General information for g515.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Farnesol dehydrogenase.
Parent gene
- The parent gene g515 is located on chr_3: 3859000..3860128 (+ 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 | g515 | g515.t1 | TSS | g515.t1 | 3858942 | 3858942 |
| chr_3 | g515 | g515.t1 | isoform | g515.t1 | 3859000 | 3860128 |
| chr_3 | g515 | g515.t1 | exon | g515.t1.exon1 | 3859000 | 3859049 |
| chr_3 | g515 | g515.t1 | cds | g515.t1.CDS1 | 3859000 | 3859049 |
| chr_3 | g515 | g515.t1 | exon | g515.t1.exon2 | 3859114 | 3859639 |
| chr_3 | g515 | g515.t1 | cds | g515.t1.CDS2 | 3859114 | 3859639 |
| chr_3 | g515 | g515.t1 | exon | g515.t1.exon3 | 3859922 | 3860128 |
| chr_3 | g515 | g515.t1 | cds | g515.t1.CDS3 | 3859922 | 3860128 |
| chr_3 | g515 | g515.t1 | TTS | g515.t1 | 3860261 | 3860261 |
Sequences
>g515.t1 Gene=g515 Length=783
ATGTCAATTTCACGTTGGTCTGGTCGTGTTGCAGTTGTGACTGGTGCAAGTGCTGGAATT
GGGGAAGCGACTTGTATCGAATTTTGTAAACATGGACTCATAACTATCGGTCTAGCACGT
CGTGTCGAAAAAATGGAAGAAATTCGTAAAAGCCTCTCGCCTGAGCAATCAAAACTCTTT
CATGCCATGAAATGTGATGTCTCAAATGAAGCGGAAATTGTTCAAGTTTTTGCGGAAATT
GAGAAAAAGTTTGGTGGCGTCGATGTTTTGGTCAATAATGCTGGTGTAATTGCAAAATAT
AATATGATAGATGAGAATAGTGCGTCTGATATGAAGCGAGTGATTGACACTAATGTGTTT
GGAGTTATCAATTGTACAAGAGAAGCAGTCAAAACAATGAGAAAGAAAAATGAAGCTCAT
GTTATTCATATCAATAGCGTTGCTGGTCATAGTATGCCTTTTATTGCTGAATTTCCCGCA
TTTGGAATTTATACAGCAAGCAAATATGCAGTCACAGCAATTGCTGAACAACATCGACAA
GAATTTATTAAGGAAAAGCTGAATATTAAAGTTACAAGTCTCAGTCCTGGAGCAGTTGCA
ACAGAAATTTTTGACACAATGAATACAGAAAAAACAGATCCAGAAAAAATTAAAGAATTT
ATGGCAAAAATACCATTTTTAGCATCCAAAGACATTGCTGATTCAATTGTGTTCTTACTC
AGCACACCACCAAATGTTTTGATCACAGAACTCACAATTCGCCCAATGAATGAAGCATTT
TAA
>g515.t1 Gene=g515 Length=260
MSISRWSGRVAVVTGASAGIGEATCIEFCKHGLITIGLARRVEKMEEIRKSLSPEQSKLF
HAMKCDVSNEAEIVQVFAEIEKKFGGVDVLVNNAGVIAKYNMIDENSASDMKRVIDTNVF
GVINCTREAVKTMRKKNEAHVIHINSVAGHSMPFIAEFPAFGIYTASKYAVTAIAEQHRQ
EFIKEKLNIKVTSLSPGAVATEIFDTMNTEKTDPEKIKEFMAKIPFLASKDIADSIVFLL
STPPNVLITELTIRPMNEAF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g515.t1 | Gene3D | G3DSA:3.40.50.720 | - | 2 | 258 | 6.9E-62 |
| 2 | g515.t1 | PANTHER | PTHR43115 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 4 | 260 | 1.2E-100 |
| 3 | g515.t1 | PANTHER | PTHR43115:SF4 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 4 | 260 | 1.2E-100 |
| 9 | g515.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 10 | 27 | 1.8E-25 |
| 5 | g515.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 85 | 96 | 4.7E-7 |
| 10 | g515.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 85 | 96 | 1.8E-25 |
| 7 | g515.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 133 | 149 | 1.8E-25 |
| 4 | g515.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 139 | 147 | 4.7E-7 |
| 6 | g515.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 164 | 183 | 4.7E-7 |
| 11 | g515.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 164 | 183 | 1.8E-25 |
| 8 | g515.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 187 | 204 | 1.8E-25 |
| 12 | g515.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 222 | 242 | 1.8E-25 |
| 1 | g515.t1 | Pfam | PF00106 | short chain dehydrogenase | 10 | 210 | 3.3E-47 |
| 17 | g515.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 25 | - |
| 18 | g515.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 9 | - |
| 19 | g515.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 10 | 20 | - |
| 20 | g515.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 21 | 25 | - |
| 16 | g515.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 26 | 260 | - |
| 14 | g515.t1 | ProSitePatterns | PS00061 | Short-chain dehydrogenases/reductases family signature. | 151 | 179 | - |
| 13 | g515.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 4 | 245 | 5.64E-58 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g515/g515.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g515.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0055114 | NA | NA |
| GO:0016491 | oxidoreductase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K15890 (NADP+-dependent farnesol 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