General information for g13527.t1
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.t1 | TSS | g13527.t1 | 30721237 | 30721237 |
| chr_1 | g13527 | g13527.t1 | isoform | g13527.t1 | 30721359 | 30722460 |
| chr_1 | g13527 | g13527.t1 | exon | g13527.t1.exon1 | 30721359 | 30721660 |
| chr_1 | g13527 | g13527.t1 | cds | g13527.t1.CDS1 | 30721359 | 30721660 |
| chr_1 | g13527 | g13527.t1 | exon | g13527.t1.exon2 | 30721730 | 30722106 |
| chr_1 | g13527 | g13527.t1 | cds | g13527.t1.CDS2 | 30721730 | 30722106 |
| chr_1 | g13527 | g13527.t1 | exon | g13527.t1.exon3 | 30722174 | 30722460 |
| chr_1 | g13527 | g13527.t1 | cds | g13527.t1.CDS3 | 30722174 | 30722460 |
| chr_1 | g13527 | g13527.t1 | TTS | g13527.t1 | 30723430 | 30723430 |
Sequences
>g13527.t1 Gene=g13527 Length=966
ATGGGACAGCATGTTTCGAAAACCGATTTTGAATGGTCGTATGACGATGAGCCGCATAAA
ACAAGAAGAACTGAAATTTTAAAGAAATATCCAGAGATTAAACAATTATTTGGATGTGAT
CCTAATTTTAAATATGTTTGCACTGCAATGGTTCTTACTCAAATAGCTTCACTGTACTTT
TTGCAAGATAAATCATGGACATTTCTATTCATTGCGGCTTATTGTTTTGGTGGAGTTTTA
AACCATAGTTTGAGTCTAGCTGTTCATGAAATTTCACACAATTTAAGTTTCGGTCATTCG
CGACCAATGGCAAATCGACTTTTTGGATTTTTCTGTAATCTTCCACTCGGCGTTCCAATG
TCAATTTCTTTTAAAAGATATCATTTGGAACATCACAGATATCAGGGAGATGAAGTGCTT
GATACTGATTTGCCTACACTTCTTGAAGCAAAATTATTTTGTACAACTTTTGGAAAATTT
TGTTGGGTTTGTTTGCAGCCATTCTTTTACCTTTTTCGTCCATTGGTCGTTAATCCAAAG
AAACCATGCAAGCTTGAAGTTGTTAACACAATCATTCAATTGATCTTTGACTCGATAATC
GTTTATGTTTTCGGTTGGAAAATGCTTGTTTATCTGATCATGGGTACATTGCTAGCTATG
GGTTTACATCCTGTCGCTGGTCATTTTATTAGTGAACACTATTGCTTCAAAAAAGGTTTC
GAAACATACTCATATTATGGCCCTTTGAATTTCATTACATTCAATGTTGGCTATCACAAT
GAACACCATGATTTTCCTGCTGTCCCCGGCTCACGTTTGCCGCTTGTTAAAAAAATTGCA
CCAGAATTTTATGATGATTTACCACAACATAATTCATGGATTAGAGTCATCTATGAGTTT
ATTATGGATCCAGAAATTGGACCTTATGCAAGAGTCAAACGTAAGACAAGAGGATTAAGT
TCATAA
>g13527.t1 Gene=g13527 Length=321
MGQHVSKTDFEWSYDDEPHKTRRTEILKKYPEIKQLFGCDPNFKYVCTAMVLTQIASLYF
LQDKSWTFLFIAAYCFGGVLNHSLSLAVHEISHNLSFGHSRPMANRLFGFFCNLPLGVPM
SISFKRYHLEHHRYQGDEVLDTDLPTLLEAKLFCTTFGKFCWVCLQPFFYLFRPLVVNPK
KPCKLEVVNTIIQLIFDSIIVYVFGWKMLVYLIMGTLLAMGLHPVAGHFISEHYCFKKGF
ETYSYYGPLNFITFNVGYHNEHHDFPAVPGSRLPLVKKIAPEFYDDLPQHNSWIRVIYEF
IMDPEIGPYARVKRKTRGLSS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 20 | g13527.t1 | CDD | cd03508 | Delta4-sphingolipid-FADS-like | 26 | 315 | 2.05572E-172 |
| 3 | g13527.t1 | PANTHER | PTHR12879 | SPHINGOLIPID DELTA 4 DESATURASE/C-4 HYDROXYLASE PROTEIN DES2 | 4 | 317 | 2.8E-146 |
| 19 | g13527.t1 | PIRSF | PIRSF017228 | Sphnglp_dlt4_des | 1 | 321 | 2.2E-161 |
| 1 | g13527.t1 | Pfam | PF08557 | Sphingolipid Delta4-desaturase (DES) | 6 | 42 | 3.4E-20 |
| 2 | g13527.t1 | Pfam | PF00487 | Fatty acid desaturase | 65 | 285 | 1.5E-24 |
| 13 | g13527.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 42 | - |
| 14 | g13527.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 43 | 61 | - |
| 9 | g13527.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 62 | 67 | - |
| 18 | g13527.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 68 | 87 | - |
| 12 | g13527.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 88 | 106 | - |
| 16 | g13527.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 107 | 124 | - |
| 10 | g13527.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 125 | 186 | - |
| 15 | g13527.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 187 | 204 | - |
| 11 | g13527.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 205 | 209 | - |
| 17 | g13527.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 210 | 230 | - |
| 8 | g13527.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 231 | 321 | - |
| 7 | g13527.t1 | SMART | SM01269 | Lipid_DES_2 | 5 | 43 | 5.8E-21 |
| 4 | g13527.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 65 | 87 | - |
| 6 | g13527.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 102 | 124 | - |
| 5 | g13527.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 199 | 221 | - |
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 |
| GO:0006629 | lipid metabolic process | BP |
KEGG
Orthology
- This transcript has been annotated with K04712 (sphingolipid 4-desaturase/C4-monooxygenase)
Pathway
- This transcript belongs to the following pathways
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.
