Gene loci information

Transcript annotation

  • This transcript has been annotated as Acyl-CoA desaturase 3.

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 g1406 g1406.t6 TTS g1406.t6 10674847 10674847
chr_3 g1406 g1406.t6 isoform g1406.t6 10675030 10676688
chr_3 g1406 g1406.t6 exon g1406.t6.exon1 10675030 10675301
chr_3 g1406 g1406.t6 cds g1406.t6.CDS1 10675030 10675301
chr_3 g1406 g1406.t6 exon g1406.t6.exon2 10675362 10675469
chr_3 g1406 g1406.t6 cds g1406.t6.CDS2 10675362 10675469
chr_3 g1406 g1406.t6 exon g1406.t6.exon3 10675983 10676035
chr_3 g1406 g1406.t6 cds g1406.t6.CDS3 10675983 10676035
chr_3 g1406 g1406.t6 exon g1406.t6.exon4 10676103 10676489
chr_3 g1406 g1406.t6 cds g1406.t6.CDS4 10676103 10676489
chr_3 g1406 g1406.t6 exon g1406.t6.exon5 10676554 10676688
chr_3 g1406 g1406.t6 cds g1406.t6.CDS5 10676554 10676591
chr_3 g1406 g1406.t6 TSS g1406.t6 NA NA

Sequences

>g1406.t6 Gene=g1406 Length=955
CGTTGTATATGGAATTTGTGGTGGCTTCGGAATAACAGCAGGTGCTCATCGACTTTGGGC
TCATAATTCATACAAAACAAATACAGCCTACAAAATTATGCTTCTTATTTTCCAAACAAT
CGCATTTCAGAACAGTGCATACGAATGGACAAGAGATCATCGTGTCCATCACAAATTTAC
TGATACAAATGCAGATCCACATAATGCACGTCGTGGTTTTTTCTTCTCACATATGGGCTG
GTTGTTGTGCAAAAAACATCCGGATGTTAAAAAGTTTGGTGCAAGAGTTAGCATGGCTGA
TTTAGAAGCTGATCCAATCATTATGTTTCAACATAGACATTACCTTAAGCTCATGTTGTT
CTTCAGTCTTATTTTGCCAGTTTTTATTCCGTGGTATTTCTGGGGTGAAAGTTTTTGGGC
TTCATTTTTAATTGCTGGCGTTTTACGTTACATTACTTCACTTCATATTACATGGCTTAT
TAATTCTGCTGCACATACTTATGGAATGAAACCTTTTGATAAGAATATTTCACCATCTGA
CAGCTATCTTGTTGGATTTTTAGCTATGGGAGAAGGCTGGCATAATTATCATCACGTCTT
TCCTTATGATTACAAAACTTCAGAATTAGGATTTTACGTGTTCAACTTAACGACAGCTTT
TATTGATTTTTTCTCACTGTTTGGATGGACATATGACCTTAAAACAGTGTCACCTGAAAT
GATCAGACGTCGTGTGTTGAGAACAGGTGATGGAAGTCATCCAGCATCAAAAGAAATGGA
TACAAAGGAATTATTGAATAAATTTATCCTAAGTCAAGCAATTGACAAAAATGGAAATAT
AATTCATAATGAAGAAGACTCAATATGGGGATTTAATGATGAAATGCTTCCAGCTGAAGA
TAGAAAATACATTAAAATTATTAACAAACATTCAAATTTAAAGAAAAGAAATTAA

>g1406.t6 Gene=g1406 Length=285
MLLIFQTIAFQNSAYEWTRDHRVHHKFTDTNADPHNARRGFFFSHMGWLLCKKHPDVKKF
GARVSMADLEADPIIMFQHRHYLKLMLFFSLILPVFIPWYFWGESFWASFLIAGVLRYIT
SLHITWLINSAAHTYGMKPFDKNISPSDSYLVGFLAMGEGWHNYHHVFPYDYKTSELGFY
VFNLTTAFIDFFSLFGWTYDLKTVSPEMIRRRVLRTGDGSHPASKEMDTKELLNKFILSQ
AIDKNGNIIHNEEDSIWGFNDEMLPAEDRKYIKIINKHSNLKKRN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g1406.t6 CDD cd03505 Delta9-FADS-like 2 202 1.92416E-54
2 g1406.t6 PANTHER PTHR11351 ACYL-COA DESATURASE 1 225 9.9E-104
3 g1406.t6 PANTHER PTHR11351:SF91 DESATURASE 1, ISOFORM A-RELATED 1 225 9.9E-104
6 g1406.t6 PRINTS PR00075 Fatty acid desaturase family 1 signature 21 50 1.3E-37
5 g1406.t6 PRINTS PR00075 Fatty acid desaturase family 1 signature 82 100 1.3E-37
7 g1406.t6 PRINTS PR00075 Fatty acid desaturase family 1 signature 115 136 1.3E-37
4 g1406.t6 PRINTS PR00075 Fatty acid desaturase family 1 signature 158 172 1.3E-37
1 g1406.t6 Pfam PF00487 Fatty acid desaturase 6 169 4.3E-13
11 g1406.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 81 -
16 g1406.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 82 101 -
14 g1406.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 102 106 -
17 g1406.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 107 128 -
12 g1406.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 129 148 -
18 g1406.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 149 165 -
15 g1406.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 166 176 -
19 g1406.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 177 201 -
13 g1406.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 202 285 -
8 g1406.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 85 102 -
9 g1406.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 106 128 -
10 g1406.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 177 199 -

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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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