General information for g3472.t20
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Very-long-chain enoyl-CoA reductase.
Parent gene
- The parent gene g3472 is located on chr_3: 25772874..25773395 (+ 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 | g3472 | g3472.t20 | TSS | g3472.t20 | 25772089 | 25772089 |
| chr_3 | g3472 | g3472.t20 | isoform | g3472.t20 | 25772160 | 25773395 |
| chr_3 | g3472 | g3472.t20 | exon | g3472.t20.exon1 | 25772160 | 25772747 |
| chr_3 | g3472 | g3472.t20 | exon | g3472.t20.exon2 | 25772800 | 25773016 |
| chr_3 | g3472 | g3472.t20 | cds | g3472.t20.CDS1 | 25772882 | 25773016 |
| chr_3 | g3472 | g3472.t20 | exon | g3472.t20.exon3 | 25773075 | 25773140 |
| chr_3 | g3472 | g3472.t20 | cds | g3472.t20.CDS2 | 25773075 | 25773140 |
| chr_3 | g3472 | g3472.t20 | exon | g3472.t20.exon4 | 25773222 | 25773395 |
| chr_3 | g3472 | g3472.t20 | cds | g3472.t20.CDS3 | 25773222 | 25773395 |
| chr_3 | g3472 | g3472.t20 | TTS | g3472.t20 | 25773546 | 25773546 |
Sequences
>g3472.t20 Gene=g3472 Length=1045
ATGGAGGTAAACTTGTTAATCAAATACTGTTTAAAACACTTATCTTATAATTGTTTCTTA
ATTTAGATTGAAATTCTTGATGCACGAAATTCAAAAGGTGAGTAAATTTAAAATCAAAGT
TCTTACTCTTATATTTTACACGTAAAATTGACTTTTGGCCGGAATATGGAATACATTTTT
ATATTTGCCTATTGAATAATTTTCTTCTTTTCTTCTTCTTTACTTCTTTTTTTTTATCTG
TCTCTTCGCTAAAACAGTTATAACAAAATGTAATGTTCAATCCAGCACAACGATAAAAGA
TTTGAAATCCAGTGTATATGCGGCAAATAAAAAATTAAATGTTCATCGTCAATCATTTAA
GCTGGAAGTAAAAGGAAAAACACTTAAGGATAGTGACACAATTGAATCATTGAACTTAAG
AAATGGTAGTAAATTGTATGTTAAAGATCTTGGTCCGCAAATTGGTTGGTCAACTGTTTT
CCTTTGCGAATATGCTGGTCCACTTGTTGTTTATTTATGGGTTTATACTCGTCCTTGGTT
GTTTTATGGTGACACATCGTCATCAGCTGAAATCAGTCAAACAGCACATATTGCTGCTGC
ATGCTACACATTGCATTATGCTAAACGATTACTTGAAACAATTTTCGTTCATCGCTTTTC
ACATGCGACAATGCCTATGAGAAATTTGTTCAAAAACTGCATCTACTATTGGGGATTTAC
TGCTTACGTTGCCTATCACGTTAATCATCCTCTTTTTACATCACCATCTACTGCTCAAGT
TTATGCTAGTCTTGCCGCATTCTTGTTATGTGAACTTGGTAACTTTTCAATACATATCAA
TTTGAGAAATTTAAGACCACCAGGAACATCTTTCGGAGCTTGGCTTTCATTTTCTATCAT
GACTCAATGCTTGCCTGCTTTCCTTTTTGCTGCTGCTGGAATGTATCAAATGACAATGTG
GGCTATCGGAAAACATAAGAACTACAAAAAAGAATTCAAAGAATATCCAAAGCAAAGAAA
AGCTATTATTCCATTTTTATTGTAA
>g3472.t20 Gene=g3472 Length=124
MPMRNLFKNCIYYWGFTAYVAYHVNHPLFTSPSTAQVYASLAAFLLCELGNFSIHINLRN
LRPPGTSFGAWLSFSIMTQCLPAFLFAAAGMYQMTMWAIGKHKNYKKEFKEYPKQRKAII
PFLL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g3472.t20 | PANTHER | PTHR10556:SF31 | VERY-LONG-CHAIN ENOYL-COA REDUCTASE | 1 | 66 | 4.0E-43 |
| 4 | g3472.t20 | PANTHER | PTHR10556 | 3-OXO-5-ALPHA-STEROID 4-DEHYDROGENASE | 1 | 66 | 4.0E-43 |
| 3 | g3472.t20 | PANTHER | PTHR10556:SF31 | VERY-LONG-CHAIN ENOYL-COA REDUCTASE | 68 | 124 | 4.0E-43 |
| 5 | g3472.t20 | PANTHER | PTHR10556 | 3-OXO-5-ALPHA-STEROID 4-DEHYDROGENASE | 68 | 124 | 4.0E-43 |
| 1 | g3472.t20 | Pfam | PF02544 | 3-oxo-5-alpha-steroid 4-dehydrogenase | 70 | 124 | 1.8E-14 |
| 11 | g3472.t20 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 14 | g3472.t20 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 25 | - |
| 10 | g3472.t20 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 26 | 36 | - |
| 15 | g3472.t20 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 37 | 56 | - |
| 12 | g3472.t20 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 57 | 67 | - |
| 13 | g3472.t20 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 68 | 92 | - |
| 9 | g3472.t20 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 93 | 124 | - |
| 7 | g3472.t20 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 5 | 24 | - |
| 8 | g3472.t20 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 34 | 56 | - |
| 6 | g3472.t20 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 68 | 90 | - |
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:0016627 | oxidoreductase activity, acting on the CH-CH group of donors | MF |
| GO:0006629 | lipid metabolic process | BP |
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