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.t50 TSS g16389.t50 9313433 9313433
chr_4 g16389 g16389.t50 isoform g16389.t50 9314409 9317789
chr_4 g16389 g16389.t50 exon g16389.t50.exon1 9314409 9314539
chr_4 g16389 g16389.t50 cds g16389.t50.CDS1 9314528 9314539
chr_4 g16389 g16389.t50 exon g16389.t50.exon2 9315379 9315453
chr_4 g16389 g16389.t50 cds g16389.t50.CDS2 9315379 9315453
chr_4 g16389 g16389.t50 exon g16389.t50.exon3 9317074 9317438
chr_4 g16389 g16389.t50 cds g16389.t50.CDS3 9317074 9317438
chr_4 g16389 g16389.t50 exon g16389.t50.exon4 9317501 9317789
chr_4 g16389 g16389.t50 cds g16389.t50.CDS4 9317501 9317789
chr_4 g16389 g16389.t50 TTS g16389.t50 9317882 9317882

Sequences

>g16389.t50 Gene=g16389 Length=860
TTTTCTTCCTGACATGCTTATGCAATTTGGGTGTCACGATCGGCGTTCACAGATTATGGA
GTCACAGAAGTTTCAAATGCACTCGTCCAATTAAGCTTCTTCTTACCTTTTTTTACACAA
TGGCTGGTCAATCATCGATTTTCCATTGGGTTCAAATTCATCGAGTTCATCATAAATTTT
CTGAAACTTTAAAGGATCCATTAGATATTTATAAATTTTTTTTTATTTTAGTCGGTTGGT
ACTGTCTTTCATACCATCCAGAATGTGAAACTGAGATGAAGCGTATTGATATGGATGATA
TAAAGGCTGATAAAGACCTGATGTTCCAGTACAAGTACTATTCACATCTTTTCACACTTC
TCAATTTCCTTTCCGTTCTTATTCCATGCTATTTTTGGGGCGAATCATTCAAAATTGCTT
TTTGGGTTTGCTTTGTAACACGTTTTGCCATCAACTTTACACAATTAAATTTCACTAATA
GTGCAAATCATTTCATTGGAAAACGTCCTTATGATAAAACTCAATCAGCTACTGACAACA
TTGCTTGCACTATTTTCTCATTTGGAGAAGGGTATCATAATTATCATCATGTCTTTCCTT
ATGATTACCGTACTGGTGAATTTGGTGACATTGGTCACTACAATCTCTCAGCTGTCATCA
TTGATTTCTGGTACAAAATGGGATGGGTTTGGGATCGTAAACTTGTTTCACAAGACATGA
TCAATCGAAGAGTCTTAAGAACTGGCGATGGAAGTCATTGGTTGTCACATGATGAAGCCC
ATAAAAATTCAATCTATGGTTATGGTGATAAAGATATTGATGAAGCTGATCAGAAAGAAT
TAGAAAGAATGATTGGCTAA

>g16389.t50 Gene=g16389 Length=246
MAGQSSIFHWVQIHRVHHKFSETLKDPLDIYKFFFILVGWYCLSYHPECETEMKRIDMDD
IKADKDLMFQYKYYSHLFTLLNFLSVLIPCYFWGESFKIAFWVCFVTRFAINFTQLNFTN
SANHFIGKRPYDKTQSATDNIACTIFSFGEGYHNYHHVFPYDYRTGEFGDIGHYNLSAVI
IDFWYKMGWVWDRKLVSQDMINRRVLRTGDGSHWLSHDEAHKNSIYGYGDKDIDEADQKE
LERMIG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g16389.t50 CDD cd03505 Delta9-FADS-like 1 194 9.04043E-33
2 g16389.t50 PANTHER PTHR11351 ACYL-COA DESATURASE 2 244 2.7E-78
3 g16389.t50 PANTHER PTHR11351:SF61 RH14937P 2 244 2.7E-78
5 g16389.t50 PRINTS PR00075 Fatty acid desaturase family 1 signature 14 43 5.2E-16
4 g16389.t50 PRINTS PR00075 Fatty acid desaturase family 1 signature 73 91 5.2E-16
6 g16389.t50 PRINTS PR00075 Fatty acid desaturase family 1 signature 106 127 5.2E-16
7 g16389.t50 PRINTS PR00075 Fatty acid desaturase family 1 signature 149 163 5.2E-16
1 g16389.t50 Pfam PF00487 Fatty acid desaturase 4 178 1.2E-13
13 g16389.t50 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 29 -
16 g16389.t50 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 30 46 -
10 g16389.t50 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 47 72 -
15 g16389.t50 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 73 94 -
12 g16389.t50 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 95 99 -
14 g16389.t50 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 100 119 -
11 g16389.t50 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 120 246 -
9 g16389.t50 ProSitePatterns PS00476 Fatty acid desaturases family 1 signature. 149 163 -
8 g16389.t50 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 73 95 -

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