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_3 g2254 g2254.t2 TSS g2254.t2 16302050 16302050
chr_3 g2254 g2254.t2 isoform g2254.t2 16302197 16304255
chr_3 g2254 g2254.t2 exon g2254.t2.exon1 16302197 16302328
chr_3 g2254 g2254.t2 cds g2254.t2.CDS1 16302197 16302328
chr_3 g2254 g2254.t2 exon g2254.t2.exon2 16302388 16302518
chr_3 g2254 g2254.t2 cds g2254.t2.CDS2 16302388 16302518
chr_3 g2254 g2254.t2 exon g2254.t2.exon3 16302574 16302815
chr_3 g2254 g2254.t2 cds g2254.t2.CDS3 16302574 16302814
chr_3 g2254 g2254.t2 exon g2254.t2.exon4 16303398 16303495
chr_3 g2254 g2254.t2 exon g2254.t2.exon5 16304032 16304147
chr_3 g2254 g2254.t2 exon g2254.t2.exon6 16304218 16304255
chr_3 g2254 g2254.t2 TTS g2254.t2 16304443 16304443

Sequences

>g2254.t2 Gene=g2254 Length=757
ATGGAAAAGTGGGAAGGAAAAGTAGCTGTTGTCACTGGTGCTTCTGTTGGAATAGGGGCC
GCTTTGTGTCGTGCACTTGTCGAAGCTGGAATGATCGTTTGTGGATTATCAAAACGCAAG
GATAAAATGGAAGCTATTCGACGAACACTTTTTGGTGTTAAAGGGCAATTTAATTGCGTT
GAATGTGACATTCGTGATGAAAATCAAGTCGCTGCTGCTTTTAGATGGATTGAGGATGTT
TGTGGTGGAGTCGATTTATTGATAAACAATGCTGGTGTTATCACTAAAGGTCTTCTCTTG
GACGCAAAAAATACATCCGAACTCTACAGAACTATGGAGACTAACATCATTGGTCTCTGT
CTCATTACTCGTGAAGCTGTTAAACTTATGAAAAAGCGCGATGAAGAACGAGGAACTGTA
GGACATATTGTGAACATCAATAGCATATTCGGTCACAAGATTCATGCCTGTGTTGTACGT
ATTTATAATAGATGTGTCTCATGAAATTCGCTGTCACTGCAATCACAGAATGTGTCCGTC
AAGAATTATTGTATTTAGGAACAAAAATCAAAATCACAAGTATTTCACCGGGATTGGTCG
AAGGTGACATTGGTACTTTAAACACTTCTCATGACATGATCAAATTGATGCCAAAGCTTA
ATCCACAAGATGTTGCAGATGCAGTTCTTTATGCTATTTCTACACCAGAAAATGTTTTGA
TTCACGAATTGATAATCAAACCAGTCGGAGAATTTCT

>g2254.t2 Gene=g2254 Length=167
MEKWEGKVAVVTGASVGIGAALCRALVEAGMIVCGLSKRKDKMEAIRRTLFGVKGQFNCV
ECDIRDENQVAAAFRWIEDVCGGVDLLINNAGVITKGLLLDAKNTSELYRTMETNIIGLC
LITREAVKLMKKRDEERGTVGHIVNINSIFGHKIHACVVRIYNRCVS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g2254.t2 Gene3D G3DSA:3.40.50.720 - 1 159 4.9E-38
2 g2254.t2 PANTHER PTHR43115 DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 1 155 1.7E-57
3 g2254.t2 PANTHER PTHR43115:SF4 DEHYDROGENASE/REDUCTASE SDR FAMILY MEMBER 11 1 155 1.7E-57
6 g2254.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 8 25 1.4E-14
4 g2254.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 82 93 1.2E-5
8 g2254.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 82 93 1.4E-14
7 g2254.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 135 151 1.4E-14
5 g2254.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 141 149 1.2E-5
1 g2254.t2 Pfam PF00106 short chain dehydrogenase 7 155 2.7E-31
13 g2254.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 25 -
14 g2254.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 7 -
15 g2254.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 8 18 -
16 g2254.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 19 25 -
12 g2254.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 26 167 -
10 g2254.t2 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 3 154 4.27E-37
9 g2254.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 15 37 -

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.

Raw TPM values