Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Farnesol dehydrogenase.

Parent gene

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_4 g15376 g15376.t1 isoform g15376.t1 5164708 5165445
chr_4 g15376 g15376.t1 exon g15376.t1.exon1 5164708 5165445
chr_4 g15376 g15376.t1 cds g15376.t1.CDS1 5164708 5165445
chr_4 g15376 g15376.t1 TSS g15376.t1 NA NA
chr_4 g15376 g15376.t1 TTS g15376.t1 NA NA

Sequences

>g15376.t1 Gene=g15376 Length=738
ATGGAAAAGTGGACAGGAAAGACAGCAGTGATTACAGGTGGATGTTCAGGCATGGGTGCA
GCAATTCTTTCAAAATTTACTAAACATGGTTTGAAAGTCATCAATTTAGACTTAAATGTT
ACTAAAAATAGTTTAAAATTTGATGAAAATTCAAAAGTTTTCAATCGTAAATGTGATGTT
GCAAACTTGGATTCAATAAGAGAAAATTTCAAATGGATTGAAGAAAATTTTAGTGTTGTT
CATGTTCTTATCAAAAATGCTGGAATTGTGAGAAATGTAAATGTTCTTGATGAAAATTCA
GCTGAAGCTGTGAGTAAAGTGATTGATGTGAATTTCATTGGCGTTGTACATTGCACTCGT
GAAGCTGCAAAACTAATGAAAAAATCAGATGATTACTGCATAATTGTTAATATTTGCTCA
ATCGCTGGTCATACGGTTCCATTTCCAAATCAATTAAATATTTATCCAGCTACGAAATTC
GCTGTTAGAGCTTTTTCTGAAATTGTCAAACAAGAGCTGACCGTTGAAGAAAATGACAAA
ATTCGTGTGACTAATGTGAGTCCAGGATTTGTTAGGACAAACCTTTTTAATGACACTGGC
TTTCCTGAAATCGATGTACTTAGAGAAAAATATAAAGCAAAAATTACTGAACCAAAAAAT
ATCGCTGAAGCTGTTTGCTATATTTTGAGCACTCCAGTTAATGTTAATGTTACTGAGTTG
ACAATTACGGGAGTATAA

>g15376.t1 Gene=g15376 Length=245
MEKWTGKTAVITGGCSGMGAAILSKFTKHGLKVINLDLNVTKNSLKFDENSKVFNRKCDV
ANLDSIRENFKWIEENFSVVHVLIKNAGIVRNVNVLDENSAEAVSKVIDVNFIGVVHCTR
EAAKLMKKSDDYCIIVNICSIAGHTVPFPNQLNIYPATKFAVRAFSEIVKQELTVEENDK
IRVTNVSPGFVRTNLFNDTGFPEIDVLREKYKAKITEPKNIAEAVCYILSTPVNVNVTEL
TITGV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g15376.t1 Gene3D G3DSA:3.40.50.720 - 1 242 0.0e+00
2 g15376.t1 PANTHER PTHR43115 DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 1 244 0.0e+00
8 g15376.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 8 25 0.0e+00
3 g15376.t1 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 78 89 6.1e-06
7 g15376.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 78 89 0.0e+00
11 g15376.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 127 143 0.0e+00
4 g15376.t1 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 133 141 6.1e-06
5 g15376.t1 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 155 174 6.1e-06
10 g15376.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 155 174 0.0e+00
9 g15376.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 179 196 0.0e+00
6 g15376.t1 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 211 231 0.0e+00
1 g15376.t1 Pfam PF00106 short chain dehydrogenase 7 197 0.0e+00
12 g15376.t1 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 4 242 0.0e+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. There were no conditions that were differentially expressed