General information for g11836.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t3 | isoform | g11836.t3 | 18685068 | 18687136 |
| chr_1 | g11836 | g11836.t3 | exon | g11836.t3.exon1 | 18685068 | 18685174 |
| chr_1 | g11836 | g11836.t3 | exon | g11836.t3.exon2 | 18685501 | 18685722 |
| chr_1 | g11836 | g11836.t3 | cds | g11836.t3.CDS1 | 18685624 | 18685722 |
| chr_1 | g11836 | g11836.t3 | exon | g11836.t3.exon3 | 18685783 | 18687136 |
| chr_1 | g11836 | g11836.t3 | cds | g11836.t3.CDS2 | 18685783 | 18686409 |
| chr_1 | g11836 | g11836.t3 | TTS | g11836.t3 | 18687146 | 18687146 |
| chr_1 | g11836 | g11836.t3 | TSS | g11836.t3 | NA | NA |
Sequences
>g11836.t3 Gene=g11836 Length=1683
CAATTGGTCGATCATTGGGTATCAAGGCAACAAAAGCAAAAGCACCACTGTCAAATACAG
TTTTGGAAGCGACTTATTCGAAACATTCAAAACTCAATCATAAAATAATTGTTCCATTGA
CAAAACAATTAGATCTATCTGAGCGTCAAATTGAAAGATGGTGGAGAAGGCGTAAAGCGC
AAGATAAACCTACAACATTAAAAAAATTCTGTGAAAATGTATGGCGATGTATGTATTATA
CTTATAGTTTCATTTTCGGAGCCATAGTAATGTGGGATAAGCCATGGTTATGGGATATTA
AGCAATGCTGGTATAACTATCCGCATCAGTCTATTCTAAATGACGTATGGTGGTACTATA
TGATCTCAATGGCGTTTTATTGGTCATTAACTTTTTCGCAATGCTTCGACAATAAGCGCA
AAGACTTTTGGCAAATGTTCATTCATCATGTTTTGACTCTAGTATTGATATCTCTTAGTT
GGATTTGCAATTTACATCGTGTTGGTTCATTAGTATTAATTGTACATGATTTTGCTGACA
TATTTTTGGAAGCTGCAAAGTTTTTGAAATATGCAAGTCTACAGAAAGCTTGCGATATTG
TTTTTGGAGTTTTCACAGTGTCTTGGCTTGTAACAAGATTAGGATTATATCCGAGAATAA
TTTATAGTTCTACAATAGAAGCACCGCAAATTTTACCAATGTATCCTGTTTATTACATAT
TTAATTCATTACTTATTATGCTTCTCGTGCTTCATCTCATATGGACTTATATGATCTTGC
AAGTTGTAGTGCAAACAATTAAAGCTGGACAAATGGAAGGCGATGTTCGTTCAAGTTCTG
ATGAAGTTTCTGATAGTTCTGAAAATCGCGATAAACCTATGCATAATGGGAATGCTGAAT
CACCTAAAAAAGAAAATCATTCTTACAACAACACATCACCTAAAAAGATAAATTGATTTG
TAAATAATCAATTATTCACATTTCTTCATTCCAAAATATTTTGGAGAATGATCATAACAA
GATGGGTATTTCATTTCAATCAGTTTCGAAGATCTAATTTTACACTATCTAGAATTTTGA
TTATTAACTAAGAGTTTCAAACAAAAAAGTCTCAGTTTTATTAAAAAGCAGTTAGAAAAG
ATCGAATAATTACGTATTTTAGGGAATTTGAAATGTTTAAAATGAATGAATGAAAGACTT
TGATTCTCTAGTGAAAGATATTTTTTTACCTATCTTTATTGGTAGATAAAACATTAAATG
ATGATTAACCTAAGTGTAAAAACTAAAAAGATTTTACCAAGATATTACTGTTGTAGAAAT
CAATTTTTTTAATCATAAATCTCTTATATCCTAAAATACTAAATCTTTAAAAAGTAATGA
GAAAATATTTTTAGATTGCTTATTTGCAATTTAAAAGAAGAAAATGAGGCGACAAACAAC
AGAATGATTAAAAACCATATCTACATTTGATTGTTTTATTAGTTTTTTTATCTGCTTTAA
GAAACGAACCAAATTTATTGTTCTTAAGCTTATTTGTGACTTTCATTTGAAAGTTTTTGT
TGATCAGTTATGTATGTTAGTCTAATTAATTGATCTACTAATTCATTATTGCATTGAACA
ATTTTTATATTATTAAAATCATTAGAACTAATTAATGTGTCATTTTTTGGAATAAATATT
TTT
>g11836.t3 Gene=g11836 Length=241
MYYTYSFIFGAIVMWDKPWLWDIKQCWYNYPHQSILNDVWWYYMISMAFYWSLTFSQCFD
NKRKDFWQMFIHHVLTLVLISLSWICNLHRVGSLVLIVHDFADIFLEAAKFLKYASLQKA
CDIVFGVFTVSWLVTRLGLYPRIIYSSTIEAPQILPMYPVYYIFNSLLIMLLVLHLIWTY
MILQVVVQTIKAGQMEGDVRSSSDEVSDSSENRDKPMHNGNAESPKKENHSYNNTSPKKI
N
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 23 | g11836.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 198 | 241 | - |
| 22 | g11836.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 201 | 225 | - |
| 21 | g11836.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 226 | 241 | - |
| 2 | g11836.t3 | PANTHER | PTHR12560 | LONGEVITY ASSURANCE FACTOR 1 LAG1 | 1 | 228 | 2.9E-102 |
| 3 | g11836.t3 | PANTHER | PTHR12560:SF56 | LD18904P | 1 | 228 | 2.9E-102 |
| 15 | g11836.t3 | PIRSF | PIRSF005225 | LAG1_LAC1 | 1 | 233 | 5.0E-78 |
| 1 | g11836.t3 | Pfam | PF03798 | TLC domain | 2 | 183 | 9.6E-42 |
| 8 | g11836.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 39 | - |
| 14 | g11836.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 40 | 59 | - |
| 6 | g11836.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 60 | 65 | - |
| 11 | g11836.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 66 | 85 | - |
| 9 | g11836.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 86 | 90 | - |
| 13 | g11836.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 91 | 109 | - |
| 4 | g11836.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 110 | 120 | - |
| 12 | g11836.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 121 | 140 | - |
| 7 | g11836.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 141 | 159 | - |
| 10 | g11836.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 160 | 183 | - |
| 5 | g11836.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 184 | 241 | - |
| 24 | g11836.t3 | ProSiteProfiles | PS50922 | TLC domain profile. | 1 | 191 | 17.449 |
| 20 | g11836.t3 | SMART | SM00724 | lag1_27 | 1 | 191 | 2.1E-63 |
| 19 | g11836.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 39 | 56 | - |
| 16 | g11836.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 66 | 88 | - |
| 18 | g11836.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 123 | 145 | - |
| 17 | g11836.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 160 | 182 | - |
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: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.
