General information for g3472.t4
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.t4 | TSS | g3472.t4 | 25772089 | 25772089 |
| chr_3 | g3472 | g3472.t4 | isoform | g3472.t4 | 25772160 | 25772939 |
| chr_3 | g3472 | g3472.t4 | exon | g3472.t4.exon1 | 25772160 | 25772165 |
| chr_3 | g3472 | g3472.t4 | cds | g3472.t4.CDS1 | 25772160 | 25772165 |
| chr_3 | g3472 | g3472.t4 | exon | g3472.t4.exon2 | 25772226 | 25772256 |
| chr_3 | g3472 | g3472.t4 | cds | g3472.t4.CDS2 | 25772226 | 25772256 |
| chr_3 | g3472 | g3472.t4 | exon | g3472.t4.exon3 | 25772417 | 25772747 |
| chr_3 | g3472 | g3472.t4 | cds | g3472.t4.CDS3 | 25772417 | 25772747 |
| chr_3 | g3472 | g3472.t4 | exon | g3472.t4.exon4 | 25772800 | 25772939 |
| chr_3 | g3472 | g3472.t4 | cds | g3472.t4.CDS4 | 25772800 | 25772938 |
| chr_3 | g3472 | g3472.t4 | TTS | g3472.t4 | 25773546 | 25773546 |
Sequences
>g3472.t4 Gene=g3472 Length=508
ATGGAGATTGAAATTCTTGATGCACGAAATTCAAAAGTTATAACAAAATGTAATGTTCAA
TCCAGCACAACGATAAAAGATTTGAAATCCAGTGTATATGCGGCAAATAAAAAATTAAAT
GTTCATCGTCAATCATTTAAGCTGGAAGTAAAAGGAAAAACACTTAAGGATAGTGACACA
ATTGAATCATTGAACTTAAGAAATGGTAGTAAATTGTATGTTAAAGATCTTGGTCCGCAA
ATTGGTTGGTCAACTGTTTTCCTTTGCGAATATGCTGGTCCACTTGTTGTTTATTTATGG
GTTTATACTCGTCCTTGGTTGTTTTATGGTGACACATCGTCATCAGCTGAAATCAGTCAA
ACAGCACATATTGCTGCTGCATGCTACACATTGCATTATGCTAAACGATTACTTGAAACA
ATTTTCGTTCATCGCTTTTCACATGCGACAATGCCTATGAGAAATTTGTTCAAAAACTGC
ATCTACTATTGGGGATTTACTGCTTACG
>g3472.t4 Gene=g3472 Length=169
MEIEILDARNSKVITKCNVQSSTTIKDLKSSVYAANKKLNVHRQSFKLEVKGKTLKDSDT
IESLNLRNGSKLYVKDLGPQIGWSTVFLCEYAGPLVVYLWVYTRPWLFYGDTSSSAEISQ
TAHIAAACYTLHYAKRLLETIFVHRFSHATMPMRNLFKNCIYYWGFTAY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g3472.t4 | CDD | cd01801 | Ubl_TECR_like | 2 | 77 | 0.0000000 |
| 6 | g3472.t4 | Gene3D | G3DSA:3.10.20.90 | - | 1 | 77 | 0.0000000 |
| 2 | g3472.t4 | PANTHER | PTHR10556:SF28 | SC2 | 1 | 169 | 0.0000000 |
| 3 | g3472.t4 | PANTHER | PTHR10556 | 3-OXO-5-ALPHA-STEROID 4-DEHYDROGENASE | 1 | 169 | 0.0000000 |
| 1 | g3472.t4 | Pfam | PF00240 | Ubiquitin family | 18 | 74 | 0.0000001 |
| 7 | g3472.t4 | ProSiteProfiles | PS50053 | Ubiquitin domain profile. | 1 | 74 | 11.4420000 |
| 5 | g3472.t4 | SMART | SM00213 | ubq_7 | 3 | 77 | 0.0004900 |
| 4 | g3472.t4 | SUPERFAMILY | SSF54236 | Ubiquitin-like | 12 | 74 | 0.0000000 |
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:0005515 | protein binding | 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.
