General information for g521.t1
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Farnesol dehydrogenase.
Parent gene
- The parent gene g521 is located on chr_3: 3873364..3874136 (+ 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 | g521 | g521.t1 | isoform | g521.t1 | 3871408 | 3873364 |
| chr_3 | g521 | g521.t1 | exon | g521.t1.exon1 | 3871408 | 3871457 |
| chr_3 | g521 | g521.t1 | cds | g521.t1.CDS1 | 3871408 | 3871457 |
| chr_3 | g521 | g521.t1 | exon | g521.t1.exon2 | 3872476 | 3872526 |
| chr_3 | g521 | g521.t1 | cds | g521.t1.CDS2 | 3872476 | 3872526 |
| chr_3 | g521 | g521.t1 | exon | g521.t1.exon3 | 3872583 | 3873111 |
| chr_3 | g521 | g521.t1 | cds | g521.t1.CDS3 | 3872583 | 3873111 |
| chr_3 | g521 | g521.t1 | exon | g521.t1.exon4 | 3873164 | 3873364 |
| chr_3 | g521 | g521.t1 | cds | g521.t1.CDS4 | 3873164 | 3873364 |
| chr_3 | g521 | g521.t1 | TTS | g521.t1 | 3874037 | 3874037 |
| chr_3 | g521 | g521.t1 | TSS | g521.t1 | NA | NA |
Sequences
>g521.t1 Gene=g521 Length=831
ATGACAATTTCACGTTGGTTTGGTCGTGTTGCGGTTGTGACTGGAACAAGAATGTCAATT
TCACGTTGGTCTGGTCGTGTTGCGGTTGTGACGGGAGCAAGCGCTGGAATTGGTGCTGCA
ACTGCAATTGAATTAGCTAGAAATGGTTTGATCACAATCGGATTAGCGAGAAGAGTTGAA
AAAGTTGAAGAACTTCGATCACAATTGACACCGGAACAACAGCAAAATTTTCATGCCATG
AAATGTGATGTTTCAGTTGAGTCCGAAATTATTCAAGTTTTTGATGAGATTGTGAATAAA
TTTGGTGGAGTCGATGTTTTAATAAATAATGCAGCAGTTGTGACACAAAAAAAATTAATC
GATTTTGATAATTCAAGTGAAGTTCAAAAACTTATCAACACAAATCTACTCGGTGCTATC
AACTGTACGCGCGAAGTAGTGAAATCACTTCGTGAAAGAAATGCTGAAGGACATATAATT
CACATTAATAGTGTGTATGGACATTTCATGCCATATTATCCTGATCGTCCTACAGTTGGA
ATTTATACTACTAGCAAATTTGCACTTACAGCTATGGCTGAACAACAACGACAAGAATTT
ATGAGCGAAAATTTAAATATCAAGGTCACTTCTTTAAGTCCAGGACTTGTTGAAACTGAA
ATTATGCAAACAATTCAAGGAATGACAAAAGAAATGATTGAAGGATTTTATGAAATGACA
CCACATATGGAGTCAAAAGATATTGCAGATGCTATAATTTATCTTCTTAGTACACCACAA
CATGTTCTTATCACTGAACTCACTATAAGACCAATGAATGGAATATTTTAG
>g521.t1 Gene=g521 Length=276
MTISRWFGRVAVVTGTRMSISRWSGRVAVVTGASAGIGAATAIELARNGLITIGLARRVE
KVEELRSQLTPEQQQNFHAMKCDVSVESEIIQVFDEIVNKFGGVDVLINNAAVVTQKKLI
DFDNSSEVQKLINTNLLGAINCTREVVKSLRERNAEGHIIHINSVYGHFMPYYPDRPTVG
IYTTSKFALTAMAEQQRQEFMSENLNIKVTSLSPGLVETEIMQTIQGMTKEMIEGFYEMT
PHMESKDIADAIIYLLSTPQHVLITELTIRPMNGIF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g521.t1 | Gene3D | G3DSA:3.40.50.720 | - | 16 | 274 | 0.0e+00 |
| 2 | g521.t1 | PANTHER | PTHR43115 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 18 | 273 | 0.0e+00 |
| 3 | g521.t1 | PANTHER | PTHR43115:SF4 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 18 | 273 | 0.0e+00 |
| 12 | g521.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 27 | 44 | 0.0e+00 |
| 4 | g521.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 102 | 113 | 1.2e-06 |
| 10 | g521.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 102 | 113 | 0.0e+00 |
| 9 | g521.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 151 | 167 | 0.0e+00 |
| 6 | g521.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 157 | 165 | 1.2e-06 |
| 5 | g521.t1 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 182 | 201 | 1.2e-06 |
| 11 | g521.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 182 | 201 | 0.0e+00 |
| 8 | g521.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 205 | 222 | 0.0e+00 |
| 7 | g521.t1 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 238 | 258 | 0.0e+00 |
| 1 | g521.t1 | Pfam | PF00106 | short chain dehydrogenase | 27 | 226 | 0.0e+00 |
| 13 | g521.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 18 | 262 | 0.0e+00 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g521/g521.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g521.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
## [1] "No matching GO terms"KEGG
Orthology
- This transcript has been annotated with K22970 (17beta-estradiol 17-dehydrogenase / 3beta-hydroxysteroid 3-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.
