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.t6 TTS g1402.t6 10653242 10653242
chr_3 g1402 g1402.t6 isoform g1402.t6 10653331 10654892
chr_3 g1402 g1402.t6 exon g1402.t6.exon1 10653331 10653380
chr_3 g1402 g1402.t6 cds g1402.t6.CDS1 10653331 10653380
chr_3 g1402 g1402.t6 exon g1402.t6.exon2 10653456 10653773
chr_3 g1402 g1402.t6 cds g1402.t6.CDS2 10653456 10653773
chr_3 g1402 g1402.t6 exon g1402.t6.exon3 10653838 10653890
chr_3 g1402 g1402.t6 cds g1402.t6.CDS3 10653838 10653890
chr_3 g1402 g1402.t6 exon g1402.t6.exon4 10653950 10654132
chr_3 g1402 g1402.t6 cds g1402.t6.CDS4 10653950 10654132
chr_3 g1402 g1402.t6 exon g1402.t6.exon5 10654185 10654892
chr_3 g1402 g1402.t6 cds g1402.t6.CDS5 10654185 10654465
chr_3 g1402 g1402.t6 TSS g1402.t6 NA NA

Sequences

>g1402.t6 Gene=g1402 Length=1312
ATGGTACCAGATCCATACGATGTAGTTTTCAAATCAACAGACGAAAATGGAAATGTGGTC
GCTAACAAATCTAACGGAGTCATTGTAAGTTTTATTTTAAGTCTTTTGCATAATTTATTC
AAAAGTTCATTAACATTTTTTGCATCTCCATCATAGCGTGACTATCCGAGAAAAAATCCG
TACGACACAAAGCCGGGTGAGAAACCTTATGTGTTAGAAATTGTTTGGCGTAATGTTTTC
ATCATGCTTTATGCTCATTGTGCTGCTTTGAAAGTATTTTGGACACCTTGTCAACTCTCA
ACAATTTTAATTGGTAAATTATTTAAATTTTATTATTTTTAATTGTTAATTTTTAAGTTT
TTTTATTGCAGCTGTTGGTTACGGGATTTTAGGCTCATGGGGAATTGCAGCAGGTGCTCA
TAGGCTTATGGCTCATAAATCATACAAAGCAAATAGAAACCTTCAACTTCTTTTAATATT
TTTTCAAACTATTGCACTACAAAATTCTTGTATAGAATGGGTTAGAGATCATCGAGTTCA
TCATAAATATTCTGATACAAATGCAGATCCACATAATGCTAGTCGTGGATTCTTCTTTTC
ACATATGGGCTGGTTATTATGTAAGAAACATCCCGATGTGAGGAAATATGGAAGTAGAAT
TAGTATGGCTGATTTAGAATGTGATCCAGTTCTTCGATTTCAACATAAATATTATGTTTG
GCTAGTGCTTCTTATTTCACTCTCAATTCCAATTTTTATATCAACTTATATTTTTGGTGA
TACATTTTCGGCTGCTTATCATATGAACATTTTTAGAATTGTCTTAGCATGGCATATAAC
TTGGAGTATAAATTCTGTTTCACATATTTGGGGAAATCGACCCTTTGAAAAAGATATTTT
GCCAACTGATACTTTCATAATTGGTTTTCTTGCTTTTGGAGAAGGATGGCATAATTTTCA
TCATGTTTATCCGTGGGACTATAAAGTTTCTGAATTGCCCAATTATTATTGCAATTTTAC
AATTCCATTTATTGATTTCTTCGCATGGCTTGGTTGGGCGACAGATTTAAAAATGGCATC
AGATGAGATGATCAGAAAAAGAATAATGAAAAGTGGTGATGGAACTCATAGATATTCAAT
AGAGGAAGCAAAAAAGAAAAAGACAGCTAAAGAATTGTTAGATTTATTCAATAACAAAGT
CTTACAAAAAAGCAATCCACATGAACTTGAAGGCGATTTTGCTGACACATATTGGGGATA
TGAAGAAGAAATAAAAGATATCACAATATTAAAACCAACAAAGGGAAAATAA

>g1402.t6 Gene=g1402 Length=294
MAHKSYKANRNLQLLLIFFQTIALQNSCIEWVRDHRVHHKYSDTNADPHNASRGFFFSHM
GWLLCKKHPDVRKYGSRISMADLECDPVLRFQHKYYVWLVLLISLSIPIFISTYIFGDTF
SAAYHMNIFRIVLAWHITWSINSVSHIWGNRPFEKDILPTDTFIIGFLAFGEGWHNFHHV
YPWDYKVSELPNYYCNFTIPFIDFFAWLGWATDLKMASDEMIRKRIMKSGDGTHRYSIEE
AKKKKTAKELLDLFNNKVLQKSNPHELEGDFADTYWGYEEEIKDITILKPTKGK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
21 g1402.t6 CDD cd03505 Delta9-FADS-like 2 215 7.08992E-59
2 g1402.t6 PANTHER PTHR11351 ACYL-COA DESATURASE 2 246 3.5E-95
3 g1402.t6 PANTHER PTHR11351:SF31 RE43130P 2 246 3.5E-95
5 g1402.t6 PRINTS PR00075 Fatty acid desaturase family 1 signature 35 64 4.2E-31
4 g1402.t6 PRINTS PR00075 Fatty acid desaturase family 1 signature 96 114 4.2E-31
6 g1402.t6 PRINTS PR00075 Fatty acid desaturase family 1 signature 128 149 4.2E-31
7 g1402.t6 PRINTS PR00075 Fatty acid desaturase family 1 signature 171 185 4.2E-31
1 g1402.t6 Pfam PF00487 Fatty acid desaturase 2 184 4.0E-10
14 g1402.t6 Phobius SIGNAL_PEPTIDE Signal peptide region 1 25 -
15 g1402.t6 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 11 -
16 g1402.t6 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 12 20 -
20 g1402.t6 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 21 25 -
12 g1402.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 26 94 -
17 g1402.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 95 116 -
11 g1402.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 117 127 -
18 g1402.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 128 148 -
13 g1402.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 149 196 -
19 g1402.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 197 217 -
10 g1402.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 218 294 -
9 g1402.t6 SignalP_EUK SignalP-noTM SignalP-noTM 1 27 -
8 g1402.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 95 117 -

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