Gene loci information

Transcript annotation

  • This transcript has been annotated as Acyl-CoA Delta(11) desaturase.

Parent gene

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 g1404 g1404.t1 isoform g1404.t1 10666259 10667504
chr_3 g1404 g1404.t1 exon g1404.t1.exon1 10666259 10666476
chr_3 g1404 g1404.t1 cds g1404.t1.CDS1 10666259 10666476
chr_3 g1404 g1404.t1 exon g1404.t1.exon2 10666531 10666638
chr_3 g1404 g1404.t1 cds g1404.t1.CDS2 10666531 10666638
chr_3 g1404 g1404.t1 exon g1404.t1.exon3 10666699 10666814
chr_3 g1404 g1404.t1 cds g1404.t1.CDS3 10666699 10666814
chr_3 g1404 g1404.t1 exon g1404.t1.exon4 10666872 10667325
chr_3 g1404 g1404.t1 cds g1404.t1.CDS4 10666872 10667325
chr_3 g1404 g1404.t1 exon g1404.t1.exon5 10667384 10667504
chr_3 g1404 g1404.t1 cds g1404.t1.CDS5 10667384 10667504
chr_3 g1404 g1404.t1 TSS g1404.t1 NA NA
chr_3 g1404 g1404.t1 TTS g1404.t1 NA NA

Sequences

>g1404.t1 Gene=g1404 Length=1017
ATGGGAGTAAAAAAATTCAGTTGGACCAACATTATTGTGTTTATTATATTACATTGGGCA
TTTATTGTTGGATCAATAGAAACTTTTACTTTTCGTATGAATTTGCCACTTTATTTATTT
AATTTATTCTATGGATTCTTCATTGGTTTCGGTATAACAGCTGGAACACATCGTTTATGG
GCTCATGGAGCTTACAAGGCAAATTTACCTTTAAGACTTTTCCTAACATTTTGGCAAACA
GCAGCATTTCAAAAGAGCATTTACAAATGGGTTCGAGATCACAGACTTCATCATAAATTT
ACTGACACGAATGCTGATCCTCACAATTCACTTCGTGGCTTCTTCTTTTCACATATAGGT
TGGTTGTTGTGTGAAAAACATCCCGATGTGATAAAATTTGGCAAGAAAATTGACTTGAGT
GATTTAGAACGTGATCCAATTGTGATGTTTCAACATAAATATTATTATATGCTTATGCCA
TTTTGTTGCTGGATAATTCCAATTTATATACCAACACTTTGGGGCATTTCTATTTATGAT
TCAACTATTATGTGTTGTGTACGTTATGTATCTATTCTTCATTTTACTTGGTTGGTGAAT
TCATATGCACATTTCTGGGGAAATAAACCTTATGATAAAAATCTTACATCAACTGAATCT
TATACTGTTTCAATGCTGGCATTTGGCGAAGGCTGGCACAATTATCATCATGTCTTTCCT
TATGATTATAAAACTTCAGAACATGGAAAATATTGGTGCAATTACACGACTGGATTTTTG
GAATTTTGTGCTAAAATTGGTTGGGCAACAGATTTAAAAACAGTCAGTCCAGAAGTAATT
TGTAAACGTGTGTTAAGGACAGGCGATGGAAGTCATCCTTTTGCCAAAAATCAATTCAAT
CAAATGACAAGTGAAGAAGAAAATAAATATGAAGAATTTGTATGGGGTTGGCAAGATAAA
TTGTTGACTAAAGAAGAAAGAAAATATGTTACTGTTATTAACAAGACTTTGACATAA

>g1404.t1 Gene=g1404 Length=338
MGVKKFSWTNIIVFIILHWAFIVGSIETFTFRMNLPLYLFNLFYGFFIGFGITAGTHRLW
AHGAYKANLPLRLFLTFWQTAAFQKSIYKWVRDHRLHHKFTDTNADPHNSLRGFFFSHIG
WLLCEKHPDVIKFGKKIDLSDLERDPIVMFQHKYYYMLMPFCCWIIPIYIPTLWGISIYD
STIMCCVRYVSILHFTWLVNSYAHFWGNKPYDKNLTSTESYTVSMLAFGEGWHNYHHVFP
YDYKTSEHGKYWCNYTTGFLEFCAKIGWATDLKTVSPEVICKRVLRTGDGSHPFAKNQFN
QMTSEEENKYEEFVWGWQDKLLTKEERKYVTVINKTLT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
22 g1404.t1 CDD cd03505 Delta9-FADS-like 34 273 3.78694E-68
2 g1404.t1 PANTHER PTHR11351 ACYL-COA DESATURASE 5 295 5.6E-115
3 g1404.t1 PANTHER PTHR11351:SF91 DESATURASE 1, ISOFORM A-RELATED 5 295 5.6E-115
4 g1404.t1 PRINTS PR00075 Fatty acid desaturase family 1 signature 8 28 2.7E-49
9 g1404.t1 PRINTS PR00075 Fatty acid desaturase family 1 signature 57 77 2.7E-49
7 g1404.t1 PRINTS PR00075 Fatty acid desaturase family 1 signature 94 123 2.7E-49
5 g1404.t1 PRINTS PR00075 Fatty acid desaturase family 1 signature 155 173 2.7E-49
8 g1404.t1 PRINTS PR00075 Fatty acid desaturase family 1 signature 186 207 2.7E-49
6 g1404.t1 PRINTS PR00075 Fatty acid desaturase family 1 signature 229 243 2.7E-49
1 g1404.t1 Pfam PF00487 Fatty acid desaturase 37 240 1.9E-13
15 g1404.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
20 g1404.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 26 -
14 g1404.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 27 37 -
19 g1404.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 38 57 -
16 g1404.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 58 68 -
18 g1404.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 69 88 -
13 g1404.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 89 153 -
21 g1404.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 154 176 -
17 g1404.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 177 338 -
10 g1404.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 7 29 -
11 g1404.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 39 61 -
12 g1404.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 154 176 -

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

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