Gene loci information

Transcript annotation

  • This transcript has been annotated as 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_3 g2254 g2254.t5 TSS g2254.t5 16302050 16302050
chr_3 g2254 g2254.t5 isoform g2254.t5 16302197 16304255
chr_3 g2254 g2254.t5 exon g2254.t5.exon1 16302197 16302328
chr_3 g2254 g2254.t5 cds g2254.t5.CDS1 16302197 16302328
chr_3 g2254 g2254.t5 exon g2254.t5.exon2 16302388 16302518
chr_3 g2254 g2254.t5 cds g2254.t5.CDS2 16302388 16302518
chr_3 g2254 g2254.t5 exon g2254.t5.exon3 16302574 16302788
chr_3 g2254 g2254.t5 cds g2254.t5.CDS3 16302574 16302788
chr_3 g2254 g2254.t5 exon g2254.t5.exon4 16302898 16302934
chr_3 g2254 g2254.t5 cds g2254.t5.CDS4 16302898 16302934
chr_3 g2254 g2254.t5 exon g2254.t5.exon5 16303398 16303495
chr_3 g2254 g2254.t5 cds g2254.t5.CDS5 16303398 16303495
chr_3 g2254 g2254.t5 exon g2254.t5.exon6 16304032 16304147
chr_3 g2254 g2254.t5 cds g2254.t5.CDS6 16304032 16304147
chr_3 g2254 g2254.t5 exon g2254.t5.exon7 16304218 16304255
chr_3 g2254 g2254.t5 cds g2254.t5.CDS7 16304218 16304253
chr_3 g2254 g2254.t5 TTS g2254.t5 16304443 16304443

Sequences

>g2254.t5 Gene=g2254 Length=767
ATGGAAAAGTGGGAAGGAAAAGTAGCTGTTGTCACTGGTGCTTCTGTTGGAATAGGGGCC
GCTTTGTGTCGTGCACTTGTCGAAGCTGGAATGATCGTTTGTGGATTATCAAAACGCAAG
GATAAAATGGAAGCTATTCGACGAACACTTTTTGGTGTTAAAGGGCAATTTAATTGCGTT
GAATGTGACATTCGTGATGAAAATCAAGTCGCTGCTGCTTTTAGATGGATTGAGGATGTT
TGTGGTGGAGTCGATTTATTGATAAACAATGCTGGTGTTATCACTAAAGGTCTTCTCTTG
GACGCAAAAAATACATCCGAACTCTACAGAACTATGGAGACTAACATCATTGGTCTCTGT
CTCATTACTCGTGAAGCTGTTAAACTTATGAAAAAGCGCGATGAAGAACGAGGAACTGTA
GGACATATTGTGAACATCAATAGCATATTCGGTCACAAGATTCATGCCTGTGTTGTACCC
GGGAACAAAGCCTCTAAATGGGATGTATCCGGTGAATTCGCTGTCACTGCAATCACAGAA
TGTGTCCGTCAAGAATTATTGTATTTAGGAACAAAAATCAAAATCACAAGTATTTCACCG
GGATTGGTCGAAGGTGACATTGGTACTTTAAACACTTCTCATGACATGATCAAATTGATG
CCAAAGCTTAATCCACAAGATGTTGCAGATGCAGTTCTTTATGCTATTTCTACACCAGAA
AATGTTTTGATTCACGAATTGATAATCAAACCAGTCGGAGAATTTCT

>g2254.t5 Gene=g2254 Length=255
MEKWEGKVAVVTGASVGIGAALCRALVEAGMIVCGLSKRKDKMEAIRRTLFGVKGQFNCV
ECDIRDENQVAAAFRWIEDVCGGVDLLINNAGVITKGLLLDAKNTSELYRTMETNIIGLC
LITREAVKLMKKRDEERGTVGHIVNINSIFGHKIHACVVPGNKASKWDVSGEFAVTAITE
CVRQELLYLGTKIKITSISPGLVEGDIGTLNTSHDMIKLMPKLNPQDVADAVLYAISTPE
NVLIHELIIKPVGEF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g2254.t5 Gene3D G3DSA:3.40.50.720 - 1 254 6.5E-49
2 g2254.t5 PANTHER PTHR43115 DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 1 254 2.0E-93
3 g2254.t5 PANTHER PTHR43115:SF4 DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 1 254 2.0E-93
8 g2254.t5 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 8 25 5.5E-21
4 g2254.t5 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 82 93 2.3E-5
10 g2254.t5 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 82 93 5.5E-21
9 g2254.t5 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 135 151 5.5E-21
5 g2254.t5 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 141 149 2.3E-5
7 g2254.t5 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 191 208 5.5E-21
6 g2254.t5 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 218 238 5.5E-21
1 g2254.t5 Pfam PF00106 short chain dehydrogenase 7 208 7.5E-36
14 g2254.t5 Phobius SIGNAL_PEPTIDE Signal peptide region 1 25 -
15 g2254.t5 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 7 -
16 g2254.t5 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 8 18 -
17 g2254.t5 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 19 25 -
13 g2254.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 26 255 -
11 g2254.t5 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 2 251 5.83E-47

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