General information for g520.t1
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Farnesol dehydrogenase.
Parent gene
- The parent gene g520 is located on chr_3: 3870279..3871171 (+ 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 | g520 | g520.t1 | TSS | g520.t1 | 3870230 | 3870230 |
| chr_3 | g520 | g520.t1 | isoform | g520.t1 | 3870279 | 3871171 |
| chr_3 | g520 | g520.t1 | exon | g520.t1.exon1 | 3870279 | 3870328 |
| chr_3 | g520 | g520.t1 | cds | g520.t1.CDS1 | 3870279 | 3870328 |
| chr_3 | g520 | g520.t1 | exon | g520.t1.exon2 | 3870386 | 3870914 |
| chr_3 | g520 | g520.t1 | cds | g520.t1.CDS2 | 3870386 | 3870914 |
| chr_3 | g520 | g520.t1 | exon | g520.t1.exon3 | 3870971 | 3871171 |
| chr_3 | g520 | g520.t1 | cds | g520.t1.CDS3 | 3870971 | 3871171 |
| chr_3 | g520 | g520.t1 | TTS | g520.t1 | 3871302 | 3871302 |
Sequences
>g520.t1 Gene=g520 Length=780
ATGACAATTTCACGTTGGTCTGGTCGTGTCGCAGTTGTGACTGGCGCAAGCGCTGGAATT
GGAGCAGCAACTGCAATAGAATTAGCTAAAAATGGTTTGATCACAATCGGATTAGCGAGA
AGAGTCGAAAAGATTGAAGAACTTCGATCACAATTGACTTCAGAGCAGCAGAAAAATTTT
CATGCCATGAAATGTGATGTTTCAGTTGAAGCCGAAATTATTCGTACATTTGCTGAAATA
GAAAGAAAATTCGGTGGAGTCGATGTTCTTATTAATAATGCAGGAGTGATTCCTCAGACT
TCTTTAACTGATTTAAATAATTCAAGCGAAATGCAAAGAATAATTAACACAAATGTGTTT
GGTGTCATCAATTGTACAAGAGAATTTGTAAAATCAATTCGTGAAAGAAATGCTGAAGGT
CATGTAATTCATATTAATAGCATTGCTGGTCATTTTATGCCTTTCCAAAAAGATTCTCCT
TCAATGGGAATTTACAGTGCAAGCAAATATGCAGTCACAGCTTTGGCTGAACAACATCGT
CAAGAGTTTATTAAAGAAAAACTGAACATTAAAGTTACAAGTCTCAGTCCAGGAGCAGTT
TTGACTGAAATTATGCATACAGTTTCAATTTTTCCTAAAGAAGTTATGGAAGAAATGATC
AAAAACACTCCATTTTTGGAATCAAAAGACATTGCTGATGCTATTATTTATTTATTGAGC
ACACCACAGAATGTTTTGATCACTGAACTCACAATTCGACCAATGAATGAAACATTTTAA
>g520.t1 Gene=g520 Length=259
MTISRWSGRVAVVTGASAGIGAATAIELAKNGLITIGLARRVEKIEELRSQLTSEQQKNF
HAMKCDVSVEAEIIRTFAEIERKFGGVDVLINNAGVIPQTSLTDLNNSSEMQRIINTNVF
GVINCTREFVKSIRERNAEGHVIHINSIAGHFMPFQKDSPSMGIYSASKYAVTALAEQHR
QEFIKEKLNIKVTSLSPGAVLTEIMHTVSIFPKEVMEEMIKNTPFLESKDIADAIIYLLS
TPQNVLITELTIRPMNETF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g520.t1 | Coils | Coil | Coil | 38 | 58 | - |
| 14 | g520.t1 | Gene3D | G3DSA:3.40.50.720 | - | 2 | 257 | 2.7E-62 |
| 2 | g520.t1 | PANTHER | PTHR43115 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 4 | 259 | 7.0E-103 |
| 3 | g520.t1 | PANTHER | PTHR43115:SF4 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 4 | 259 | 7.0E-103 |
| 8 | g520.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 10 | 27 | 2.5E-27 |
| 5 | g520.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 85 | 96 | 7.7E-9 |
| 11 | g520.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 85 | 96 | 2.5E-27 |
| 10 | g520.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 134 | 150 | 2.5E-27 |
| 6 | g520.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 140 | 148 | 7.7E-9 |
| 4 | g520.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 165 | 184 | 7.7E-9 |
| 7 | g520.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 165 | 184 | 2.5E-27 |
| 12 | g520.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 188 | 205 | 2.5E-27 |
| 9 | g520.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 221 | 241 | 2.5E-27 |
| 1 | g520.t1 | Pfam | PF00106 | short chain dehydrogenase | 10 | 207 | 1.6E-46 |
| 17 | g520.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 25 | - |
| 18 | g520.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 9 | - |
| 19 | g520.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 10 | 20 | - |
| 20 | g520.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 21 | 25 | - |
| 16 | g520.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 26 | 259 | - |
| 13 | g520.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 3 | 246 | 7.37E-58 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g520/g520.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g520.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
## [1] "No matching GO terms"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.
