General information for g5156.t2
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Farnesol dehydrogenase.
Parent gene
- The parent gene g5156 is located on chr_2: 7327604..7328703 (- 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_2 | g5156 | g5156.t2 | isoform | g5156.t2 | 7326449 | 7328703 |
| chr_2 | g5156 | g5156.t2 | exon | g5156.t2.exon1 | 7326449 | 7327541 |
| chr_2 | g5156 | g5156.t2 | exon | g5156.t2.exon2 | 7327604 | 7327843 |
| chr_2 | g5156 | g5156.t2 | cds | g5156.t2.CDS1 | 7327833 | 7327843 |
| chr_2 | g5156 | g5156.t2 | exon | g5156.t2.exon3 | 7328016 | 7328385 |
| chr_2 | g5156 | g5156.t2 | cds | g5156.t2.CDS2 | 7328016 | 7328385 |
| chr_2 | g5156 | g5156.t2 | exon | g5156.t2.exon4 | 7328448 | 7328555 |
| chr_2 | g5156 | g5156.t2 | cds | g5156.t2.CDS3 | 7328448 | 7328555 |
| chr_2 | g5156 | g5156.t2 | exon | g5156.t2.exon5 | 7328617 | 7328703 |
| chr_2 | g5156 | g5156.t2 | cds | g5156.t2.CDS4 | 7328617 | 7328703 |
| chr_2 | g5156 | g5156.t2 | TSS | g5156.t2 | 7328803 | 7328803 |
| chr_2 | g5156 | g5156.t2 | TTS | g5156.t2 | NA | NA |
Sequences
>g5156.t2 Gene=g5156 Length=1898
ATGGATGGTGTTGAGAATGAAATTCCAATTCCATGGCAAGAAAAACTTGATAATGGTGTA
AAAAGATGGGAAGGAAGAGTTGCAGTTGTGACAGGAGCAAGCAGTCCAATTGGCAGAGCT
ATTTGTGAAGATTTAGTAAAACATGGATTGATAGTTTGTGGATTAGCAACAAGATCAGGA
AAACATGAACTTGAAGATTTAGGCAAAAAACTCGAACGACAACAAGAAAAAGGAAAATTG
CTGGCTTTTGAATGTGACATCAAAGAAGAAGGTCATATACAACCTATTTTTCGGTACATT
GAAGATCACTACGACGGAATAGATTTACTTGTCAATAATGCAAATGTTATGTGTAAAGGT
CTAATTCTCGATGAAGACAACACACCGCTAATGCGAGACGTTATGGAAACAAATATTATT
GGTATGTGTATTGTCACTCGCGAGGCTGCAAGATTGATGAAAATGAGAAAAGAAGAACGC
AAAAATTTGGGTCATGTTGTCAACATTCTCTCAATCGTCGGACATAAGTTTGGACCTTCA
AATTCACGATCGAAGCCTATTAATGCTAAAAATTGAAATATTTCACAGGCATGCAGCAAC
AGCAATCACAGAATGTATTCGTCAAGAATTCCTTTTTCTTTATGAAAACGTAAAAATCAC
AGCGATCAGTCCAGGTTTAGTGGAAGGTCAAGATACTGATATTCTCACAGAAGAAGAACG
TGCACATGGAAAAATGCCAGCATTAGAGCCAAAAGATGTTAGTGCTGCTGTATTGTATGC
AATATCAGTAAAAGATACAGTTCAAATTCATGAAATTAAAATTAAACCTGTTGGAGAATT
TATTTAGGCAGTTAAAGTCAACATTTTCTTTATTATCGTAGGCGAAAATGATGATGAGAA
ATATGAAGTAGTGGAAGAAGTATTTATAGTCAAAAAAGTGTGTGTCGCATATCAAAAATA
GCTCTCATAGATCATGTTTATTCAGTGTCACAGACATTTCATATCATATGAGTGCGATGT
CATATTTAATTCAATTTCATCATAAATGAACTGCTGAGCTACTGACGAGAATGAAAAATT
ATTGTTGATGTTATTTTTAAAATAGTTGAAAGTGCAATTAATTACAAGTCATTGTATGAA
AATTATTCATCGTTCTTTCTCTCTGAATGTTAGAGAATTTAAATGCAGCGTAAATAATGT
GAAGACACAGATTGATTAATCCTAGTGATTTCTTTAAAATTTACAAGCATTTTTGAAAAT
ATACAAAATCGCAATTGAATAGTTTTTATATAAGCTTCGTTATTTCTAGTTTTTCTCAAA
TGTGACATTTTCTAGCTAAATATGTCAATCTTTTAAAAACATTGAAAGAATTTTCCTTTT
TTAAAATCTTTTGTTTACATTAAAACATTTTTGTTTTGATTTCTTTGTTTACATTTCGTA
AATGTTTATTTACATTTAAGATTTTATTTGCAAAATTTTCATTTTAGCAAAAATTAAGTG
AAAATGCAATAATTACAAAGAAATCAACTCTATAAAATTCTTCATTTAATGATGACAAAA
AATTTCGAGCTTCCTTGTATTTAATAATTTAAAAATCACAGTGTCTTCACCTTGAACAAA
AATCTTTTTCTTTAGATAAAATTTCAAAATTTCTTTTCATCATTTTCGCATTCAATATAA
ATTATTGTTAGATACTTCAACCAAACATTCACTAATTTTTCACTTTTTCCCTCTTTTTGA
TGTTTTTCTTTTATGAAAATAAAGATTTAATTTGAGAACTCACTACTAATTTTATAAATA
ACATTCAGAAAATGTATTCGAAAAATAATTTATAGCCATAGATTTTTAGAATGAATCTAA
TTTATTTAAATAAATAAATAAATATAAAATAAAAAGTT
>g5156.t2 Gene=g5156 Length=191
MDGVENEIPIPWQEKLDNGVKRWEGRVAVVTGASSPIGRAICEDLVKHGLIVCGLATRSG
KHELEDLGKKLERQQEKGKLLAFECDIKEEGHIQPIFRYIEDHYDGIDLLVNNANVMCKG
LILDEDNTPLMRDVMETNIIGMCIVTREAARLMKMRKEERKNLGHVVNILSIVGHKFGPS
NSRSKPINAKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g5156.t2 | Gene3D | G3DSA:3.40.50.720 | - | 23 | 187 | 0 |
| 2 | g5156.t2 | PANTHER | PTHR43115 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 22 | 179 | 0 |
| 4 | g5156.t2 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 27 | 44 | 0 |
| 5 | g5156.t2 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 105 | 116 | 0 |
| 3 | g5156.t2 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 158 | 174 | 0 |
| 1 | g5156.t2 | Pfam | PF00106 | short chain dehydrogenase | 27 | 179 | 0 |
| 6 | g5156.t2 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 21 | 180 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5156/g5156.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5156.t2.fa.iupred3.txt does not exist
GO terms from InterProScan
## [1] "No matching GO terms"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