General information for g3472.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable very-long-chain enoyl-CoA reductase art-1.
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.t1 | TSS | g3472.t1 | 25772089 | 25772089 |
| chr_3 | g3472 | g3472.t1 | isoform | g3472.t1 | 25772160 | 25773395 |
| chr_3 | g3472 | g3472.t1 | exon | g3472.t1.exon1 | 25772160 | 25772165 |
| chr_3 | g3472 | g3472.t1 | cds | g3472.t1.CDS1 | 25772160 | 25772165 |
| chr_3 | g3472 | g3472.t1 | exon | g3472.t1.exon2 | 25772226 | 25772256 |
| chr_3 | g3472 | g3472.t1 | cds | g3472.t1.CDS2 | 25772226 | 25772256 |
| chr_3 | g3472 | g3472.t1 | exon | g3472.t1.exon3 | 25772417 | 25772747 |
| chr_3 | g3472 | g3472.t1 | cds | g3472.t1.CDS3 | 25772417 | 25772747 |
| chr_3 | g3472 | g3472.t1 | exon | g3472.t1.exon4 | 25772800 | 25773016 |
| chr_3 | g3472 | g3472.t1 | cds | g3472.t1.CDS4 | 25772800 | 25773016 |
| chr_3 | g3472 | g3472.t1 | exon | g3472.t1.exon5 | 25773075 | 25773395 |
| chr_3 | g3472 | g3472.t1 | cds | g3472.t1.CDS5 | 25773075 | 25773395 |
| chr_3 | g3472 | g3472.t1 | TTS | g3472.t1 | 25773546 | 25773546 |
Sequences
>g3472.t1 Gene=g3472 Length=906
ATGGAGATTGAAATTCTTGATGCACGAAATTCAAAAGTTATAACAAAATGTAATGTTCAA
TCCAGCACAACGATAAAAGATTTGAAATCCAGTGTATATGCGGCAAATAAAAAATTAAAT
GTTCATCGTCAATCATTTAAGCTGGAAGTAAAAGGAAAAACACTTAAGGATAGTGACACA
ATTGAATCATTGAACTTAAGAAATGGTAGTAAATTGTATGTTAAAGATCTTGGTCCGCAA
ATTGGTTGGTCAACTGTTTTCCTTTGCGAATATGCTGGTCCACTTGTTGTTTATTTATGG
GTTTATACTCGTCCTTGGTTGTTTTATGGTGACACATCGTCATCAGCTGAAATCAGTCAA
ACAGCACATATTGCTGCTGCATGCTACACATTGCATTATGCTAAACGATTACTTGAAACA
ATTTTCGTTCATCGCTTTTCACATGCGACAATGCCTATGAGAAATTTGTTCAAAAACTGC
ATCTACTATTGGGGATTTACTGCTTACGTTGCCTATCACGTTAATCATCCTCTTTTTACA
TCACCATCTACTGCTCAAGTTTATGCTAGTCTTGCCGCATTCTTGTTATGTGAACTTGGT
AACTTTTCAATACATATCAATTTGAGAAATTTAAGACCACCAGGAACATCTGTAAGAAAA
ATTCCAATGTCTGATTCAAATCCGCTAACTGCTCTCTTTAACTTCGTTTCGTGTCCAAAT
TATACTTACGAGTTCGGAGCTTGGCTTTCATTTTCTATCATGACTCAATGCTTGCCTGCT
TTCCTTTTTGCTGCTGCTGGAATGTATCAAATGACAATGTGGGCTATCGGAAAACATAAG
AACTACAAAAAAGAATTCAAAGAATATCCAAAGCAAAGAAAAGCTATTATTCCATTTTTA
TTGTAA
>g3472.t1 Gene=g3472 Length=301
MEIEILDARNSKVITKCNVQSSTTIKDLKSSVYAANKKLNVHRQSFKLEVKGKTLKDSDT
IESLNLRNGSKLYVKDLGPQIGWSTVFLCEYAGPLVVYLWVYTRPWLFYGDTSSSAEISQ
TAHIAAACYTLHYAKRLLETIFVHRFSHATMPMRNLFKNCIYYWGFTAYVAYHVNHPLFT
SPSTAQVYASLAAFLLCELGNFSIHINLRNLRPPGTSVRKIPMSDSNPLTALFNFVSCPN
YTYEFGAWLSFSIMTQCLPAFLFAAAGMYQMTMWAIGKHKNYKKEFKEYPKQRKAIIPFL
L
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g3472.t1 | CDD | cd01801 | Ubl_TECR_like | 2 | 77 | 4.55481E-24 |
| 6 | g3472.t1 | Gene3D | G3DSA:3.10.20.90 | - | 1 | 77 | 2.8E-22 |
| 3 | g3472.t1 | PANTHER | PTHR10556:SF28 | SC2 | 1 | 301 | 3.0E-110 |
| 4 | g3472.t1 | PANTHER | PTHR10556 | 3-OXO-5-ALPHA-STEROID 4-DEHYDROGENASE | 1 | 301 | 3.0E-110 |
| 2 | g3472.t1 | Pfam | PF00240 | Ubiquitin family | 18 | 74 | 2.1E-7 |
| 1 | g3472.t1 | Pfam | PF02544 | 3-oxo-5-alpha-steroid 4-dehydrogenase | 150 | 301 | 4.1E-30 |
| 8 | g3472.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 257 | - |
| 9 | g3472.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 258 | 277 | - |
| 7 | g3472.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 278 | 301 | - |
| 15 | g3472.t1 | ProSiteProfiles | PS50053 | Ubiquitin domain profile. | 1 | 74 | 11.442 |
| 16 | g3472.t1 | ProSiteProfiles | PS50244 | Steroid 5-alpha reductase C-terminal domain profile. | 190 | 276 | 22.185 |
| 14 | g3472.t1 | SMART | SM00213 | ubq_7 | 3 | 77 | 4.9E-4 |
| 5 | g3472.t1 | SUPERFAMILY | SSF54236 | Ubiquitin-like | 12 | 74 | 9.69E-9 |
| 12 | g3472.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 80 | 102 | - |
| 11 | g3472.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 160 | 179 | - |
| 13 | g3472.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 245 | 267 | - |
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:0005515 | protein binding | MF |
| GO:0006629 | lipid metabolic process | BP |
KEGG
Orthology
- This transcript has been annotated with K10258 (very-long-chain enoyl-CoA reductase)
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.
