General information for g3030.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Acyl-CoA Delta(11) desaturase.
Parent gene
- The parent gene g3030 is located on chr_3: 22212931..22220089 (+ 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 | g3030 | g3030.t1 | isoform | g3030.t1 | 22208326 | 22213559 |
| chr_3 | g3030 | g3030.t1 | exon | g3030.t1.exon1 | 22208326 | 22208333 |
| chr_3 | g3030 | g3030.t1 | cds | g3030.t1.CDS1 | 22208326 | 22208333 |
| chr_3 | g3030 | g3030.t1 | exon | g3030.t1.exon2 | 22209050 | 22209447 |
| chr_3 | g3030 | g3030.t1 | cds | g3030.t1.CDS2 | 22209050 | 22209447 |
| chr_3 | g3030 | g3030.t1 | exon | g3030.t1.exon3 | 22212182 | 22212358 |
| chr_3 | g3030 | g3030.t1 | cds | g3030.t1.CDS3 | 22212182 | 22212358 |
| chr_3 | g3030 | g3030.t1 | exon | g3030.t1.exon4 | 22212422 | 22212581 |
| chr_3 | g3030 | g3030.t1 | cds | g3030.t1.CDS4 | 22212422 | 22212581 |
| chr_3 | g3030 | g3030.t1 | exon | g3030.t1.exon5 | 22212931 | 22213116 |
| chr_3 | g3030 | g3030.t1 | cds | g3030.t1.CDS5 | 22212931 | 22213116 |
| chr_3 | g3030 | g3030.t1 | exon | g3030.t1.exon6 | 22213177 | 22213462 |
| chr_3 | g3030 | g3030.t1 | cds | g3030.t1.CDS6 | 22213177 | 22213462 |
| chr_3 | g3030 | g3030.t1 | exon | g3030.t1.exon7 | 22213521 | 22213559 |
| chr_3 | g3030 | g3030.t1 | cds | g3030.t1.CDS7 | 22213521 | 22213559 |
| chr_3 | g3030 | g3030.t1 | TTS | g3030.t1 | 22214491 | 22214491 |
| chr_3 | g3030 | g3030.t1 | TSS | g3030.t1 | NA | NA |
Sequences
>g3030.t1 Gene=g3030 Length=1254
ATGGGAGTTGCCAACGATAGCGATAGTGATTTTGAAGAAATAACAAACATAAACGACAAA
ATGAATCATGTACAAGCGGTAACAGTGGTTGAAACCACTCTTGATGAGAATAGCAAGTGT
GTGAATAATCAGATAAAATCTAACATAACAAAGCGCAATGTGTTTAAAGATAGCAATAAT
AATGTGCAACAAATAACAAAAGAGTCGCTTAATGTCGATAGTAGTAAGCAAACTTCCACC
AATGATGAGGATGATCAACCTATGGAGTACACTTTGCTCGGCTTCATTAAGTTCAAATCA
CCTATCAAATGGCTCAACACAGTCTCCATCATTCTCATTCATCTCATATTTATTTTTGGA
TTTTTCACATATCCTCTTTATGGAAAAATTTTAACTACACTCTGGGGCTTCGTCGTGGGA
GGAATTTGCGGATTTGGTGTAACCGGTGGAGCCCATAGATTTTGGTGTCATCGATCATAT
AAAGCTAAATTGCCACTTCGTATCATTCTTATGCTCTGCTATTGTACGGCTGGACAAAAC
ACTCTCTATGATTGGGTACGAGATCATCGAGTTCATCATAAATATTCAGAGACTGACGCA
GATCCACATAACTCAAACAGAGGCTTCTTCTTTGCTCATGTTGGATGGTTGATGTTGCAA
AAGCATCCAGAAGTTATTAAAAAAGGTCGTGCCATTGACATGAGTGATGTTTTGGCCGAT
CCAGTTATTCAATTTCATCAAAAATATTTCATCCCTCTTAAAATTCTGTGTTGCTTCATT
CTACCAACAATTGTGCCTGTCTATTTCTGGGGTGAATCATGGTATATGGCTTTCATGTCA
CAAGCAGTTTTACGTTATCTCTTCAGTTTGAACTTTACTTGGTTGGTTAATTCGGCTGCT
CACATGTGGGGCTATAAACCTTACGACAGGAGAATAAATCCAGTCGAGAATGTTGCAGTT
GCTGTTGTTGCTATGGGCGAAGGATGGCATAATTATCATCATGTATTTCCTTGGGATTAC
AAAGCAGCTGAATTGGGAGATTATAAATTAAACATTACAACTTTCTGGATAGACTTATTT
GCTAAAATTGGTTGGGCTTATGACTTAAAACAACCTTCTGAAGACTTGGTGAGAAAGACA
GTTCAAAAATATGGTGATGGTTGTCATTCTGTGTGGGGACATGGACAATCAGAAAATATT
CATGCACCTGTCGAGGCAATTCCTGCACCAGGCGAAGAAAACCTTGGCTATTGA
>g3030.t1 Gene=g3030 Length=417
MGVANDSDSDFEEITNINDKMNHVQAVTVVETTLDENSKCVNNQIKSNITKRNVFKDSNN
NVQQITKESLNVDSSKQTSTNDEDDQPMEYTLLGFIKFKSPIKWLNTVSIILIHLIFIFG
FFTYPLYGKILTTLWGFVVGGICGFGVTGGAHRFWCHRSYKAKLPLRIILMLCYCTAGQN
TLYDWVRDHRVHHKYSETDADPHNSNRGFFFAHVGWLMLQKHPEVIKKGRAIDMSDVLAD
PVIQFHQKYFIPLKILCCFILPTIVPVYFWGESWYMAFMSQAVLRYLFSLNFTWLVNSAA
HMWGYKPYDRRINPVENVAVAVVAMGEGWHNYHHVFPWDYKAAELGDYKLNITTFWIDLF
AKIGWAYDLKQPSEDLVRKTVQKYGDGCHSVWGHGQSENIHAPVEAIPAPGEENLGY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 26 | g3030.t1 | CDD | cd03505 | Delta9-FADS-like | 129 | 370 | 4.69146E-74 |
| 2 | g3030.t1 | PANTHER | PTHR11351 | ACYL-COA DESATURASE | 37 | 398 | 1.4E-176 |
| 3 | g3030.t1 | PANTHER | PTHR11351:SF21 | GH07782P | 37 | 398 | 1.4E-176 |
| 25 | g3030.t1 | PIRSF | PIRSF000345 | OLE1 | 24 | 386 | 9.3E-80 |
| 5 | g3030.t1 | PRINTS | PR00075 | Fatty acid desaturase family 1 signature | 104 | 124 | 3.4E-62 |
| 10 | g3030.t1 | PRINTS | PR00075 | Fatty acid desaturase family 1 signature | 129 | 151 | 3.4E-62 |
| 4 | g3030.t1 | PRINTS | PR00075 | Fatty acid desaturase family 1 signature | 152 | 172 | 3.4E-62 |
| 7 | g3030.t1 | PRINTS | PR00075 | Fatty acid desaturase family 1 signature | 189 | 218 | 3.4E-62 |
| 9 | g3030.t1 | PRINTS | PR00075 | Fatty acid desaturase family 1 signature | 250 | 268 | 3.4E-62 |
| 8 | g3030.t1 | PRINTS | PR00075 | Fatty acid desaturase family 1 signature | 283 | 304 | 3.4E-62 |
| 6 | g3030.t1 | PRINTS | PR00075 | Fatty acid desaturase family 1 signature | 326 | 340 | 3.4E-62 |
| 1 | g3030.t1 | Pfam | PF00487 | Fatty acid desaturase | 134 | 337 | 6.5E-13 |
| 17 | g3030.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 103 | - |
| 23 | g3030.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 104 | 127 | - |
| 20 | g3030.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 128 | 132 | - |
| 24 | g3030.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 133 | 155 | - |
| 16 | g3030.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 156 | 252 | - |
| 22 | g3030.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 253 | 271 | - |
| 19 | g3030.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 272 | 282 | - |
| 21 | g3030.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 283 | 303 | - |
| 18 | g3030.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 304 | 417 | - |
| 15 | g3030.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 104 | 126 | - |
| 14 | g3030.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 130 | 152 | - |
| 13 | g3030.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 164 | 186 | - |
| 12 | g3030.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 249 | 271 | - |
| 11 | g3030.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 283 | 305 | - |
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:0006636 | unsaturated fatty acid biosynthetic process | BP |
| GO:0016021 | integral component of membrane | CC |
| GO:0004768 | stearoyl-CoA 9-desaturase activity | MF |
| GO:0055114 | NA | NA |
| GO:0016717 | oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water | MF |
| GO:0006629 | lipid metabolic process | BP |
KEGG
Orthology
- This transcript has been annotated with K00507 (stearoyl-CoA desaturase (Delta-9 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.
