General information for g13527.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Sphingolipid delta(4)-desaturase DES1.
Parent gene
- The parent gene g13527 is located on chr_1: 30722460..30723456 (+ strand)
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.t3 | TSS | g13527.t3 | 30721237 | 30721237 |
| chr_1 | g13527 | g13527.t3 | isoform | g13527.t3 | 30721359 | 30722460 |
| chr_1 | g13527 | g13527.t3 | exon | g13527.t3.exon1 | 30721359 | 30721396 |
| chr_1 | g13527 | g13527.t3 | exon | g13527.t3.exon2 | 30721618 | 30722106 |
| chr_1 | g13527 | g13527.t3 | cds | g13527.t3.CDS1 | 30721734 | 30722106 |
| chr_1 | g13527 | g13527.t3 | exon | g13527.t3.exon3 | 30722174 | 30722460 |
| chr_1 | g13527 | g13527.t3 | cds | g13527.t3.CDS2 | 30722174 | 30722460 |
| chr_1 | g13527 | g13527.t3 | TTS | g13527.t3 | 30723430 | 30723430 |
Sequences
>g13527.t3 Gene=g13527 Length=814
ATGGGACAGCATGTTTCGAAAACCGATTTTGAATGGTCCTGTTCATGAAATTTCACACAA
TTTAAGTTTCGGTCATTCGCGGTAAGCATGATTCATTTGCATTTTTATGTAATACATTGA
CTCATTTCTTATCACTCGCTTTTTTGACAGACCAATGGCAAATCGACTTTTTGGATTTTT
CTGTAATCTTCCACTCGGCGTTCCAATGTCAATTTCTTTTAAAAGATATCATTTGGAACA
TCACAGATATCAGGGAGATGAAGTGCTTGATACTGATTTGCCTACACTTCTTGAAGCAAA
ATTATTTTGTACAACTTTTGGAAAATTTTGTTGGGTTTGTTTGCAGCCATTCTTTTACCT
TTTTCGTCCATTGGTCGTTAATCCAAAGAAACCATGCAAGCTTGAAGTTGTTAACACAAT
CATTCAATTGATCTTTGACTCGATAATCGTTTATGTTTTCGGTTGGAAAATGCTTGTTTA
TCTGATCATGGGTACATTGCTAGCTATGGGTTTACATCCTGTCGCTGGTCATTTTATTAG
TGAACACTATTGCTTCAAAAAAGGTTTCGAAACATACTCATATTATGGCCCTTTGAATTT
CATTACATTCAATGTTGGCTATCACAATGAACACCATGATTTTCCTGCTGTCCCCGGCTC
ACGTTTGCCGCTTGTTAAAAAAATTGCACCAGAATTTTATGATGATTTACCACAACATAA
TTCATGGATTAGAGTCATCTATGAGTTTATTATGGATCCAGAAATTGGACCTTATGCAAG
AGTCAAACGTAAGACAAGAGGATTAAGTTCATAA
>g13527.t3 Gene=g13527 Length=219
MANRLFGFFCNLPLGVPMSISFKRYHLEHHRYQGDEVLDTDLPTLLEAKLFCTTFGKFCW
VCLQPFFYLFRPLVVNPKKPCKLEVVNTIIQLIFDSIIVYVFGWKMLVYLIMGTLLAMGL
HPVAGHFISEHYCFKKGFETYSYYGPLNFITFNVGYHNEHHDFPAVPGSRLPLVKKIAPE
FYDDLPQHNSWIRVIYEFIMDPEIGPYARVKRKTRGLSS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g13527.t3 | PANTHER | PTHR12879 | SPHINGOLIPID DELTA 4 DESATURASE/C-4 HYDROXYLASE PROTEIN DES2 | 2 | 215 | 1.8E-105 |
| 1 | g13527.t3 | Pfam | PF00487 | Fatty acid desaturase | 3 | 183 | 2.2E-21 |
| 7 | g13527.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 47 | - |
| 8 | g13527.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 48 | 70 | - |
| 5 | g13527.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 71 | 81 | - |
| 10 | g13527.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 82 | 102 | - |
| 6 | g13527.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 103 | 107 | - |
| 9 | g13527.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 108 | 128 | - |
| 4 | g13527.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 129 | 219 | - |
| 3 | g13527.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 97 | 119 | - |
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: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.
