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 g16445 g16445.t2 isoform g16445.t2 9463903 9465030
chr_4 g16445 g16445.t2 exon g16445.t2.exon1 9463903 9464066
chr_4 g16445 g16445.t2 cds g16445.t2.CDS1 9464026 9464066
chr_4 g16445 g16445.t2 exon g16445.t2.exon2 9464298 9465030
chr_4 g16445 g16445.t2 cds g16445.t2.CDS2 9464298 9465030
chr_4 g16445 g16445.t2 TSS g16445.t2 9465083 9465083
chr_4 g16445 g16445.t2 TTS g16445.t2 NA NA

Sequences

>g16445.t2 Gene=g16445 Length=897
ATGGAAAAGTGGACAGAAAAAACAGCAGTGATCACAGGAGGAAATTCAGGCATTGGTGCA
GCAATTCTTTCGCAATTTATTAAACATGATTTAAAAGTCATCAATTTAGACATAAATGTC
ACTGAAAAAGACTCAAATTTTGACGAAAATTCAAAAGTTTTCAATCGCAAATGTGATGTT
GCAAATTTGGATTCAATCAAGGAAAATTTCAAATGGATTGAAGAAAATTTTGGTGTTGTT
CATATTTTGGTTAATTGTGCTGGAATTGTAGCTGTAAATCCAATGATTGATCCACGTGAT
GAGAACACAGAAAAAGTTGATAAAACACTTGACATCAACCTTCGTGGAACAATTCATTGC
ACACGTGAAGCGATGAAATTGATGGTTAAATCTGATGATTATTGCATGATTATAAATTTT
TGTTCAATTCTTGGTCACATTATTCCTTATGTCGGTTATAGTCTTGGTGCTTATCATACT
ACAAAGCATGCAATTAGAGCATTTTCCGAGACAATCAGACAAGAACTCTGTCTTTGTAAA
AGTGAAAAAATTCGTGTAAGCAATGTAAGTCCTGGTGGTGTTAGAACAAATATGATTATT
GGCACTGGTTTATCAGAGGAACAACTTTCAAAGTTCAAATTTATTGAAGCAGAACAAGTT
GCCGAAACAATTTTATTTTTGCTGACTACACCTTATAATGTAAACATCACAGAATTAACA
GTTCGACCTGTTGTAAATTACGAAGTATTAATTGGGTTGACTTTTAATTATTGAGTCCAA
AATCATTTTTAATCCAGTAAATTTACTCGACTAAAATTCATTTTATTATTTTGTTGATTT
TTAGTTTATTGTAATAAAAATTTAAAACACTTTCAGACTCTCATTAATTTTTCTTAT

>g16445.t2 Gene=g16445 Length=257
MEKWTEKTAVITGGNSGIGAAILSQFIKHDLKVINLDINVTEKDSNFDENSKVFNRKCDV
ANLDSIKENFKWIEENFGVVHILVNCAGIVAVNPMIDPRDENTEKVDKTLDINLRGTIHC
TREAMKLMVKSDDYCMIINFCSILGHIIPYVGYSLGAYHTTKHAIRAFSETIRQELCLCK
SEKIRVSNVSPGGVRTNMIIGTGLSEEQLSKFKFIEAEQVAETILFLLTTPYNVNITELT
VRPVVNYEVLIGLTFNY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g16445.t2 Gene3D G3DSA:3.40.50.720 - 1 252 1.8E-50
2 g16445.t2 PANTHER PTHR43115 DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 1 250 3.5E-51
3 g16445.t2 PANTHER PTHR43115:SF4 DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 1 250 3.5E-51
10 g16445.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 8 25 4.2E-22
6 g16445.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 78 89 2.8E-5
8 g16445.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 78 89 4.2E-22
9 g16445.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 129 145 4.2E-22
5 g16445.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 135 143 2.8E-5
4 g16445.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 158 177 2.8E-5
7 g16445.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 158 177 4.2E-22
12 g16445.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 182 199 4.2E-22
11 g16445.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 210 230 4.2E-22
1 g16445.t2 Pfam PF00106 short chain dehydrogenase 7 198 8.5E-37
15 g16445.t2 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 3 241 7.16E-49
14 g16445.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 77 96 -
13 g16445.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 136 158 -

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