Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Acyl-CoA desaturase 2.

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.t8 isoform g16389.t8 9313332 9317437
chr_4 g16389 g16389.t8 exon g16389.t8.exon1 9313332 9313563
chr_4 g16389 g16389.t8 cds g16389.t8.CDS1 9313562 9313563
chr_4 g16389 g16389.t8 exon g16389.t8.exon2 9313627 9313817
chr_4 g16389 g16389.t8 cds g16389.t8.CDS2 9313627 9313817
chr_4 g16389 g16389.t8 exon g16389.t8.exon3 9314409 9314539
chr_4 g16389 g16389.t8 cds g16389.t8.CDS3 9314409 9314539
chr_4 g16389 g16389.t8 exon g16389.t8.exon4 9315379 9315455
chr_4 g16389 g16389.t8 cds g16389.t8.CDS4 9315379 9315455
chr_4 g16389 g16389.t8 exon g16389.t8.exon5 9316625 9316650
chr_4 g16389 g16389.t8 cds g16389.t8.CDS5 9316625 9316650
chr_4 g16389 g16389.t8 exon g16389.t8.exon6 9317099 9317437
chr_4 g16389 g16389.t8 cds g16389.t8.CDS6 9317099 9317436
chr_4 g16389 g16389.t8 TTS g16389.t8 9317882 9317882
chr_4 g16389 g16389.t8 TSS g16389.t8 NA NA

Sequences

>g16389.t8 Gene=g16389 Length=996
ATGTTATTTTGCAAACCGGCATCGACGCCACTGACTTTATATGTTCCAATGTGTGTGCAA
AAAAAAGTTTAAATTATTTTTTTCCGATTTTTTAGAACGTTCAGTTGACGTGCATCAGTC
TCGGGATATTGAAGTAATTTTTAGTTCTTCCCGTTTTTTAATTGTCGATTTTTTCTTTCG
TGCTTTGTGAATTTTTTTAAATTTAATTAATACAAAAAAGGAAGAAAAAAATGGCGCCTG
ACGCAAAAGTACATCAAAATGTGATGAAAACGGAGAGTGATGAAAATTTAAAGTCTAATG
CACCCTTTCGTGCTGAAATTCAATGGCGTAATGTTGCCGTCAACTTGTTTATTCATCTTG
GTTTCTTCGTTGGACTCTATTATATAATTACATTCAAATTGCAACTAAAAACTTTCATTT
ACTTTTTCTTCCTGACATGCTTATGCAATTTGGGTGTCACGATCGGCGTTCACAGATTAT
GGAGTCACAGAAGTTTCAAATGCACTCGTCCAATTAAGCTTCTTCTTACCTTTTTTTACA
CAATGGCTGGTCAATCATCGATTTTCCATTGGGTTCAAATTCATCGAGTTCATCATAAAT
TTTCTGAAACTTTAAAGGATCCATTAGATGTTAATCGTGGATTCTTTTTTGCACATGTCG
GTTGGTACTGTCTTTCATACCATCCAGAATGTGAAACTGAGATGAAGCGTATTGATATGG
ATGATATAAAGGCTGATAAAGACCTGATGTTCCAGTACAAGTACTATTCACATCTTTTCA
CACTTCTCAATTTCCTTTCCGTTCTTATTCCATGCTATTTTTGGGGCGAATCATTCAAAA
TTGCTTTTTGGGTTTGCTTTGTAACACGTTTTGCCATCAACTTTACACAATTAAATTTCA
CTAATAGTGCAAATCATTTCATTGGAAAACGTCCTTATGATAAAACTCAATCAGCTACTG
ACAACATTGCTTGCACTATTTTCTCATTTGGAGAAG

>g16389.t8 Gene=g16389 Length=255
MAPDAKVHQNVMKTESDENLKSNAPFRAEIQWRNVAVNLFIHLGFFVGLYYIITFKLQLK
TFIYFFFLTCLCNLGVTIGVHRLWSHRSFKCTRPIKLLLTFFYTMAGQSSIFHWVQIHRV
HHKFSETLKDPLDVNRGFFFAHVGWYCLSYHPECETEMKRIDMDDIKADKDLMFQYKYYS
HLFTLLNFLSVLIPCYFWGESFKIAFWVCFVTRFAINFTQLNFTNSANHFIGKRPYDKTQ
SATDNIACTIFSFGE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
24 g16389.t8 CDD cd03505 Delta9-FADS-like 58 255 4.2798E-37
2 g16389.t8 PANTHER PTHR11351 ACYL-COA DESATURASE 7 255 2.9E-73
3 g16389.t8 PANTHER PTHR11351:SF61 RH14937P 7 255 2.9E-73
4 g16389.t8 PRINTS PR00075 Fatty acid desaturase family 1 signature 32 52 2.2E-28
6 g16389.t8 PRINTS PR00075 Fatty acid desaturase family 1 signature 81 101 2.2E-28
8 g16389.t8 PRINTS PR00075 Fatty acid desaturase family 1 signature 118 147 2.2E-28
5 g16389.t8 PRINTS PR00075 Fatty acid desaturase family 1 signature 178 196 2.2E-28
7 g16389.t8 PRINTS PR00075 Fatty acid desaturase family 1 signature 211 232 2.2E-28
1 g16389.t8 Pfam PF00487 Fatty acid desaturase 65 254 2.1E-11
17 g16389.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 34 -
22 g16389.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 35 53 -
13 g16389.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 54 61 -
20 g16389.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 62 83 -
16 g16389.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 84 94 -
23 g16389.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 95 115 -
14 g16389.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 116 177 -
19 g16389.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 178 199 -
18 g16389.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 200 204 -
21 g16389.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 205 224 -
15 g16389.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 225 255 -
10 g16389.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 34 53 -
12 g16389.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 63 85 -
9 g16389.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 98 117 -
11 g16389.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 178 200 -

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