General information for g1406.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Acyl-CoA desaturase 1.
Parent gene
- The parent gene g1406 is located on chr_3: 10676480..10687218 (- 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 | g1406 | g1406.t1 | TTS | g1406.t1 | 10674847 | 10674847 |
| chr_3 | g1406 | g1406.t1 | isoform | g1406.t1 | 10675030 | 10679470 |
| chr_3 | g1406 | g1406.t1 | exon | g1406.t1.exon1 | 10675030 | 10675301 |
| chr_3 | g1406 | g1406.t1 | cds | g1406.t1.CDS1 | 10675030 | 10675301 |
| chr_3 | g1406 | g1406.t1 | exon | g1406.t1.exon2 | 10675362 | 10675469 |
| chr_3 | g1406 | g1406.t1 | cds | g1406.t1.CDS2 | 10675362 | 10675469 |
| chr_3 | g1406 | g1406.t1 | exon | g1406.t1.exon3 | 10675983 | 10676035 |
| chr_3 | g1406 | g1406.t1 | cds | g1406.t1.CDS3 | 10675983 | 10676035 |
| chr_3 | g1406 | g1406.t1 | exon | g1406.t1.exon4 | 10676103 | 10676489 |
| chr_3 | g1406 | g1406.t1 | cds | g1406.t1.CDS4 | 10676103 | 10676489 |
| chr_3 | g1406 | g1406.t1 | exon | g1406.t1.exon5 | 10676554 | 10676689 |
| chr_3 | g1406 | g1406.t1 | cds | g1406.t1.CDS5 | 10676554 | 10676689 |
| chr_3 | g1406 | g1406.t1 | exon | g1406.t1.exon6 | 10679170 | 10679353 |
| chr_3 | g1406 | g1406.t1 | cds | g1406.t1.CDS6 | 10679170 | 10679353 |
| chr_3 | g1406 | g1406.t1 | exon | g1406.t1.exon7 | 10679411 | 10679470 |
| chr_3 | g1406 | g1406.t1 | cds | g1406.t1.CDS7 | 10679411 | 10679470 |
| chr_3 | g1406 | g1406.t1 | TSS | g1406.t1 | NA | NA |
Sequences
>g1406.t1 Gene=g1406 Length=1200
ATGGTGCACAAAGTTAGCAACTCGACAATGGCGATAGCTGAAGTCGATAAAAATGAAAAT
ATGATCAAGACAAAAAATTCGCTAAATGTTAGCGATGAAAAGCCACGAGACTTTCCTGCT
GAATTACCAGGACCAGAATATAAACTAGAATTAGTGTGGCGAAATATCATCATTTTTGCA
TTACTTCATATAGGCTATGTTGCTGCATTTTTCATCGATAAATTTACAATTACTAAAGTC
TTTGGCGTTGTATATGGAATTTGTGGTGGCTTCGGAATAACAGCAGGTGCTCATCGACTT
TGGGCTCATAATTCATACAAAACAAATACAGCCTACAAAATTATGCTTCTTATTTTCCAA
ACAATCGCATTTCAGAACAGTGCATACGAATGGACAAGAGATCATCGTGTCCATCACAAA
TTTACTGATACAAATGCAGATCCACATAATGCACGTCGTGGTTTTTTCTTCTCACATATG
GGCTGGTTGTTGTGCAAAAAACATCCGGATGTTAAAAAGTTTGGTGCAAGAGTTAGCATG
GCTGATTTAGAAGCTGATCCAATCATTATGTTTCAACATAGACATTACCTTAAGCTCATG
TTGTTCTTCAGTCTTATTTTGCCAGTTTTTATTCCGTGGTATTTCTGGGGTGAAAGTTTT
TGGGCTTCATTTTTAATTGCTGGCGTTTTACGTTACATTACTTCACTTCATATTACATGG
CTTATTAATTCTGCTGCACATACTTATGGAATGAAACCTTTTGATAAGAATATTTCACCA
TCTGACAGCTATCTTGTTGGATTTTTAGCTATGGGAGAAGGCTGGCATAATTATCATCAC
GTCTTTCCTTATGATTACAAAACTTCAGAATTAGGATTTTACGTGTTCAACTTAACGACA
GCTTTTATTGATTTTTTCTCACTGTTTGGATGGACATATGACCTTAAAACAGTGTCACCT
GAAATGATCAGACGTCGTGTGTTGAGAACAGGTGATGGAAGTCATCCAGCATCAAAAGAA
ATGGATACAAAGGAATTATTGAATAAATTTATCCTAAGTCAAGCAATTGACAAAAATGGA
AATATAATTCATAATGAAGAAGACTCAATATGGGGATTTAATGATGAAATGCTTCCAGCT
GAAGATAGAAAATACATTAAAATTATTAACAAACATTCAAATTTAAAGAAAAGAAATTAA
>g1406.t1 Gene=g1406 Length=399
MVHKVSNSTMAIAEVDKNENMIKTKNSLNVSDEKPRDFPAELPGPEYKLELVWRNIIIFA
LLHIGYVAAFFIDKFTITKVFGVVYGICGGFGITAGAHRLWAHNSYKTNTAYKIMLLIFQ
TIAFQNSAYEWTRDHRVHHKFTDTNADPHNARRGFFFSHMGWLLCKKHPDVKKFGARVSM
ADLEADPIIMFQHRHYLKLMLFFSLILPVFIPWYFWGESFWASFLIAGVLRYITSLHITW
LINSAAHTYGMKPFDKNISPSDSYLVGFLAMGEGWHNYHHVFPYDYKTSELGFYVFNLTT
AFIDFFSLFGWTYDLKTVSPEMIRRRVLRTGDGSHPASKEMDTKELLNKFILSQAIDKNG
NIIHNEEDSIWGFNDEMLPAEDRKYIKIINKHSNLKKRN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 30 | g1406.t1 | CDD | cd03505 | Delta9-FADS-like | 80 | 316 | 3.91241E-73 |
| 2 | g1406.t1 | PANTHER | PTHR11351 | ACYL-COA DESATURASE | 47 | 338 | 9.9E-125 |
| 3 | g1406.t1 | PANTHER | PTHR11351:SF91 | DESATURASE 1, ISOFORM A-RELATED | 47 | 338 | 9.9E-125 |
| 4 | g1406.t1 | PRINTS | PR00075 | Fatty acid desaturase family 1 signature | 53 | 73 | 4.5E-51 |
| 6 | g1406.t1 | PRINTS | PR00075 | Fatty acid desaturase family 1 signature | 98 | 118 | 4.5E-51 |
| 8 | g1406.t1 | PRINTS | PR00075 | Fatty acid desaturase family 1 signature | 135 | 164 | 4.5E-51 |
| 7 | g1406.t1 | PRINTS | PR00075 | Fatty acid desaturase family 1 signature | 196 | 214 | 4.5E-51 |
| 9 | g1406.t1 | PRINTS | PR00075 | Fatty acid desaturase family 1 signature | 229 | 250 | 4.5E-51 |
| 5 | g1406.t1 | PRINTS | PR00075 | Fatty acid desaturase family 1 signature | 272 | 286 | 4.5E-51 |
| 1 | g1406.t1 | Pfam | PF00487 | Fatty acid desaturase | 80 | 283 | 3.5E-16 |
| 20 | g1406.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 50 | - |
| 29 | g1406.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 51 | 72 | - |
| 15 | g1406.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 73 | 78 | - |
| 27 | g1406.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 79 | 98 | - |
| 22 | g1406.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 99 | 109 | - |
| 24 | g1406.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 110 | 129 | - |
| 16 | g1406.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 130 | 195 | - |
| 26 | g1406.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 196 | 215 | - |
| 19 | g1406.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 216 | 220 | - |
| 28 | g1406.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 221 | 242 | - |
| 17 | g1406.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 243 | 262 | - |
| 23 | g1406.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 263 | 279 | - |
| 21 | g1406.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 280 | 290 | - |
| 25 | g1406.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 291 | 315 | - |
| 18 | g1406.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 316 | 399 | - |
| 14 | g1406.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 51 | 70 | - |
| 10 | g1406.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 80 | 102 | - |
| 13 | g1406.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 199 | 216 | - |
| 12 | g1406.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 220 | 242 | - |
| 11 | g1406.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 291 | 313 | - |
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: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. There were no conditions that were differentially expressed