Gene loci information

Transcript annotation

  • This transcript has been annotated as 3-hydroxyacyl-CoA dehydrogenase type-2.

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 g332 g332.t10 TTS g332.t10 2782221 2782221
chr_3 g332 g332.t10 isoform g332.t10 2782762 2783271
chr_3 g332 g332.t10 exon g332.t10.exon1 2782762 2783195
chr_3 g332 g332.t10 cds g332.t10.CDS1 2782764 2783195
chr_3 g332 g332.t10 exon g332.t10.exon2 2783263 2783271
chr_3 g332 g332.t10 cds g332.t10.CDS2 2783263 2783271
chr_3 g332 g332.t10 TSS g332.t10 2783302 2783302

Sequences

>g332.t10 Gene=g332 Length=443
ATGTTTAAGAACGCTGTTGCATTAGTGACTGGAGGTGGAAGTGGATTGGGAAGAGCTGTA
GTTGAGAGGTTTGCTCGAGCCGGATCAAAGGTTGTAATCGGCGATTTGAAACAATCTCCA
GGCGAGGAATTAGCGAAAGAACTTGGCAATAATGTAACTTTTGTTCCAATGGATGTCACA
TCAGAGAACGATGTTAATGAGGCATTGCACGTGGCAAAAAGTAAATTCGGAGGACTGCAT
GTAGCTGTAAATTGTGCTGGAATTGCAGTGGCAGTGAAAACTTACAATTTCAATAAGAAA
ACTGCACATAGCCTCGAATCATTTGCGAAGGTCATTAATGTCAACACTAATGGTACTTTC
AATGTCACACGATTGGCAGCTGGTTTAATTGGAGAAAATGATCCTGATAAAGATGGACAA
CGTGGTGTAATTATAAATACAGC

>g332.t10 Gene=g332 Length=147
MFKNAVALVTGGGSGLGRAVVERFARAGSKVVIGDLKQSPGEELAKELGNNVTFVPMDVT
SENDVNEALHVAKSKFGGLHVAVNCAGIAVAVKTYNFNKKTAHSLESFAKVINVNTNGTF
NVTRLAAGLIGENDPDKDGQRGVIINT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g332.t10 Gene3D G3DSA:3.40.50.720 - 1 147 6.6E-42
2 g332.t10 PANTHER PTHR43658:SF11 3-HYDROXYACYL-COA DEHYDROGENASE TYPE-2 2 147 1.5E-56
3 g332.t10 PANTHER PTHR43658 SHORT-CHAIN DEHYDROGENASE/REDUCTASE 2 147 1.5E-56
6 g332.t10 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 6 23 6.6E-11
4 g332.t10 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 77 88 6.6E-11
5 g332.t10 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 136 147 6.6E-11
1 g332.t10 Pfam PF00106 short chain dehydrogenase 6 147 2.8E-27
10 g332.t10 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
11 g332.t10 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 4 -
12 g332.t10 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 5 12 -
13 g332.t10 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 13 19 -
9 g332.t10 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 147 -
7 g332.t10 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 2 147 8.65E-38

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