General information for g1402.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 g1402 is located on chr_3: 10654225..10656742 (- 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 | g1402 | g1402.t1 | TTS | g1402.t1 | 10653242 | 10653242 |
| chr_3 | g1402 | g1402.t1 | isoform | g1402.t1 | 10653331 | 10654892 |
| chr_3 | g1402 | g1402.t1 | exon | g1402.t1.exon1 | 10653331 | 10653398 |
| chr_3 | g1402 | g1402.t1 | cds | g1402.t1.CDS1 | 10653331 | 10653398 |
| chr_3 | g1402 | g1402.t1 | exon | g1402.t1.exon2 | 10653456 | 10653773 |
| chr_3 | g1402 | g1402.t1 | cds | g1402.t1.CDS2 | 10653456 | 10653773 |
| chr_3 | g1402 | g1402.t1 | exon | g1402.t1.exon3 | 10653838 | 10653890 |
| chr_3 | g1402 | g1402.t1 | cds | g1402.t1.CDS3 | 10653838 | 10653890 |
| chr_3 | g1402 | g1402.t1 | exon | g1402.t1.exon4 | 10653950 | 10654132 |
| chr_3 | g1402 | g1402.t1 | cds | g1402.t1.CDS4 | 10653950 | 10654132 |
| chr_3 | g1402 | g1402.t1 | exon | g1402.t1.exon5 | 10654185 | 10654521 |
| chr_3 | g1402 | g1402.t1 | cds | g1402.t1.CDS5 | 10654185 | 10654521 |
| chr_3 | g1402 | g1402.t1 | exon | g1402.t1.exon6 | 10654580 | 10654736 |
| chr_3 | g1402 | g1402.t1 | cds | g1402.t1.CDS6 | 10654580 | 10654736 |
| chr_3 | g1402 | g1402.t1 | exon | g1402.t1.exon7 | 10654809 | 10654892 |
| chr_3 | g1402 | g1402.t1 | cds | g1402.t1.CDS7 | 10654809 | 10654892 |
| chr_3 | g1402 | g1402.t1 | TSS | g1402.t1 | NA | NA |
Sequences
>g1402.t1 Gene=g1402 Length=1200
ATGGTACCAGATCCATACGATGTAGTTTTCAAATCAACAGACGAAAATGGAAATGTGGTC
GCTAACAAATCTAACGGAGTCATTCGTGACTATCCGAGAAAAAATCCGTACGACACAAAG
CCGGGTGAGAAACCTTATGTGTTAGAAATTGTTTGGCGTAATGTTTTCATCATGCTTTAT
GCTCATTGTGCTGCTTTGAAAGTATTTTGGACACCTTGTCAACTCTCAACAATTTTAATT
GCTGTTGGTTACGGGATTTTAGGCTCATGGGGAATTGCAGCAGGTGCTCATAGGCTTATG
GCTCATAAATCATACAAAGCAAATAGAAACCTTCAACTTCTTTTAATATTTTTTCAAACT
ATTGCACTACAAAATTCTTGTATAGAATGGGTTAGAGATCATCGAGTTCATCATAAATAT
TCTGATACAAATGCAGATCCACATAATGCTAGTCGTGGATTCTTCTTTTCACATATGGGC
TGGTTATTATGTAAGAAACATCCCGATGTGAGGAAATATGGAAGTAGAATTAGTATGGCT
GATTTAGAATGTGATCCAGTTCTTCGATTTCAACATAAATATTATGTTTGGCTAGTGCTT
CTTATTTCACTCTCAATTCCAATTTTTATATCAACTTATATTTTTGGTGATACATTTTCG
GCTGCTTATCATATGAACATTTTTAGAATTGTCTTAGCATGGCATATAACTTGGAGTATA
AATTCTGTTTCACATATTTGGGGAAATCGACCCTTTGAAAAAGATATTTTGCCAACTGAT
ACTTTCATAATTGGTTTTCTTGCTTTTGGAGAAGGATGGCATAATTTTCATCATGTTTAT
CCGTGGGACTATAAAGTTTCTGAATTGCCCAATTATTATTGCAATTTTACAATTCCATTT
ATTGATTTCTTCGCATGGCTTGGTTGGGCGACAGATTTAAAAATGGCATCAGATGAGATG
ATCAGAAAAAGAATAATGAAAAGTGGTGATGGAACTCATAGATATTCAATAGAGGAAGCA
AAAAAGAAAAAGACAGCTAAAGAATTGTTAGATTTATTCAATAACAAAGTCTTACAAAAA
AGCAATCCACATGAACTTGAAGGCGATTTTGCTGACACATATTGGGGATATGGTGACAAT
GATATACCAGAAGAAGAAATAAAAGATATCACAATATTAAAACCAACAAAGGGAAAATAA
>g1402.t1 Gene=g1402 Length=399
MVPDPYDVVFKSTDENGNVVANKSNGVIRDYPRKNPYDTKPGEKPYVLEIVWRNVFIMLY
AHCAALKVFWTPCQLSTILIAVGYGILGSWGIAAGAHRLMAHKSYKANRNLQLLLIFFQT
IALQNSCIEWVRDHRVHHKYSDTNADPHNASRGFFFSHMGWLLCKKHPDVRKYGSRISMA
DLECDPVLRFQHKYYVWLVLLISLSIPIFISTYIFGDTFSAAYHMNIFRIVLAWHITWSI
NSVSHIWGNRPFEKDILPTDTFIIGFLAFGEGWHNFHHVYPWDYKVSELPNYYCNFTIPF
IDFFAWLGWATDLKMASDEMIRKRIMKSGDGTHRYSIEEAKKKKTAKELLDLFNNKVLQK
SNPHELEGDFADTYWGYGDNDIPEEEIKDITILKPTKGK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 25 | g1402.t1 | CDD | cd03505 | Delta9-FADS-like | 77 | 314 | 2.98825E-69 |
| 2 | g1402.t1 | PANTHER | PTHR11351 | ACYL-COA DESATURASE | 35 | 345 | 4.5E-111 |
| 3 | g1402.t1 | PANTHER | PTHR11351:SF31 | RE43130P | 35 | 345 | 4.5E-111 |
| 7 | g1402.t1 | PRINTS | PR00075 | Fatty acid desaturase family 1 signature | 52 | 72 | 3.5E-41 |
| 6 | g1402.t1 | PRINTS | PR00075 | Fatty acid desaturase family 1 signature | 97 | 117 | 3.5E-41 |
| 5 | g1402.t1 | PRINTS | PR00075 | Fatty acid desaturase family 1 signature | 134 | 163 | 3.5E-41 |
| 8 | g1402.t1 | PRINTS | PR00075 | Fatty acid desaturase family 1 signature | 195 | 213 | 3.5E-41 |
| 4 | g1402.t1 | PRINTS | PR00075 | Fatty acid desaturase family 1 signature | 227 | 248 | 3.5E-41 |
| 9 | g1402.t1 | PRINTS | PR00075 | Fatty acid desaturase family 1 signature | 270 | 284 | 3.5E-41 |
| 1 | g1402.t1 | Pfam | PF00487 | Fatty acid desaturase | 80 | 283 | 2.8E-11 |
| 15 | g1402.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 49 | - |
| 19 | g1402.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 50 | 70 | - |
| 18 | g1402.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 71 | 75 | - |
| 21 | g1402.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 76 | 96 | - |
| 12 | g1402.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 97 | 193 | - |
| 24 | g1402.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 194 | 215 | - |
| 17 | g1402.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 216 | 226 | - |
| 20 | g1402.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 227 | 244 | - |
| 14 | g1402.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 245 | 255 | - |
| 22 | g1402.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 256 | 276 | - |
| 16 | g1402.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 277 | 295 | - |
| 23 | g1402.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 296 | 316 | - |
| 13 | g1402.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 317 | 399 | - |
| 10 | g1402.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 77 | 99 | - |
| 11 | g1402.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 194 | 216 | - |
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 K20416 (palmitoyl-[glycerolipid] 7-desaturase)
Pathway
This gene does not belong to any 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