General information for g11836.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ceramide synthase 6.
Parent gene
- The parent gene g11836 is located on chr_1: 18685911..18687152 (+ 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 | g11836 | g11836.t1 | TSS | g11836.t1 | 18683882 | 18683882 |
| chr_1 | g11836 | g11836.t1 | isoform | g11836.t1 | 18684039 | 18686409 |
| chr_1 | g11836 | g11836.t1 | exon | g11836.t1.exon1 | 18684039 | 18684083 |
| chr_1 | g11836 | g11836.t1 | cds | g11836.t1.CDS1 | 18684039 | 18684083 |
| chr_1 | g11836 | g11836.t1 | exon | g11836.t1.exon2 | 18684219 | 18684358 |
| chr_1 | g11836 | g11836.t1 | cds | g11836.t1.CDS2 | 18684219 | 18684358 |
| chr_1 | g11836 | g11836.t1 | exon | g11836.t1.exon3 | 18685054 | 18685174 |
| chr_1 | g11836 | g11836.t1 | cds | g11836.t1.CDS3 | 18685054 | 18685174 |
| chr_1 | g11836 | g11836.t1 | exon | g11836.t1.exon4 | 18685501 | 18685722 |
| chr_1 | g11836 | g11836.t1 | cds | g11836.t1.CDS4 | 18685501 | 18685722 |
| chr_1 | g11836 | g11836.t1 | exon | g11836.t1.exon5 | 18685783 | 18686409 |
| chr_1 | g11836 | g11836.t1 | cds | g11836.t1.CDS5 | 18685783 | 18686409 |
| chr_1 | g11836 | g11836.t1 | TTS | g11836.t1 | 18687146 | 18687146 |
Sequences
>g11836.t1 Gene=g11836 Length=1155
ATGGATTTATTAAGAAAATTCTCAGAAACTTTTTGGAATGAAGATGTTTGGCTTCCACCG
AATATTACATGGAAAGATATTGATCCTCGAAATAGCAATGAAATTGTGTATACTGATTAT
AGGCATCTTCTGTGGCCGATCCCTATGTCATTTGTCATTATATTGTTGCGATTTATTATT
GAAAGATATTGGATAACACCAATTGGTCGATCATTGGGTATCAAGGCAACAAAAGCAAAA
GCACCACTGTCAAATACAGTTTTGGAAGCGACTTATTCGAAACATTCAAAACTCAATCAT
AAAATAATTGTTCCATTGACAAAACAATTAGATCTATCTGAGCGTCAAATTGAAAGATGG
TGGAGAAGGCGTAAAGCGCAAGATAAACCTACAACATTAAAAAAATTCTGTGAAAATGTA
TGGCGATGTATGTATTATACTTATAGTTTCATTTTCGGAGCCATAGTAATGTGGGATAAG
CCATGGTTATGGGATATTAAGCAATGCTGGTATAACTATCCGCATCAGTCTATTCTAAAT
GACGTATGGTGGTACTATATGATCTCAATGGCGTTTTATTGGTCATTAACTTTTTCGCAA
TGCTTCGACAATAAGCGCAAAGACTTTTGGCAAATGTTCATTCATCATGTTTTGACTCTA
GTATTGATATCTCTTAGTTGGATTTGCAATTTACATCGTGTTGGTTCATTAGTATTAATT
GTACATGATTTTGCTGACATATTTTTGGAAGCTGCAAAGTTTTTGAAATATGCAAGTCTA
CAGAAAGCTTGCGATATTGTTTTTGGAGTTTTCACAGTGTCTTGGCTTGTAACAAGATTA
GGATTATATCCGAGAATAATTTATAGTTCTACAATAGAAGCACCGCAAATTTTACCAATG
TATCCTGTTTATTACATATTTAATTCATTACTTATTATGCTTCTCGTGCTTCATCTCATA
TGGACTTATATGATCTTGCAAGTTGTAGTGCAAACAATTAAAGCTGGACAAATGGAAGGC
GATGTTCGTTCAAGTTCTGATGAAGTTTCTGATAGTTCTGAAAATCGCGATAAACCTATG
CATAATGGGAATGCTGAATCACCTAAAAAAGAAAATCATTCTTACAACAACACATCACCT
AAAAAGATAAATTGA
>g11836.t1 Gene=g11836 Length=384
MDLLRKFSETFWNEDVWLPPNITWKDIDPRNSNEIVYTDYRHLLWPIPMSFVIILLRFII
ERYWITPIGRSLGIKATKAKAPLSNTVLEATYSKHSKLNHKIIVPLTKQLDLSERQIERW
WRRRKAQDKPTTLKKFCENVWRCMYYTYSFIFGAIVMWDKPWLWDIKQCWYNYPHQSILN
DVWWYYMISMAFYWSLTFSQCFDNKRKDFWQMFIHHVLTLVLISLSWICNLHRVGSLVLI
VHDFADIFLEAAKFLKYASLQKACDIVFGVFTVSWLVTRLGLYPRIIYSSTIEAPQILPM
YPVYYIFNSLLIMLLVLHLIWTYMILQVVVQTIKAGQMEGDVRSSSDEVSDSSENRDKPM
HNGNAESPKKENHSYNNTSPKKIN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 23 | g11836.t1 | CDD | cd00086 | homeodomain | 87 | 131 | 4.43226E-4 |
| 6 | g11836.t1 | Gene3D | G3DSA:1.10.10.60 | - | 82 | 131 | 8.0E-14 |
| 31 | g11836.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 341 | 384 | - |
| 33 | g11836.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 344 | 368 | - |
| 32 | g11836.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 369 | 384 | - |
| 3 | g11836.t1 | PANTHER | PTHR12560 | LONGEVITY ASSURANCE FACTOR 1 LAG1 | 5 | 371 | 1.6E-154 |
| 4 | g11836.t1 | PANTHER | PTHR12560:SF56 | LD18904P | 5 | 371 | 1.6E-154 |
| 22 | g11836.t1 | PIRSF | PIRSF005225 | LAG1_LAC1 | 4 | 376 | 1.3E-93 |
| 1 | g11836.t1 | Pfam | PF00046 | Homeodomain | 86 | 129 | 3.2E-6 |
| 2 | g11836.t1 | Pfam | PF03798 | TLC domain | 135 | 326 | 1.1E-44 |
| 14 | g11836.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 42 | - |
| 17 | g11836.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 43 | 60 | - |
| 9 | g11836.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 61 | 142 | - |
| 21 | g11836.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 143 | 163 | - |
| 12 | g11836.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 164 | 182 | - |
| 20 | g11836.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 183 | 202 | - |
| 8 | g11836.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 203 | 208 | - |
| 16 | g11836.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 209 | 228 | - |
| 11 | g11836.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 229 | 233 | - |
| 15 | g11836.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 234 | 252 | - |
| 10 | g11836.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 253 | 263 | - |
| 18 | g11836.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 264 | 283 | - |
| 13 | g11836.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 284 | 302 | - |
| 19 | g11836.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 303 | 326 | - |
| 7 | g11836.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 327 | 384 | - |
| 35 | g11836.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 88 | 131 | 8.697 |
| 34 | g11836.t1 | ProSiteProfiles | PS50922 | TLC domain profile. | 134 | 334 | 17.728 |
| 30 | g11836.t1 | SMART | SM00724 | lag1_27 | 134 | 334 | 3.7E-75 |
| 5 | g11836.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 81 | 136 | 2.82E-7 |
| 26 | g11836.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 43 | 60 | - |
| 24 | g11836.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 139 | 158 | - |
| 29 | g11836.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 182 | 199 | - |
| 28 | g11836.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 212 | 234 | - |
| 27 | g11836.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 266 | 283 | - |
| 25 | g11836.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 303 | 325 | - |
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:0003677 | DNA binding | MF |
| GO:0016021 | integral component of membrane | CC |
KEGG
Orthology
- This transcript has been annotated with K23727 (sphingoid base N-palmitoyltransferase)
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.
