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.t8 TTS g332.t8 2782221 2782221
chr_3 g332 g332.t8 isoform g332.t8 2782378 2783271
chr_3 g332 g332.t8 exon g332.t8.exon1 2782378 2782596
chr_3 g332 g332.t8 cds g332.t8.CDS1 2782378 2782596
chr_3 g332 g332.t8 exon g332.t8.exon2 2782656 2782913
chr_3 g332 g332.t8 cds g332.t8.CDS2 2782656 2782913
chr_3 g332 g332.t8 exon g332.t8.exon3 2783052 2783195
chr_3 g332 g332.t8 cds g332.t8.CDS3 2783052 2783195
chr_3 g332 g332.t8 exon g332.t8.exon4 2783263 2783271
chr_3 g332 g332.t8 cds g332.t8.CDS4 2783263 2783271
chr_3 g332 g332.t8 TSS g332.t8 2783302 2783302

Sequences

>g332.t8 Gene=g332 Length=630
ATGTTTAAGAACGCTGTTGCATTAGTGACTGGAGGTGGAAGTGGATTGGGAAGAGCTGTA
GTTGAGAGGTTTGCTCGAGCCGGATCAAAGGTTGTAATCGGCGATTTGAAACAATCTCCA
GGCGAGGAATTAGCGAAAGAACTTGGCAATAATAATAAGAAAACTGCACATAGCCTCGAA
TCATTTGCGAAGGTCATTAATGTCAACACTAATGGTACTTTCAATGTCACACGATTGGCA
GCTGGTTTAATTGGAGAAAATGATCCTGATAAAGATGGACAACGTGGTGTAATTATAAAT
ACAGCTTCGGTTGCTGCTTTTGACGGTCAGATTGGACAAGCAGCTTATGCTGCATCAAAA
GCAGCTGTTGTAGGAATGACTTTGCCTATTGCAAGAGATTTATCAGTTCAAGGAATCCGT
GTTGTAACAATTGCACCAGGACTTTTTGATACACCAATGTTGCAAGCTTTGCCTGATAAA
ATTCGTTCGTTTTTGGCGAAAACTGTTCCATTTCCTCAACGTCTTGGCGATCCTGATGAA
TTTGCACAATTGGTTGAATCAATCGTTGATAATCCAATGCTTAATGGTGAAGTCATCCGT
TTGGATGGAGCTTTGAGAATGATGCCATAA

>g332.t8 Gene=g332 Length=209
MFKNAVALVTGGGSGLGRAVVERFARAGSKVVIGDLKQSPGEELAKELGNNNKKTAHSLE
SFAKVINVNTNGTFNVTRLAAGLIGENDPDKDGQRGVIINTASVAAFDGQIGQAAYAASK
AAVVGMTLPIARDLSVQGIRVVTIAPGLFDTPMLQALPDKIRSFLAKTVPFPQRLGDPDE
FAQLVESIVDNPMLNGEVIRLDGALRMMP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g332.t8 Gene3D G3DSA:3.40.50.720 - 1 53 2.2E-12
16 g332.t8 Gene3D G3DSA:3.40.50.720 - 54 209 3.6E-43
3 g332.t8 PANTHER PTHR43658:SF11 3-HYDROXYACYL-COA DEHYDROGENASE TYPE-2 2 51 1.2E-96
5 g332.t8 PANTHER PTHR43658 SHORT-CHAIN DEHYDROGENASE/REDUCTASE 2 51 1.2E-96
2 g332.t8 PANTHER PTHR43658:SF11 3-HYDROXYACYL-COA DEHYDROGENASE TYPE-2 51 209 1.2E-96
4 g332.t8 PANTHER PTHR43658 SHORT-CHAIN DEHYDROGENASE/REDUCTASE 51 209 1.2E-96
11 g332.t8 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 6 23 2.0E-26
8 g332.t8 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 90 106 2.0E-26
7 g332.t8 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 96 104 3.3E-6
6 g332.t8 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 116 135 3.3E-6
9 g332.t8 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 116 135 2.0E-26
10 g332.t8 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 137 154 2.0E-26
12 g332.t8 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 171 191 2.0E-26
1 g332.t8 Pfam PF00106 short chain dehydrogenase 57 159 9.6E-25
18 g332.t8 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
19 g332.t8 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 4 -
20 g332.t8 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 5 12 -
21 g332.t8 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 13 19 -
17 g332.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 209 -
14 g332.t8 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature. 103 131 -
13 g332.t8 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 2 207 9.45E-49

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.

Raw TPM values