Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Sphingolipid delta(4)-desaturase DES1.

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_1 g13527 g13527.t2 TSS g13527.t2 30721237 30721237
chr_1 g13527 g13527.t2 isoform g13527.t2 30721359 30721732
chr_1 g13527 g13527.t2 exon g13527.t2.exon1 30721359 30721660
chr_1 g13527 g13527.t2 cds g13527.t2.CDS1 30721359 30721660
chr_1 g13527 g13527.t2 exon g13527.t2.exon2 30721730 30721732
chr_1 g13527 g13527.t2 cds g13527.t2.CDS2 30721730 30721730
chr_1 g13527 g13527.t2 TTS g13527.t2 NA NA

Sequences

>g13527.t2 Gene=g13527 Length=305
ATGGGACAGCATGTTTCGAAAACCGATTTTGAATGGTCGTATGACGATGAGCCGCATAAA
ACAAGAAGAACTGAAATTTTAAAGAAATATCCAGAGATTAAACAATTATTTGGATGTGAT
CCTAATTTTAAATATGTTTGCACTGCAATGGTTCTTACTCAAATAGCTTCACTGTACTTT
TTGCAAGATAAATCATGGACATTTCTATTCATTGCGGCTTATTGTTTTGGTGGAGTTTTA
AACCATAGTTTGAGTCTAGCTGTTCATGAAATTTCACACAATTTAAGTTTCGGTCATTCG
CGACC

>g13527.t2 Gene=g13527 Length=101
MGQHVSKTDFEWSYDDEPHKTRRTEILKKYPEIKQLFGCDPNFKYVCTAMVLTQIASLYF
LQDKSWTFLFIAAYCFGGVLNHSLSLAVHEISHNLSFGHSR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g13527.t2 PANTHER PTHR12879 SPHINGOLIPID DELTA 4 DESATURASE/C-4 HYDROXYLASE PROTEIN DES2 1 101 8.3E-33
3 g13527.t2 PANTHER PTHR12879:SF2 SPHINGOLIPID DELTA(4)-DESATURASE DES1 1 101 8.3E-33
1 g13527.t2 Pfam PF08557 Sphingolipid Delta4-desaturase (DES) 6 42 4.8E-21
8 g13527.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 42 -
9 g13527.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 43 61 -
6 g13527.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 62 67 -
10 g13527.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 68 88 -
7 g13527.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 89 101 -
5 g13527.t2 SMART SM01269 Lipid_DES_2 5 43 5.8E-21
4 g13527.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 66 88 -

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:0042284 sphingolipid delta-4 desaturase activity MF
GO:0030148 sphingolipid biosynthetic process BP
GO:0016021 integral component of membrane CC

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