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.t7 TTS g332.t7 2782221 2782221
chr_3 g332 g332.t7 isoform g332.t7 2782378 2783271
chr_3 g332 g332.t7 exon g332.t7.exon1 2782378 2782596
chr_3 g332 g332.t7 cds g332.t7.CDS1 2782378 2782596
chr_3 g332 g332.t7 exon g332.t7.exon2 2782662 2783195
chr_3 g332 g332.t7 cds g332.t7.CDS2 2782662 2783195
chr_3 g332 g332.t7 exon g332.t7.exon3 2783263 2783271
chr_3 g332 g332.t7 cds g332.t7.CDS3 2783263 2783271
chr_3 g332 g332.t7 TSS g332.t7 2783302 2783302

Sequences

>g332.t7 Gene=g332 Length=762
ATGTTTAAGAACGCTGTTGCATTAGTGACTGGAGGTGGAAGTGGATTGGGAAGAGCTGTA
GTTGAGAGGTTTGCTCGAGCCGGATCAAAGGTTGTAATCGGCGATTTGAAACAATCTCCA
GGCGAGGAATTAGCGAAAGAACTTGGCAATAATGTAACTTTTGTTCCAATGGATGTCACA
TCAGAGAACGATGTTAATGAGGCATTGCACGTGGCAAAAAGTAAATTCGGAGGACTGCAT
GTAGCTGTAAATTGTGCTGGAATTGCAGTGGCAGTGAAAACTTACAATTTCAATAAGAAA
ACTGCACATAGCCTCGAATCATTTGCGAAGGTCATTAATGTCAACACTAATGGTACTTTC
AATGTCACACGATTGGCAGCTGGTTTAATTGGAGAAAATGATCCTGATAAAGATGGACAA
CGTGGTGTAATTATAAATACAGCTTCGGTTGCTGCTTTTGACGGTCAGATTGGACAAGCA
GCTTATGCTGCATCAAAAGCAGCTGTTGTAGGAATGACTTTGCCTATTGCAAGAGATTTA
TCAGGAATCCGTGTTGTAACAATTGCACCAGGACTTTTTGATACACCAATGTTGCAAGCT
TTGCCTGATAAAATTCGTTCGTTTTTGGCGAAAACTGTTCCATTTCCTCAACGTCTTGGC
GATCCTGATGAATTTGCACAATTGGTTGAATCAATCGTTGATAATCCAATGCTTAATGGT
GAAGTCATCCGTTTGGATGGAGCTTTGAGAATGATGCCATAA

>g332.t7 Gene=g332 Length=253
MFKNAVALVTGGGSGLGRAVVERFARAGSKVVIGDLKQSPGEELAKELGNNVTFVPMDVT
SENDVNEALHVAKSKFGGLHVAVNCAGIAVAVKTYNFNKKTAHSLESFAKVINVNTNGTF
NVTRLAAGLIGENDPDKDGQRGVIINTASVAAFDGQIGQAAYAASKAAVVGMTLPIARDL
SGIRVVTIAPGLFDTPMLQALPDKIRSFLAKTVPFPQRLGDPDEFAQLVESIVDNPMLNG
EVIRLDGALRMMP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g332.t7 CDD cd05371 HSD10-like_SDR_c 3 253 2.05762E-141
14 g332.t7 Gene3D G3DSA:3.40.50.720 - 1 253 1.2E-76
2 g332.t7 PANTHER PTHR43658:SF11 3-HYDROXYACYL-COA DEHYDROGENASE TYPE-2 2 253 5.4E-122
3 g332.t7 PANTHER PTHR43658 SHORT-CHAIN DEHYDROGENASE/REDUCTASE 2 253 5.4E-122
11 g332.t7 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 6 23 1.1E-29
4 g332.t7 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 77 88 7.2E-10
7 g332.t7 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 77 88 1.1E-29
9 g332.t7 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 136 152 1.1E-29
6 g332.t7 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 142 150 7.2E-10
5 g332.t7 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 162 181 7.2E-10
10 g332.t7 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 162 181 1.1E-29
12 g332.t7 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 181 198 1.1E-29
8 g332.t7 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 215 235 1.1E-29
1 g332.t7 Pfam PF00106 short chain dehydrogenase 6 203 1.4E-46
16 g332.t7 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
17 g332.t7 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 4 -
18 g332.t7 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 5 12 -
19 g332.t7 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 13 19 -
15 g332.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 253 -
21 g332.t7 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature. 149 177 -
13 g332.t7 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 2 251 4.14E-65

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

Pathway

  • This transcript belongs to the following pathways

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