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 g1402 g1402.t15 TTS g1402.t15 10653242 10653242
chr_3 g1402 g1402.t15 isoform g1402.t15 10653840 10656742
chr_3 g1402 g1402.t15 exon g1402.t15.exon1 10653840 10653890
chr_3 g1402 g1402.t15 cds g1402.t15.CDS1 10653842 10653890
chr_3 g1402 g1402.t15 exon g1402.t15.exon2 10653950 10654132
chr_3 g1402 g1402.t15 cds g1402.t15.CDS2 10653950 10654132
chr_3 g1402 g1402.t15 exon g1402.t15.exon3 10654185 10654521
chr_3 g1402 g1402.t15 cds g1402.t15.CDS3 10654185 10654521
chr_3 g1402 g1402.t15 exon g1402.t15.exon4 10654580 10654736
chr_3 g1402 g1402.t15 cds g1402.t15.CDS4 10654580 10654736
chr_3 g1402 g1402.t15 exon g1402.t15.exon5 10654809 10654905
chr_3 g1402 g1402.t15 cds g1402.t15.CDS5 10654809 10654892
chr_3 g1402 g1402.t15 exon g1402.t15.exon6 10656635 10656742
chr_3 g1402 g1402.t15 TSS g1402.t15 10656745 10656745

Sequences

>g1402.t15 Gene=g1402 Length=933
TTTATTTTGGACATCGTAGAGTGAAGACCTGAAAAAGGAAAAAAAAAGTTGTTCAAGAAA
AATTTTGTTTATTAAATTCTTTGAAGAAAAAAGTTGAAAATTATTGTGGAATTTTCATAT
CATGGTACCAGATCCATACGATGTAGTTTTCAAATCAACAGACGAAAATGGAAATGTGGT
CGCTAACAAATCTAACGGAGTCATTCGTGACTATCCGAGAAAAAATCCGTACGACACAAA
GCCGGGTGAGAAACCTTATGTGTTAGAAATTGTTTGGCGTAATGTTTTCATCATGCTTTA
TGCTCATTGTGCTGCTTTGAAAGTATTTTGGACACCTTGTCAACTCTCAACAATTTTAAT
TGCTGTTGGTTACGGGATTTTAGGCTCATGGGGAATTGCAGCAGGTGCTCATAGGCTTAT
GGCTCATAAATCATACAAAGCAAATAGAAACCTTCAACTTCTTTTAATATTTTTTCAAAC
TATTGCACTACAAAATTCTTGTATAGAATGGGTTAGAGATCATCGAGTTCATCATAAATA
TTCTGATACAAATGCAGATCCACATAATGCTAGTCGTGGATTCTTCTTTTCACATATGGG
CTGGTTATTATGTAAGAAACATCCCGATGTGAGGAAATATGGAAGTAGAATTAGTATGGC
TGATTTAGAATGTGATCCAGTTCTTCGATTTCAACATAAATATTATGTTTGGCTAGTGCT
TCTTATTTCACTCTCAATTCCAATTTTTATATCAACTTATATTTTTGGTGATACATTTTC
GGCTGCTTATCATATGAACATTTTTAGAATTGTCTTAGCATGGCATATAACTTGGAGTAT
AAATTCTGTTTCACATATTTGGGGAAATCGACCCTTTGAAAAAGATATTTTGCCAACTGA
TACTTTCATAATTGGTTTTCTTGCTTTTGGAGA

>g1402.t15 Gene=g1402 Length=270
MVPDPYDVVFKSTDENGNVVANKSNGVIRDYPRKNPYDTKPGEKPYVLEIVWRNVFIMLY
AHCAALKVFWTPCQLSTILIAVGYGILGSWGIAAGAHRLMAHKSYKANRNLQLLLIFFQT
IALQNSCIEWVRDHRVHHKYSDTNADPHNASRGFFFSHMGWLLCKKHPDVRKYGSRISMA
DLECDPVLRFQHKYYVWLVLLISLSIPIFISTYIFGDTFSAAYHMNIFRIVLAWHITWSI
NSVSHIWGNRPFEKDILPTDTFIIGFLAFG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g1402.t15 CDD cd03505 Delta9-FADS-like 77 270 4.85777E-48
2 g1402.t15 PANTHER PTHR11351 ACYL-COA DESATURASE 35 270 3.4E-83
3 g1402.t15 PANTHER PTHR11351:SF31 RE43130P 35 270 3.4E-83
7 g1402.t15 PRINTS PR00075 Fatty acid desaturase family 1 signature 52 72 3.9E-33
6 g1402.t15 PRINTS PR00075 Fatty acid desaturase family 1 signature 97 117 3.9E-33
5 g1402.t15 PRINTS PR00075 Fatty acid desaturase family 1 signature 134 163 3.9E-33
8 g1402.t15 PRINTS PR00075 Fatty acid desaturase family 1 signature 195 213 3.9E-33
4 g1402.t15 PRINTS PR00075 Fatty acid desaturase family 1 signature 227 248 3.9E-33
1 g1402.t15 Pfam PF00487 Fatty acid desaturase 80 255 2.1E-7
13 g1402.t15 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 49 -
16 g1402.t15 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 50 70 -
15 g1402.t15 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 71 75 -
17 g1402.t15 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 76 96 -
11 g1402.t15 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 97 193 -
19 g1402.t15 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 194 215 -
14 g1402.t15 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 216 226 -
18 g1402.t15 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 227 247 -
12 g1402.t15 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 248 270 -
9 g1402.t15 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 77 99 -
10 g1402.t15 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 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