Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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_4 g16389 g16389.t49 TSS g16389.t49 9313433 9313433
chr_4 g16389 g16389.t49 isoform g16389.t49 9314348 9317789
chr_4 g16389 g16389.t49 exon g16389.t49.exon1 9314348 9314539
chr_4 g16389 g16389.t49 cds g16389.t49.CDS1 9314528 9314539
chr_4 g16389 g16389.t49 exon g16389.t49.exon2 9315379 9315455
chr_4 g16389 g16389.t49 cds g16389.t49.CDS2 9315379 9315455
chr_4 g16389 g16389.t49 exon g16389.t49.exon3 9316625 9316650
chr_4 g16389 g16389.t49 cds g16389.t49.CDS3 9316625 9316650
chr_4 g16389 g16389.t49 exon g16389.t49.exon4 9317099 9317438
chr_4 g16389 g16389.t49 cds g16389.t49.CDS4 9317099 9317438
chr_4 g16389 g16389.t49 exon g16389.t49.exon5 9317501 9317789
chr_4 g16389 g16389.t49 cds g16389.t49.CDS5 9317501 9317789
chr_4 g16389 g16389.t49 TTS g16389.t49 9317882 9317882

Sequences

>g16389.t49 Gene=g16389 Length=924
AAAAAATTAAAATTTTTTCTTTACATTTTCGAACATTTCAAATTTCAATTTACTTTTCTA
GTTTTCTTCCTGACATGCTTATGCAATTTGGGTGTCACGATCGGCGTTCACAGATTATGG
AGTCACAGAAGTTTCAAATGCACTCGTCCAATTAAGCTTCTTCTTACCTTTTTTTACACA
ATGGCTGGTCAATCATCGATTTTCCATTGGGTTCAAATTCATCGAGTTCATCATAAATTT
TCTGAAACTTTAAAGGATCCATTAGATGTTAATCGTGGATTCTTTTTTGCACATGTCGGT
TGGTACTGTCTTTCATACCATCCAGAATGTGAAACTGAGATGAAGCGTATTGATATGGAT
GATATAAAGGCTGATAAAGACCTGATGTTCCAGTACAAGTACTATTCACATCTTTTCACA
CTTCTCAATTTCCTTTCCGTTCTTATTCCATGCTATTTTTGGGGCGAATCATTCAAAATT
GCTTTTTGGGTTTGCTTTGTAACACGTTTTGCCATCAACTTTACACAATTAAATTTCACT
AATAGTGCAAATCATTTCATTGGAAAACGTCCTTATGATAAAACTCAATCAGCTACTGAC
AACATTGCTTGCACTATTTTCTCATTTGGAGAAGGGTATCATAATTATCATCATGTCTTT
CCTTATGATTACCGTACTGGTGAATTTGGTGACATTGGTCACTACAATCTCTCAGCTGTC
ATCATTGATTTCTGGTACAAAATGGGATGGGTTTGGGATCGTAAACTTGTTTCACAAGAC
ATGATCAATCGAAGAGTCTTAAGAACTGGCGATGGAAGTCATTGGTTGTCACATGATGAA
GCCCATAAAAATTCAATCTATGGTTATGGTGATAAAGATATTGATGAAGCTGATCAGAAA
GAATTAGAAAGAATGATTGGCTAA

>g16389.t49 Gene=g16389 Length=247
MAGQSSIFHWVQIHRVHHKFSETLKDPLDVNRGFFFAHVGWYCLSYHPECETEMKRIDMD
DIKADKDLMFQYKYYSHLFTLLNFLSVLIPCYFWGESFKIAFWVCFVTRFAINFTQLNFT
NSANHFIGKRPYDKTQSATDNIACTIFSFGEGYHNYHHVFPYDYRTGEFGDIGHYNLSAV
IIDFWYKMGWVWDRKLVSQDMINRRVLRTGDGSHWLSHDEAHKNSIYGYGDKDIDEADQK
ELERMIG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g16389.t49 CDD cd03505 Delta9-FADS-like 1 195 2.09698E-37
2 g16389.t49 PANTHER PTHR11351 ACYL-COA DESATURASE 2 245 2.9E-84
3 g16389.t49 PANTHER PTHR11351:SF61 RH14937P 2 245 2.9E-84
6 g16389.t49 PRINTS PR00075 Fatty acid desaturase family 1 signature 14 43 2.4E-23
5 g16389.t49 PRINTS PR00075 Fatty acid desaturase family 1 signature 74 92 2.4E-23
7 g16389.t49 PRINTS PR00075 Fatty acid desaturase family 1 signature 107 128 2.4E-23
4 g16389.t49 PRINTS PR00075 Fatty acid desaturase family 1 signature 150 164 2.4E-23
1 g16389.t49 Pfam PF00487 Fatty acid desaturase 4 179 4.2E-15
11 g16389.t49 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 73 -
13 g16389.t49 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 74 95 -
12 g16389.t49 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 96 100 -
14 g16389.t49 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 101 120 -
10 g16389.t49 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 121 247 -
9 g16389.t49 ProSitePatterns PS00476 Fatty acid desaturases family 1 signature. 150 164 -
8 g16389.t49 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 74 96 -

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.

Raw TPM values