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.t3 TTS g332.t3 2782221 2782221
chr_3 g332 g332.t3 isoform g332.t3 2782378 2783271
chr_3 g332 g332.t3 exon g332.t3.exon1 2782378 2782596
chr_3 g332 g332.t3 cds g332.t3.CDS1 2782378 2782596
chr_3 g332 g332.t3 exon g332.t3.exon2 2782656 2783271
chr_3 g332 g332.t3 cds g332.t3.CDS2 2782656 2783036
chr_3 g332 g332.t3 TSS g332.t3 2783302 2783302

Sequences

>g332.t3 Gene=g332 Length=835
ATGTTTAAGGTAAAATTTGATTATTTTTCTCAATTCTATTGATTATCTAACAATTTATTC
TTAATTATTGATATAGAACGCTGTTGCATTAGTGACTGGAGGTGGAAGTGGATTGGGAAG
AGCTGTAGTTGAGAGGTTTGCTCGAGCCGGATCAAAGGTTGTAATCGGCGATTTGAAACA
ATCTCCAGGCGAGGAATTAGCGAAAGAACTTGGCAATAATGTAACTTTTGTTCCAATGGA
TGTCACATCAGAGAACGATGTTAATGAGGCATTGCACGTGGCAAAAAGTAAATTCGGAGG
ACTGCATGTAGCTGTAAATTGTGCTGGAATTGCAGTGGCAGTGAAAACTTACAATTTCAA
TAAGAAAACTGCACATAGCCTCGAATCATTTGCGAAGGTCATTAATGTCAACACTAATGG
TACTTTCAATGTCACACGATTGGCAGCTGGTTTAATTGGAGAAAATGATCCTGATAAAGA
TGGACAACGTGGTGTAATTATAAATACAGCTTCGGTTGCTGCTTTTGACGGTCAGATTGG
ACAAGCAGCTTATGCTGCATCAAAAGCAGCTGTTGTAGGAATGACTTTGCCTATTGCAAG
AGATTTATCAGTTCAAGGAATCCGTGTTGTAACAATTGCACCAGGACTTTTTGATACACC
AATGTTGCAAGCTTTGCCTGATAAAATTCGTTCGTTTTTGGCGAAAACTGTTCCATTTCC
TCAACGTCTTGGCGATCCTGATGAATTTGCACAATTGGTTGAATCAATCGTTGATAATCC
AATGCTTAATGGTGAAGTCATCCGTTTGGATGGAGCTTTGAGAATGATGCCATAA

>g332.t3 Gene=g332 Length=199
MDVTSENDVNEALHVAKSKFGGLHVAVNCAGIAVAVKTYNFNKKTAHSLESFAKVINVNT
NGTFNVTRLAAGLIGENDPDKDGQRGVIINTASVAAFDGQIGQAAYAASKAAVVGMTLPI
ARDLSVQGIRVVTIAPGLFDTPMLQALPDKIRSFLAKTVPFPQRLGDPDEFAQLVESIVD
NPMLNGEVIRLDGALRMMP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g332.t3 Gene3D G3DSA:3.40.50.720 - 1 199 6.7E-56
2 g332.t3 PANTHER PTHR43658:SF11 3-HYDROXYACYL-COA DEHYDROGENASE TYPE-2 2 199 7.4E-100
3 g332.t3 PANTHER PTHR43658 SHORT-CHAIN DEHYDROGENASE/REDUCTASE 2 199 7.4E-100
5 g332.t3 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 21 32 4.2E-10
10 g332.t3 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 21 32 1.4E-19
9 g332.t3 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 80 96 1.4E-19
6 g332.t3 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 86 94 4.2E-10
4 g332.t3 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature 106 125 4.2E-10
8 g332.t3 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 106 125 1.4E-19
11 g332.t3 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 127 144 1.4E-19
7 g332.t3 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature 161 181 1.4E-19
1 g332.t3 Pfam PF13561 Enoyl-(Acyl carrier protein) reductase 1 193 4.7E-33
13 g332.t3 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature. 93 121 -
12 g332.t3 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 1 197 1.81E-45

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