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 g333 g333.t2 TTS g333.t2 2784822 2784822
chr_3 g333 g333.t2 isoform g333.t2 2784937 2785826
chr_3 g333 g333.t2 exon g333.t2.exon1 2784937 2785155
chr_3 g333 g333.t2 cds g333.t2.CDS1 2784937 2785155
chr_3 g333 g333.t2 exon g333.t2.exon2 2785211 2785826
chr_3 g333 g333.t2 cds g333.t2.CDS2 2785211 2785591
chr_3 g333 g333.t2 TSS g333.t2 2785856 2785856

Sequences

>g333.t2 Gene=g333 Length=835
ATGTTTAAGGTAAAATTTGATTATTTTTCTCAATTCTATTGATTATCTAACAATTTATTC
TTAATTATTGATATAGAACGCTGTTGCATTAGTGACTGGAGGTGGAAGTGGATTGGGAAG
AGCTGTAGTTGAGAGGTTTGCCCGAGCCGGATCAAAGGTTGTAATCGGAGATTTGAAACA
ATCTCCAGGCGAGGAATTAGCGAAGGAACTTGGCAATAATGTAACATTTGTACCAATGGA
TGTCACATCAGAAAATGATGTTAATGAGGCATTGCACGTGGCAAAAAGTAAATTTGGAGG
GTTGCATGTCGTTGTAAATTCTGCTGCTATAGTTATGTTCAAGGAAACATACGATTTCAA
AAAGAAGACTCCTCATAGTCTTAATGAATTTGCAAACATCATCAATGTCAACCTTAATGG
TACTTTCAATGTTACACGATTGGCAGCTGGTTTAATTGGAGAAAATAAACCTGATAAGGA
TGGACAACGTGGCGTCATTATAAATGTATCTACTGTTGCTGCTTTTGATGGTGTAATTGG
ACAAGCAGCTTATGCTGCATCAAAAGCGGCTGTTGTGGGAATGACTTTACCTCTTGCAAG
AGATTTGTCAAGTCAAGGAATCCGTGTTGTAACAATTGCACCAGGTTTTTTTGATACACC
AATGTTTGATTCTTTGCCTGATAAAATTCGTATAACTTTGGCAAAAACTGTTCCATTTCC
TCAACGTTTAGGTTATGCTGAGGAGTTCGCACACTTGGTTGAAGCAGTAGTTGACAATCC
CATGATTAATGGTGAAACTATTCGACAAGATGGAGCTTTGAGAATGATGCCATAA

>g333.t2 Gene=g333 Length=199
MDVTSENDVNEALHVAKSKFGGLHVVVNSAAIVMFKETYDFKKKTPHSLNEFANIINVNL
NGTFNVTRLAAGLIGENKPDKDGQRGVIINVSTVAAFDGVIGQAAYAASKAAVVGMTLPL
ARDLSSQGIRVVTIAPGFFDTPMFDSLPDKIRITLAKTVPFPQRLGYAEEFAHLVEAVVD
NPMINGETIRQDGALRMMP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g333.t2 Gene3D G3DSA:3.40.50.720 - 1 199 0
2 g333.t2 PANTHER PTHR43658:SF11 3-HYDROXYACYL-COA DEHYDROGENASE TYPE-2 2 199 0
3 g333.t2 PANTHER PTHR43658 SHORT-CHAIN DEHYDROGENASE/REDUCTASE 2 199 0
5 g333.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 21 32 0
9 g333.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 21 32 0
8 g333.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 80 96 0
6 g333.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 86 94 0
4 g333.t2 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 106 125 0
7 g333.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 106 125 0
10 g333.t2 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 127 144 0
1 g333.t2 Pfam PF00106 short chain dehydrogenase 1 149 0
11 g333.t2 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 1 197 0

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