General information for g8422.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 g8422 is located on chr_2: 30384356..30391280 (+ 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_2 | g8422 | g8422.t1 | isoform | g8422.t1 | 30384356 | 30391280 |
| chr_2 | g8422 | g8422.t1 | exon | g8422.t1.exon1 | 30384356 | 30384370 |
| chr_2 | g8422 | g8422.t1 | cds | g8422.t1.CDS1 | 30384356 | 30384370 |
| chr_2 | g8422 | g8422.t1 | TSS | g8422.t1 | 30389447 | 30389447 |
| chr_2 | g8422 | g8422.t1 | exon | g8422.t1.exon2 | 30389752 | 30389992 |
| chr_2 | g8422 | g8422.t1 | cds | g8422.t1.CDS2 | 30389752 | 30389992 |
| chr_2 | g8422 | g8422.t1 | exon | g8422.t1.exon3 | 30390051 | 30390164 |
| chr_2 | g8422 | g8422.t1 | cds | g8422.t1.CDS3 | 30390051 | 30390164 |
| chr_2 | g8422 | g8422.t1 | exon | g8422.t1.exon4 | 30390227 | 30390418 |
| chr_2 | g8422 | g8422.t1 | cds | g8422.t1.CDS4 | 30390227 | 30390418 |
| chr_2 | g8422 | g8422.t1 | exon | g8422.t1.exon5 | 30390594 | 30390605 |
| chr_2 | g8422 | g8422.t1 | cds | g8422.t1.CDS5 | 30390594 | 30390605 |
| chr_2 | g8422 | g8422.t1 | exon | g8422.t1.exon6 | 30390681 | 30390783 |
| chr_2 | g8422 | g8422.t1 | cds | g8422.t1.CDS6 | 30390681 | 30390783 |
| chr_2 | g8422 | g8422.t1 | exon | g8422.t1.exon7 | 30390842 | 30391280 |
| chr_2 | g8422 | g8422.t1 | cds | g8422.t1.CDS7 | 30390842 | 30391280 |
| chr_2 | g8422 | g8422.t1 | TTS | g8422.t1 | 30391337 | 30391337 |
Sequences
>g8422.t1 Gene=g8422 Length=1116
ATGCTTAACACTGAGGATGATTCAAGCGATAAGCGATCAGCTGTAAATCGTGCACGAAGG
TTACGAAAGATTGGTTCAAAATTGCCACCACCTTATCCAAATGGTTGGTTTGCTATAGCA
ACATCGAAAGAAATTATGAGGGGAAAAGCAAAGAATATTGAGTGCTTGGGTGAACATTTT
GTCGTCTTTCGTGCATCAAATTCTAATGAAGTTTTTGTTCTTGATGCATATTGTCCTCAC
ATGGGTGCTAACTTAGGTGTTGGTGGAATTGTAAAAAATAATTGTGTCGAATGTCCTTTC
CATCAATGGCGATTTAATGGTGATAATGGCGAATTAGTGAATATTCCTTATAGTGAAAAT
CTCTCAGAAGTTGAGAAATTTGCAAAGATCCGCAAATGGATTTCAACAGAAGTGAATGGA
ATTATTTTTGTTTGGTATCACGCGGAAAATGAACAACCTTGGATACTTCCGACTGTTGAT
GAAGTGAATGATGGAAGTTGGGTTTATCATGGTGCTAATGAATTTACTATAAATTGTCAT
ATACAAGACATCCCAGAAAATGGCGCCGACAGAGCTCATCTGACGACAGTTCATGGAACA
AACATTGCAGCTGGCATGGATGTTTGCAAATCACGTGAGAGTATTTTTTCATTTGGAACT
CACATTTGGGATGCAAAATGGGCAGTAAATGATGACTTAAAACATCAATCGATTATCAAA
TTGACTCATGTTTTCAATGTTTTATCATTTAAATTGCTGAAAATTGACAGTGATATTCGA
CAAATCGGACCAGCATTTGTGATTTTAACAATCAAAACAATTTTTGGAAACGCTGTAATT
TTTCAAACTCTAACACCCTTGGAACCATTGGTGCAAAAACTTTCACATTATTTTTATGCA
CCATGGTATCTTGCATGGTTTGTAAAGTTCCTAATTTGGGGTGAAACAGTCAATGTTGGA
CGTGATGTGATGATTTGGAATAGCAAAGAATTTATTAAAAATCCATTGCTTCCAAAAGAA
GAGAAGCAAATTAAACTTTTTAGAAATTGGTTCTCGCAGTTTTATTCAGAAAACAGTAAG
AGCTTTCAAGATGCTCATCAATCATTAGACTGGTAG
>g8422.t1 Gene=g8422 Length=371
MLNTEDDSSDKRSAVNRARRLRKIGSKLPPPYPNGWFAIATSKEIMRGKAKNIECLGEHF
VVFRASNSNEVFVLDAYCPHMGANLGVGGIVKNNCVECPFHQWRFNGDNGELVNIPYSEN
LSEVEKFAKIRKWISTEVNGIIFVWYHAENEQPWILPTVDEVNDGSWVYHGANEFTINCH
IQDIPENGADRAHLTTVHGTNIAAGMDVCKSRESIFSFGTHIWDAKWAVNDDLKHQSIIK
LTHVFNVLSFKLLKIDSDIRQIGPAFVILTIKTIFGNAVIFQTLTPLEPLVQKLSHYFYA
PWYLAWFVKFLIWGETVNVGRDVMIWNSKEFIKNPLLPKEEKQIKLFRNWFSQFYSENSK
SFQDAHQSLDW
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g8422.t1 | Gene3D | G3DSA:2.102.10.10 | - | 31 | 167 | 0.000 |
| 6 | g8422.t1 | Gene3D | G3DSA:3.30.530.90 | - | 168 | 370 | 0.000 |
| 2 | g8422.t1 | PANTHER | PTHR21266:SF32 | NEVERLAND | 13 | 363 | 0.000 |
| 3 | g8422.t1 | PANTHER | PTHR21266 | IRON-SULFUR DOMAIN CONTAINING PROTEIN | 13 | 363 | 0.000 |
| 1 | g8422.t1 | Pfam | PF00355 | Rieske [2Fe-2S] domain | 36 | 123 | 0.000 |
| 8 | g8422.t1 | ProSiteProfiles | PS51296 | Rieske [2Fe-2S] iron-sulfur domain profile. | 36 | 144 | 24.838 |
| 5 | g8422.t1 | SUPERFAMILY | SSF50022 | ISP domain | 29 | 149 | 0.000 |
| 4 | g8422.t1 | SUPERFAMILY | SSF55961 | Bet v1-like | 140 | 357 | 0.000 |
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