General information for g12302.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cholesterol 7-desaturase.
Parent gene
- The parent gene g12302 is located on chr_1: 22277850..22279694 (+ 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_1 | g12302 | g12302.t1 | TSS | g12302.t1 | 22276007 | 22276007 |
| chr_1 | g12302 | g12302.t1 | isoform | g12302.t1 | 22276094 | 22277850 |
| chr_1 | g12302 | g12302.t1 | exon | g12302.t1.exon1 | 22276094 | 22276177 |
| chr_1 | g12302 | g12302.t1 | cds | g12302.t1.CDS1 | 22276094 | 22276177 |
| chr_1 | g12302 | g12302.t1 | exon | g12302.t1.exon2 | 22276234 | 22276588 |
| chr_1 | g12302 | g12302.t1 | cds | g12302.t1.CDS2 | 22276234 | 22276588 |
| chr_1 | g12302 | g12302.t1 | exon | g12302.t1.exon3 | 22276835 | 22277038 |
| chr_1 | g12302 | g12302.t1 | cds | g12302.t1.CDS3 | 22276835 | 22277038 |
| chr_1 | g12302 | g12302.t1 | exon | g12302.t1.exon4 | 22277169 | 22277207 |
| chr_1 | g12302 | g12302.t1 | cds | g12302.t1.CDS4 | 22277169 | 22277207 |
| chr_1 | g12302 | g12302.t1 | exon | g12302.t1.exon5 | 22277271 | 22277334 |
| chr_1 | g12302 | g12302.t1 | cds | g12302.t1.CDS5 | 22277271 | 22277334 |
| chr_1 | g12302 | g12302.t1 | exon | g12302.t1.exon6 | 22277409 | 22277850 |
| chr_1 | g12302 | g12302.t1 | cds | g12302.t1.CDS6 | 22277409 | 22277850 |
| chr_1 | g12302 | g12302.t1 | TTS | g12302.t1 | NA | NA |
Sequences
>g12302.t1 Gene=g12302 Length=1188
ATGTGGATTTATTATGTAGTTTCAATTCCTCCTATTTTAATTTTAATTTATTTTATATTT
TTCGTTCCTGTTAATTATAAAAGTAAAGATTCAAAGGACAAACGTACAGCGATAAATCGA
AGTAGAAAGTTAAGAAAAAATGGAAAAAATATTCCACCACCTTTTCCAAATGGTTGGTTT
TGTCTTATGGGTTCTAATGAACTTGAACCTGGAACTGCAAAAGATGTAAATTGTTTGGGT
GAAAATTTTGTGGTTTTTCGTTCAGCTGTCACCAAAGAAGTTTACGTCCTTGATGCTTAT
TGTACACATATGGGAGCAAATTTGGGTGTTGGTGGAATCGTTAAAGATGAATGTATCGAA
TGTCCTTTTCATCAATGGAAATTTTCAGGAAAAGATGGCTCACTTGTATCAATTCCTTAT
AGTGAAGATATTAAGAGTGTTCAAAAGATGGCAAAAATGCGTAAATGGATATCAAAGGAG
ATAAATAAATTAATTTTTGTTTGGTATCATGCTGAAAATGAAGAACCATGGGATATACCA
ATTGTACAAGAAGTTGAAAATGATAAATTTTGGTTACATGGAACCAATGATTTTATCATA
TATTCACACATACAGGACATCCCAGAAAATGGCGCTGATAGAGCTCATTTAGCAACAGTT
CATGGTCCAAATATTTTGGCTGGCACCGATATTCGAACTTTTCGCGATAAATTATTATCA
ATAGGATTGCACTTATGGGATGCCAAATGGAATGCTTGCGAAGGAAAATTAAAGCATATA
GCAAAAGCATCGATTGATCATGTTGTTGAAGTTTTAAAAGTAAAATTCTTTCAACTTGAA
GCTGACGTAACTCAAATCGGTCCTGGTTATGTAGTGTTAAAACTGAAAACTTTTTATGGA
AATGTGACTATACTACAGACTGTAACACCAATAGAACCTATGAAACAACGACTCATGCAC
TTTTTTTATGGCACACCATGGAATGGACTGTTCATGAAATTTACAATTTTTGGCGAAACT
GTCAATGTAGCTAGAGATGCTATGGTGTGGGATAACAAGACATTTATTAGAAATCCATTA
TTGCCGAAAGAAGAAAAACAAATCAGACTTTATCGAAATTGGTTTTCACAATTTTATTCT
GAAAATAGCAAAAGCTTTCAAGAAGCTTACAATGATTTAAGCTGGTAA
>g12302.t1 Gene=g12302 Length=395
MWIYYVVSIPPILILIYFIFFVPVNYKSKDSKDKRTAINRSRKLRKNGKNIPPPFPNGWF
CLMGSNELEPGTAKDVNCLGENFVVFRSAVTKEVYVLDAYCTHMGANLGVGGIVKDECIE
CPFHQWKFSGKDGSLVSIPYSEDIKSVQKMAKMRKWISKEINKLIFVWYHAENEEPWDIP
IVQEVENDKFWLHGTNDFIIYSHIQDIPENGADRAHLATVHGPNILAGTDIRTFRDKLLS
IGLHLWDAKWNACEGKLKHIAKASIDHVVEVLKVKFFQLEADVTQIGPGYVVLKLKTFYG
NVTILQTVTPIEPMKQRLMHFFYGTPWNGLFMKFTIFGETVNVARDAMVWDNKTFIRNPL
LPKEEKQIRLYRNWFSQFYSENSKSFQEAYNDLSW
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g12302.t1 | Gene3D | G3DSA:2.102.10.10 | - | 54 | 191 | 5.8E-35 |
| 7 | g12302.t1 | Gene3D | G3DSA:3.30.530.90 | - | 194 | 392 | 1.4E-23 |
| 2 | g12302.t1 | PANTHER | PTHR21266:SF32 | NEVERLAND | 26 | 386 | 1.9E-56 |
| 3 | g12302.t1 | PANTHER | PTHR21266 | IRON-SULFUR DOMAIN CONTAINING PROTEIN | 26 | 386 | 1.9E-56 |
| 1 | g12302.t1 | Pfam | PF00355 | Rieske [2Fe-2S] domain | 59 | 147 | 6.8E-18 |
| 11 | g12302.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 12 | g12302.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 26 | - |
| 10 | g12302.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 27 | 395 | - |
| 9 | g12302.t1 | ProSiteProfiles | PS51296 | Rieske [2Fe-2S] iron-sulfur domain profile. | 60 | 147 | 22.818 |
| 6 | g12302.t1 | SUPERFAMILY | SSF50022 | ISP domain | 52 | 172 | 5.63E-27 |
| 5 | g12302.t1 | SUPERFAMILY | SSF55961 | Bet v1-like | 163 | 381 | 9.06E-7 |
| 4 | g12302.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 2 | 24 | - |
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:0051537 | 2 iron, 2 sulfur cluster binding | MF |
| GO:0055114 | NA | NA |
KEGG
Orthology
- This transcript has been annotated with K14938 (cholesterol 7-desaturase)
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. There were no conditions that were differentially expressed