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.t4 TTS g332.t4 2782221 2782221
chr_3 g332 g332.t4 isoform g332.t4 2782378 2783271
chr_3 g332 g332.t4 exon g332.t4.exon1 2782378 2782596
chr_3 g332 g332.t4 cds g332.t4.CDS1 2782559 2782596
chr_3 g332 g332.t4 exon g332.t4.exon2 2782673 2783195
chr_3 g332 g332.t4 cds g332.t4.CDS2 2782673 2783195
chr_3 g332 g332.t4 exon g332.t4.exon3 2783263 2783271
chr_3 g332 g332.t4 cds g332.t4.CDS3 2783263 2783271
chr_3 g332 g332.t4 TSS g332.t4 2783302 2783302

Sequences

>g332.t4 Gene=g332 Length=751
ATGTTTAAGAACGCTGTTGCATTAGTGACTGGAGGTGGAAGTGGATTGGGAAGAGCTGTA
GTTGAGAGGTTTGCTCGAGCCGGATCAAAGGTTGTAATCGGCGATTTGAAACAATCTCCA
GGCGAGGAATTAGCGAAAGAACTTGGCAATAATGTAACTTTTGTTCCAATGGATGTCACA
TCAGAGAACGATGTTAATGAGGCATTGCACGTGGCAAAAAGTAAATTCGGAGGACTGCAT
GTAGCTGTAAATTGTGCTGGAATTGCAGTGGCAGTGAAAACTTACAATTTCAATAAGAAA
ACTGCACATAGCCTCGAATCATTTGCGAAGGTCATTAATGTCAACACTAATGGTACTTTC
AATGTCACACGATTGGCAGCTGGTTTAATTGGAGAAAATGATCCTGATAAAGATGGACAA
CGTGGTGTAATTATAAATACAGCTTCGGTTGCTGCTTTTGACGGTCAGATTGGACAAGCA
GCTTATGCTGCATCAAAAGCAGCTGTTGTAGGAATGACTTTGCCTATTGCAAGGAATCCG
TGTTGTAACAATTGCACCAGGACTTTTTGATACACCAATGTTGCAAGCTTTGCCTGATAA
AATTCGTTCGTTTTTGGCGAAAACTGTTCCATTTCCTCAACGTCTTGGCGATCCTGATGA
ATTTGCACAATTGGTTGAATCAATCGTTGATAATCCAATGCTTAATGGTGAAGTCATCCG
TTTGGATGGAGCTTTGAGAATGATGCCATAA

>g332.t4 Gene=g332 Length=189
MFKNAVALVTGGGSGLGRAVVERFARAGSKVVIGDLKQSPGEELAKELGNNVTFVPMDVT
SENDVNEALHVAKSKFGGLHVAVNCAGIAVAVKTYNFNKKTAHSLESFAKVINVNTNGTF
NVTRLAAGLIGENDPDKDGQRGVIINTASVAAFDGQIGQAAYAASKAAVVGMTLPIARNP
CCNNCTRTF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g332.t4 Gene3D G3DSA:3.40.50.720 - 1 180 5.3E-54
2 g332.t4 PANTHER PTHR43658:SF11 3-HYDROXYACYL-COA DEHYDROGENASE TYPE-2 2 179 1.0E-77
3 g332.t4 PANTHER PTHR43658 SHORT-CHAIN DEHYDROGENASE/REDUCTASE 2 179 1.0E-77
10 g332.t4 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 6 23 2.5E-19
4 g332.t4 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 77 88 1.9E-8
7 g332.t4 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 77 88 2.5E-19
8 g332.t4 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 136 152 2.5E-19
6 g332.t4 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 142 150 1.9E-8
5 g332.t4 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 162 181 1.9E-8
9 g332.t4 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 162 181 2.5E-19
1 g332.t4 Pfam PF00106 short chain dehydrogenase 6 177 3.8E-39
15 g332.t4 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
16 g332.t4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 4 -
17 g332.t4 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 5 12 -
18 g332.t4 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 13 19 -
14 g332.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 189 -
12 g332.t4 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature. 149 177 -
11 g332.t4 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 3 178 7.82E-50

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