General information for g1462.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 g1462 is located on chr_3: 11055203..11056210 (+ 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 | g1462 | g1462.t2 | TSS | g1462.t2 | 11055181 | 11055181 |
| chr_3 | g1462 | g1462.t2 | isoform | g1462.t2 | 11055203 | 11056210 |
| chr_3 | g1462 | g1462.t2 | exon | g1462.t2.exon1 | 11055203 | 11055925 |
| chr_3 | g1462 | g1462.t2 | cds | g1462.t2.CDS1 | 11055203 | 11055925 |
| chr_3 | g1462 | g1462.t2 | exon | g1462.t2.exon2 | 11056013 | 11056210 |
| chr_3 | g1462 | g1462.t2 | cds | g1462.t2.CDS2 | 11056013 | 11056039 |
| chr_3 | g1462 | g1462.t2 | TTS | g1462.t2 | 11056250 | 11056250 |
Sequences
>g1462.t2 Gene=g1462 Length=921
ATGGACAAATGGCGAGGTAAAATTGCAGTTGTGAGTGGTGCTTCTTCAGGAATTGGTGCA
GCAATAATTAAAGATTTAGCAAAACATGGAGTTACTGTCATTGGTCTAGCGAGAAGAAGT
GAAAAGGTTGAAGAAATTTCAGCAGCTTCAAGTCATTTAGATGGAAAAATTTTTGCAAAA
AAATGTGACATTTCTGATCAAAAATCTTTAAAAGAAACTTTCGAATGGATTGAAGAAAAA
TTTTCGTTCATTCACATTTTAATCAACAATGCAGGAGTTTTACATAAATTAAGTGTACTA
GATACAAGCGATGATGCAACTGATAAAATCAATAGTGTAATCAACACAAATTTTACTGCA
GTAGTTCATTGTACAAGAGAAGGAATTCGTTTAATGAGGAAATCTGAAGATTTTTCAATC
GTCATTAATATAAACTCAATAGCAGGTCACAGTGTTTATAGTGGTCTTCACATTTCAAAC
GTTTACTCACCAACAAAGCACGCGCTTACTGCTTTTTCAGAAATTTTACGACAAGAGCTC
GTTGTGAGTGGCAGTGAGAAAATTCGTGTATCAAATTTAAGTCCTGGAGTGGTTAGAACT
GAAATCATGGTACGTGGAAAAGCTTTTAAGTCCGATGAAGATTACAATGATGTTCCACAC
ATTAATTCTGAGGATATTTCAAATGGTGTTCTTTATCTTCTTTCAACTCCATACAATGTC
AATAAATTTGAATTTTTGTATTTTTCCTGATAAAGTTTTTGGAAAATCTTCAACAATGAT
GACAAATTTCGGAACTTTAAAATGAGCTAAATTGTTTTTACAAAATTCTTTAATGTCATT
TTGTGTTAGTGTTTTTGATGAATCTTTTAGCTTTATAAATGCACCCACTTCTTCGCCCAT
TCTGTCGTCTGGGATTCCAAT
>g1462.t2 Gene=g1462 Length=249
MDKWRGKIAVVSGASSGIGAAIIKDLAKHGVTVIGLARRSEKVEEISAASSHLDGKIFAK
KCDISDQKSLKETFEWIEEKFSFIHILINNAGVLHKLSVLDTSDDATDKINSVINTNFTA
VVHCTREGIRLMRKSEDFSIVININSIAGHSVYSGLHISNVYSPTKHALTAFSEILRQEL
VVSGSEKIRVSNLSPGVVRTEIMVRGKAFKSDEDYNDVPHINSEDISNGVLYLLSTPYNV
NKFEFLYFS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g1462.t2 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 241 | 0e+00 |
| 2 | g1462.t2 | PANTHER | PTHR43115 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 1 | 240 | 0e+00 |
| 3 | g1462.t2 | PANTHER | PTHR43115:SF4 | DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 | 1 | 240 | 0e+00 |
| 9 | g1462.t2 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 8 | 25 | 0e+00 |
| 6 | g1462.t2 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 82 | 93 | 1e-07 |
| 11 | g1462.t2 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 82 | 93 | 0e+00 |
| 8 | g1462.t2 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 133 | 149 | 0e+00 |
| 4 | g1462.t2 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 139 | 147 | 1e-07 |
| 5 | g1462.t2 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 162 | 181 | 1e-07 |
| 10 | g1462.t2 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 162 | 181 | 0e+00 |
| 7 | g1462.t2 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 186 | 203 | 0e+00 |
| 1 | g1462.t2 | Pfam | PF00106 | short chain dehydrogenase | 7 | 203 | 0e+00 |
| 12 | g1462.t2 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 3 | 238 | 0e+00 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
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.
