General information for g333.t3
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 3-hydroxyacyl-CoA dehydrogenase type-2.
Parent gene
- The parent gene g333 is located on chr_3: 2784937..2786466 (- strand)
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 | g333 | g333.t3 | TTS | g333.t3 | 2784822 | 2784822 |
| chr_3 | g333 | g333.t3 | isoform | g333.t3 | 2784937 | 2786466 |
| chr_3 | g333 | g333.t3 | exon | g333.t3.exon1 | 2784937 | 2785155 |
| chr_3 | g333 | g333.t3 | cds | g333.t3.CDS1 | 2784937 | 2785155 |
| chr_3 | g333 | g333.t3 | exon | g333.t3.exon2 | 2785211 | 2785750 |
| chr_3 | g333 | g333.t3 | cds | g333.t3.CDS2 | 2785211 | 2785750 |
| chr_3 | g333 | g333.t3 | exon | g333.t3.exon3 | 2785818 | 2785906 |
| chr_3 | g333 | g333.t3 | cds | g333.t3.CDS3 | 2785818 | 2785826 |
| chr_3 | g333 | g333.t3 | exon | g333.t3.exon4 | 2786160 | 2786466 |
| chr_3 | g333 | g333.t3 | TSS | g333.t3 | NA | NA |
Sequences
>g333.t3 Gene=g333 Length=1155
TGTGATATTTTCTTACAGATTGAAAAAGGCACAAAACCAAAATTTTTCTATATTATCTTT
TTACTTTGCTTAATTTACAAAACTTAAAATAAAATTTAAAAATTATCATACTGAAATTCA
CTGAACAATAAAATGCACTGGTTAATTTTCTTTATCAGTTTTTAAATTGATAAAAAAATT
TTTTTAGAAGCATAATACATCGTCTTTTCTCGAAGAAAAACGAACAAACATTTTATTCGA
ACATAACGACCTATGTAATACAATGTCTCTATCATGATTATTATCATTGACTATTAAAAA
CTACCCAAACATATTCTTTTCCGTAAGTTTGTCATCAATTACTCGTTGTCACATTACGTG
GTTTCATTAATTTTTTGAACTTTGAAAATGTTTAAGAACGCTGTTGCATTAGTGACTGGA
GGTGGAAGTGGATTGGGAAGAGCTGTAGTTGAGAGGTTTGCCCGAGCCGGATCAAAGGTT
GTAATCGGAGATTTGAAACAATCTCCAGGCGAGGAATTAGCGAAGGAACTTGGCAATAAT
GTAACATTTGTACCAATGGATGTCACATCAGAAAATGATGTTAATGAGGCATTGCACGTG
GCAAAAAGTAAATTTGGAGGGTTGCATGTCGTTGTAAATTCTGCTGCTATAGTTATGTTC
AAGGAAACATACGATTTCAAAAAGAAGACTCCTCATAGTCTTAATGAATTTGCAAACATC
ATCAATGTCAACCTTAATGGTACTTTCAATGTTACACGATTGGCAGCTGGTTTAATTGGA
GAAAATAAACCTGATAAGGATGGACAACGTGGCGTCATTATAAATGTATCTACTGTTGCT
GCTTTTGATGGTGTAATTGGACAAGCAGCTTATGCTGCATCAAAAGCGGCTGTTGTGGGA
ATGACTTTACCTCTTGCAAGAGATTTGTCAAGTCAAGGAATCCGTGTTGTAACAATTGCA
CCAGGTTTTTTTGATACACCAATGTTTGATTCTTTGCCTGATAAAATTCGTATAACTTTG
GCAAAAACTGTTCCATTTCCTCAACGTTTAGGTTATGCTGAGGAGTTCGCACACTTGGTT
GAAGCAGTAGTTGACAATCCCATGATTAATGGTGAAACTATTCGACAAGATGGAGCTTTG
AGAATGATGCCATAA
>g333.t3 Gene=g333 Length=255
MFKNAVALVTGGGSGLGRAVVERFARAGSKVVIGDLKQSPGEELAKELGNNVTFVPMDVT
SENDVNEALHVAKSKFGGLHVVVNSAAIVMFKETYDFKKKTPHSLNEFANIINVNLNGTF
NVTRLAAGLIGENKPDKDGQRGVIINVSTVAAFDGVIGQAAYAASKAAVVGMTLPLARDL
SSQGIRVVTIAPGFFDTPMFDSLPDKIRITLAKTVPFPQRLGYAEEFAHLVEAVVDNPMI
NGETIRQDGALRMMP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g333.t3 | CDD | cd05371 | HSD10-like_SDR_c | 3 | 255 | 5.12792E-127 |
| 13 | g333.t3 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 255 | 1.1E-76 |
| 2 | g333.t3 | PANTHER | PTHR43658:SF11 | 3-HYDROXYACYL-COA DEHYDROGENASE TYPE-2 | 2 | 255 | 2.4E-110 |
| 3 | g333.t3 | PANTHER | PTHR43658 | SHORT-CHAIN DEHYDROGENASE/REDUCTASE | 2 | 255 | 2.4E-110 |
| 11 | g333.t3 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 6 | 23 | 1.7E-27 |
| 4 | g333.t3 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 77 | 88 | 3.5E-10 |
| 7 | g333.t3 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 77 | 88 | 1.7E-27 |
| 9 | g333.t3 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 136 | 152 | 1.7E-27 |
| 6 | g333.t3 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 142 | 150 | 3.5E-10 |
| 5 | g333.t3 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature | 162 | 181 | 3.5E-10 |
| 10 | g333.t3 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 162 | 181 | 1.7E-27 |
| 8 | g333.t3 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature | 183 | 200 | 1.7E-27 |
| 1 | g333.t3 | Pfam | PF00106 | short chain dehydrogenase | 6 | 205 | 2.6E-49 |
| 15 | g333.t3 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 16 | g333.t3 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 4 | - |
| 17 | g333.t3 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 5 | 12 | - |
| 18 | g333.t3 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 13 | 19 | - |
| 14 | g333.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 255 | - |
| 12 | g333.t3 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 2 | 253 | 6.29E-67 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
## [1] "No matching GO terms"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.
