.t1 | exon | g1842.t1.exon1 | 13262350 | 13262599 |
| chr_3 | g1842 | g1842.t1 | cds | g1842.t1.CDS1 | 13262350 | 13262599 |
| chr_3 | g1842 | g1842.t1 | exon | g1842.t1.exon2 | 13262663 | 13263905 |
| chr_3 | g1842 | g1842.t1 | cds | g1842.t1.CDS2 | 13262663 | 13263905 |
| chr_3 | g1842 | g1842.t1 | exon | g1842.t1.exon3 | 13263965 | 13263997 |
| chr_3 | g1842 | g1842.t1 | cds | g1842.t1.CDS3 | 13263965 | 13263997 |
| chr_3 | g1842 | g1842.t1 | exon | g1842.t1.exon4 | 13264092 | 13264173 |
| chr_3 | g1842 | g1842.t1 | cds | g1842.t1.CDS4 | 13264092 | 13264173 |
| chr_3 | g1842 | g1842.t1 | exon | g1842.t1.exon5 | 13264242 | 13264384 |
| chr_3 | g1842 | g1842.t1 | cds | g1842.t1.CDS5 | 13264242 | 13264384 |
| chr_3 | g1842 | g1842.t1 | exon | g1842.t1.exon6 | 13264580 | 13264715 |
| chr_3 | g1842 | g1842.t1 | cds | g1842.t1.CDS6 | 13264580 | 13264715 |
| chr_3 | g1842 | g1842.t1 | TSS | g1842.t1 | NA | NA |
| chr_3 | g1842 | g1842.t1 | TTS | g1842.t1 | NA | NA |
Sequences
>g1842.t1 Gene=g1842 Length=1887
ATGTGGACATGTGTCAAATTATTCATAGTTTTCATTATTCTAACACAAAAAGTACAAAAA
AGTATCGGATTCTTCCCACAATTTGCGCCATTTGTTGAAAAACTCATCAAGAATAAGGCA
GATTATATAGTTGAAAGAAGGGCTTATTTGAGGGAATATGATTTCATCATTGTCGGCAGT
GGACCAGCAGGGTGCGTTGTTGCCAATCGACTTACAGAAAATCCAAATTTTAACGTTCTT
CTCATTGAGGCTGGAACTGTTGAGACGCTTGTTGAACAAGTTCCACTTTTTGCACCATAT
GAATTTTTAACACGCTACAATTGGGGATATTTAGCAGAGCGTCAACCTTACTCGTGTTTG
GGTTTAAAAGATCAACAATGTGGTTTTCCAAGAGGAAAAGCATTAGGTGGAACATCTGTT
ATCAATGGAATGCTTTATACACGAGGATTTAAAGAAGATTTTGATGAATGGGTTAGATTA
GGAAATTATAATTGGGATTATTATGAAACTGTTCTACCAGCATTTAAAAAATCTGAAAAA
GCTAGACTTAAATTTTATCATAAACCAGAATATCACAATACAAGCGGCTTATTGGGCGTT
TCACATAATCCACATCAAACACCAATAACTAAAATTTTTATGGACGCAAATAAATTAATG
GGATTAGACGAAATCGATTACAATTCCGATGACAATATTGGTGTAGCTCATTTGCAAGCT
AATACATTGAAAGGTCGCCGACATTCTGCATACAAAGCATTTATTGAACCATTCTTGCAT
CGTCGAAATCTTCACATCATGCTGAATACACGAGTCACAAAAGTTTTGATTGATAGAGTT
ACTCGTGTTGCTTACGGTGTGGAGCTTTTGCGTAAGAAGAGACGACAAAAATTTATAGCA
CGCAGAGAAGTGATACTTTCTGCAGGCACATTCCATTCACCTCAATTGTTAATGCTGTCA
GGTATAGGACCACGTGAAGATCTTGAAAAAATTGGCGTTGAAGTTATTCACGATTCACCA
GTTGGTAAAGAAATGTACGATCATATATCATTCCCAGGACTCATGTTTACGACAAATCTA
ACAAATCCAAGCGCGCCGATGTTGGAGATAAAAAATTTGGTAAAAATGATGGGTAATTTC
TTACATGGTAAGGGTTATGCTACAGTTCCGAATGGAGTTGAAAGTCTTGCATTTATACAG
ACACCAACATTTAATGCACCTAATGAGAGACTTCCAAATATTGAGCTAATCTTACTCACA
CTTGTACCTCATTCTGATAATGGTCATGCAGTTAGAAATAGTGAAAGAATGAGTGATTGG
CTTTATGATTCTGTCTATAGACCATTGGAAGGAGAAACTACTTATTCTTTCTTAATTGTT
ATCTCATTACTTCATCCTAAATCTGTTGGATATATGAAATTACGAGATAGAAACATTTTT
AGTCCACCAAAATTCTATTCAAATTTCTTTAAAGAACCTGAAGATGTGGAATCAATTTTA
GAAGCAATCAAATATACTTTTTATTTGATAAATACTGAACCTTTTAAAAATATTAATGCA
CGACTTCATAATATACCGATACCTACGTGTAAACATCTCAATTTCGGTAGTGATGATTAT
TGGCGATGTGCTATAAGAACATGGTGCGTTTCTTTACATCATCAGACAGCGACATGCAAA
ATGGGATCCACACGAGATGCGGTGGTCAACAGTGAGCTCAAAGTTTACGGTGTAAAAAAA
CTGCGAGTTATTGACACATCAATCATTCCGAATTCACCATCAAGTCACACGAATGCTGCA
AGTTTTATGATTGGAGAGGTCGGTGCTGATTTGATAAAGAAAGATTGGCAGAGGCAGCGA
CAAACTTGGTACAATTATTATCACTAA
>g1842.t1 Gene=g1842 Length=628
MWTCVKLFIVFIILTQKVQKSIGFFPQFAPFVEKLIKNKADYIVERRAYLREYDFIIVGS
GPAGCVVANRLTENPNFNVLLIEAGTVETLVEQVPLFAPYEFLTRYNWGYLAERQPYSCL
GLKDQQCGFPRGKALGGTSVINGMLYTRGFKEDFDEWVRLGNYNWDYYETVLPAFKKSEK
ARLKFYHKPEYHNTSGLLGVSHNPHQTPITKIFMDANKLMGLDEIDYNSDDNIGVAHLQA
NTLKGRRHSAYKAFIEPFLHRRNLHIMLNTRVTKVLIDRVTRVAYGVELLRKKRRQKFIA
RREVILSAGTFHSPQLLMLSGIGPREDLEKIGVEVIHDSPVGKEMYDHISFPGLMFTTNL
TNPSAPMLEIKNLVKMMGNFLHGKGYATVPNGVESLAFIQTPTFNAPNERLPNIELILLT
LVPHSDNGHAVRNSERMSDWLYDSVYRPLEGETTYSFLIVISLLHPKSVGYMKLRDRNIF
SPPKFYSNFFKEPEDVESILEAIKYTFYLINTEPFKNINARLHNIPIPTCKHLNFGSDDY
WRCAIRTWCVSLHHQTATCKMGSTRDAVVNSELKVYGVKKLRVIDTSIIPNSPSSHTNAA
SFMIGEVGADLIKKDWQRQRQTWYNYYH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g1842.t1 | Gene3D | G3DSA:3.50.50.60 | - | 53 | 613 | 3.5E-160 |
| 9 | g1842.t1 | Gene3D | G3DSA:3.30.560.10 | Glucose Oxidase | 90 | 553 | 3.5E-160 |
| 3 | g1842.t1 | PANTHER | PTHR11552:SF208 | GLUCOSE DEHYDROGENASE [FAD, QUINONE]-LIKE PROTEIN | 36 | 621 | 2.3E-217 |
| 4 | g1842.t1 | PANTHER | PTHR11552 | GLUCOSE-METHANOL-CHOLINE GMC OXIDOREDUCTASE | 36 | 621 | 2.3E-217 |
| 15 | g1842.t1 | PIRSF | PIRSF000137 | Alcohol_oxidase | 44 | 622 | 4.5E-136 |
| 1 | g1842.t1 | Pfam | PF00732 | GMC oxidoreductase | 53 | 349 | 8.8E-72 |
| 2 | g1842.t1 | Pfam | PF05199 | GMC oxidoreductase | 466 | 606 | 3.5E-30 |
| 11 | g1842.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 20 | - |
| 12 | g1842.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 6 | - |
| 13 | g1842.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 7 | 15 | - |
| 14 | g1842.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 20 | - |
| 10 | g1842.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 21 | 628 | - |
| 17 | g1842.t1 | ProSitePatterns | PS00623 | GMC oxidoreductases signature 1. | 132 | 155 | - |
| 16 | g1842.t1 | ProSitePatterns | PS00624 | GMC oxidoreductases signature 2. | 309 | 323 | - |
| 6 | g1842.t1 | SUPERFAMILY | SSF51905 | FAD/NAD(P)-binding domain | 52 | 617 | 2.78E-74 |
| 5 | g1842.t1 | SUPERFAMILY | SSF54373 | FAD-linked reductases, C-terminal domain | 390 | 558 | 3.04E-29 |
| 7 | g1842.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 23 | - |
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 K15403 (fatty acid omega-hydroxy dehydrogenase [EC:1.1.-.-])
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.
