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.t5 TTS g332.t5 2782221 2782221
chr_3 g332 g332.t5 isoform g332.t5 2782378 2783271
chr_3 g332 g332.t5 exon g332.t5.exon1 2782378 2782596
chr_3 g332 g332.t5 cds g332.t5.CDS1 2782378 2782596
chr_3 g332 g332.t5 exon g332.t5.exon2 2782656 2782762
chr_3 g332 g332.t5 cds g332.t5.CDS2 2782656 2782762
chr_3 g332 g332.t5 exon g332.t5.exon3 2782853 2783195
chr_3 g332 g332.t5 cds g332.t5.CDS3 2782853 2783195
chr_3 g332 g332.t5 exon g332.t5.exon4 2783263 2783271
chr_3 g332 g332.t5 cds g332.t5.CDS4 2783263 2783271
chr_3 g332 g332.t5 TSS g332.t5 2783302 2783302

Sequences

>g332.t5 Gene=g332 Length=678
ATGTTTAAGAACGCTGTTGCATTAGTGACTGGAGGTGGAAGTGGATTGGGAAGAGCTGTA
GTTGAGAGGTTTGCTCGAGCCGGATCAAAGGTTGTAATCGGCGATTTGAAACAATCTCCA
GGCGAGGAATTAGCGAAAGAACTTGGCAATAATGTAACTTTTGTTCCAATGGATGTCACA
TCAGAGAACGATGTTAATGAGGCATTGCACGTGGCAAAAAGTAAATTCGGAGGACTGCAT
GTAGCTGTAAATTGTGCTGGAATTGCAGTGGCAGTGAAAACTTACAATTTCAATAAGAAA
ACTGCACATAGCCTCGAATCATTTGCGAAGGTCATTAATGTCAACACTAATGCTTCGGTT
GCTGCTTTTGACGGTCAGATTGGACAAGCAGCTTATGCTGCATCAAAAGCAGCTGTTGTA
GGAATGACTTTGCCTATTGCAAGAGATTTATCAGTTCAAGGAATCCGTGTTGTAACAATT
GCACCAGGACTTTTTGATACACCAATGTTGCAAGCTTTGCCTGATAAAATTCGTTCGTTT
TTGGCGAAAACTGTTCCATTTCCTCAACGTCTTGGCGATCCTGATGAATTTGCACAATTG
GTTGAATCAATCGTTGATAATCCAATGCTTAATGGTGAAGTCATCCGTTTGGATGGAGCT
TTGAGAATGATGCCATAA

>g332.t5 Gene=g332 Length=225
MFKNAVALVTGGGSGLGRAVVERFARAGSKVVIGDLKQSPGEELAKELGNNVTFVPMDVT
SENDVNEALHVAKSKFGGLHVAVNCAGIAVAVKTYNFNKKTAHSLESFAKVINVNTNASV
AAFDGQIGQAAYAASKAAVVGMTLPIARDLSVQGIRVVTIAPGLFDTPMLQALPDKIRSF
LAKTVPFPQRLGDPDEFAQLVESIVDNPMLNGEVIRLDGALRMMP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g332.t5 Gene3D G3DSA:3.40.50.720 - 1 117 1.3E-32
15 g332.t5 Gene3D G3DSA:3.40.50.720 - 118 225 4.7E-28
3 g332.t5 PANTHER PTHR43658:SF11 3-HYDROXYACYL-COA DEHYDROGENASE TYPE-2 2 116 7.5E-102
5 g332.t5 PANTHER PTHR43658 SHORT-CHAIN DEHYDROGENASE/REDUCTASE 2 116 7.5E-102
2 g332.t5 PANTHER PTHR43658:SF11 3-HYDROXYACYL-COA DEHYDROGENASE TYPE-2 117 225 7.5E-102
4 g332.t5 PANTHER PTHR43658 SHORT-CHAIN DEHYDROGENASE/REDUCTASE 117 225 7.5E-102
11 g332.t5 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 6 23 2.7E-25
6 g332.t5 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 77 88 7.6E-6
8 g332.t5 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 77 88 2.7E-25
7 g332.t5 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 132 151 7.6E-6
12 g332.t5 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 132 151 2.7E-25
10 g332.t5 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 153 170 2.7E-25
9 g332.t5 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 187 207 2.7E-25
1 g332.t5 Pfam PF00106 short chain dehydrogenase 6 118 4.7E-22
18 g332.t5 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
19 g332.t5 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 4 -
20 g332.t5 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 5 12 -
21 g332.t5 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 13 19 -
17 g332.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 225 -
14 g332.t5 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature. 119 147 -
13 g332.t5 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 2 223 1.01E-53

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0055114 NA NA
GO:0016491 oxidoreductase activity MF

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