General information for g11917.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ceramide synthase 2.
Parent gene
- The parent gene g11917 is located on chr_1: 19280196..19285878 (+ 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 | g11917 | g11917.t1 | TSS | g11917.t1 | 19279637 | 19279637 |
| chr_1 | g11917 | g11917.t1 | isoform | g11917.t1 | 19279699 | 19281210 |
| chr_1 | g11917 | g11917.t1 | exon | g11917.t1.exon1 | 19279699 | 19279731 |
| chr_1 | g11917 | g11917.t1 | cds | g11917.t1.CDS1 | 19279699 | 19279731 |
| chr_1 | g11917 | g11917.t1 | exon | g11917.t1.exon2 | 19279808 | 19279947 |
| chr_1 | g11917 | g11917.t1 | cds | g11917.t1.CDS2 | 19279808 | 19279947 |
| chr_1 | g11917 | g11917.t1 | exon | g11917.t1.exon3 | 19280010 | 19280136 |
| chr_1 | g11917 | g11917.t1 | cds | g11917.t1.CDS3 | 19280010 | 19280136 |
| chr_1 | g11917 | g11917.t1 | exon | g11917.t1.exon4 | 19280196 | 19280417 |
| chr_1 | g11917 | g11917.t1 | cds | g11917.t1.CDS4 | 19280196 | 19280417 |
| chr_1 | g11917 | g11917.t1 | exon | g11917.t1.exon5 | 19280543 | 19280714 |
| chr_1 | g11917 | g11917.t1 | cds | g11917.t1.CDS5 | 19280543 | 19280714 |
| chr_1 | g11917 | g11917.t1 | exon | g11917.t1.exon6 | 19280768 | 19281210 |
| chr_1 | g11917 | g11917.t1 | cds | g11917.t1.CDS6 | 19280768 | 19281210 |
| chr_1 | g11917 | g11917.t1 | TTS | g11917.t1 | 19281295 | 19281295 |
Sequences
>g11917.t1 Gene=g11917 Length=1137
ATGGAAGTATTTGAAACTTTTTGGAGTGAGAAATTTTGGCTTCCGGGAAATTTGACATGG
AAAAGTATTGAGCCTGGCACAAGAGATGGGATTCAATTTAGAAATTATTATGATCTTTGG
TATTCAATTCCATTAGCAGTTGCCATTACTATTGTGAAATCAATTATGATTAGAGAAATT
TTCATGCCATTGGGAAAATATTTACAAATAAAATCCACGAAATTTAAACCTCTTAGAGAG
AATGTAATTTTAGAAAGATTTTATCAGAAATTTCATAAAGAATTGTCTTTAACTGCAATG
CAAATTGCTAATTTAAGAAAACAAACTGACCTGACAGAGCGAGAAATTCAACGATGGTTA
AGAAAACGAAAGGCACAAAATAAATCGACAACACTTGAGAAATTTTGTGAAAATTGTTGG
CGATGCAGTTTTTATTCTTTCAATTTTCTGTTTGGTCTATATGTAATGTGGAATAGAGAA
TGGCTTTGGAATCTCAATGTTATTTCAAATTATCCTTATCATTCAATTGACAATGGAATC
TTATGTTACTACAATATTACGGCTGCTTTCTACATATCATCGTCATTCACACATTTCTTT
GAGACCCGTCGTAAAGATTTTTGGCAAATGTTCATCCATCATATCATCACACTCGCCCTA
ATTTCGATAAGTTGGATCTGTAATGGAATTAGAGGTGGAGCATTAATTGTATTTGTGCAT
GATATTGCTGATATTCTTTTGGAATCATCAAAAGCCGCAAAGTATGCAAATGCTGAAAAT
CTTTGCAATGTGATTTTCGTTCTTTTCACGATTGTGTGGATTTTAACTCGATTACTTATT
TATGGACGAATTGTTTTTATTGGTCATTTTGAATTTCCAAAAATGTATCCCATTTATCCG
TTATATTATGTTTTCTCAGCTTTGACAATCGGTTTATTCCTTCTTCATCTGCTTTGGACA
TATATGATTTTTCAGGTTGCAAATCGATTGATTTTAACAAAAAAATTTGATGATGTGAGA
TCAAGTACAGAAGACACGGAGAGTGAGTTAGGCAGTGATATAAATGAACAAACAGACATC
AATAAAAATAAAGTAATTAGAAAGAAAAATGGTACTAATGGTCGAAAGCAGTGGTAA
>g11917.t1 Gene=g11917 Length=378
MEVFETFWSEKFWLPGNLTWKSIEPGTRDGIQFRNYYDLWYSIPLAVAITIVKSIMIREI
FMPLGKYLQIKSTKFKPLRENVILERFYQKFHKELSLTAMQIANLRKQTDLTEREIQRWL
RKRKAQNKSTTLEKFCENCWRCSFYSFNFLFGLYVMWNREWLWNLNVISNYPYHSIDNGI
LCYYNITAAFYISSSFTHFFETRRKDFWQMFIHHIITLALISISWICNGIRGGALIVFVH
DIADILLESSKAAKYANAENLCNVIFVLFTIVWILTRLLIYGRIVFIGHFEFPKMYPIYP
LYYVFSALTIGLFLLHLLWTYMIFQVANRLILTKKFDDVRSSTEDTESELGSDINEQTDI
NKNKVIRKKNGTNGRKQW
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 23 | g11917.t1 | CDD | cd00086 | homeodomain | 71 | 128 | 4.48755E-5 |
| 6 | g11917.t1 | Coils | Coil | Coil | 102 | 122 | - |
| 5 | g11917.t1 | Gene3D | G3DSA:1.10.10.60 | - | 79 | 129 | 3.8E-9 |
| 2 | g11917.t1 | PANTHER | PTHR12560 | LONGEVITY ASSURANCE FACTOR 1 LAG1 | 2 | 361 | 1.7E-113 |
| 3 | g11917.t1 | PANTHER | PTHR12560:SF56 | LD18904P | 2 | 361 | 1.7E-113 |
| 22 | g11917.t1 | PIRSF | PIRSF005225 | LAG1_LAC1 | 1 | 371 | 8.9E-82 |
| 1 | g11917.t1 | Pfam | PF03798 | TLC domain | 134 | 324 | 2.1E-34 |
| 14 | g11917.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 38 | - |
| 19 | g11917.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 39 | 61 | - |
| 7 | g11917.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 62 | 137 | - |
| 20 | g11917.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 138 | 157 | - |
| 13 | g11917.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 158 | 182 | - |
| 18 | g11917.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 183 | 200 | - |
| 10 | g11917.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 201 | 206 | - |
| 17 | g11917.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 207 | 226 | - |
| 12 | g11917.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 227 | 231 | - |
| 21 | g11917.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 232 | 249 | - |
| 8 | g11917.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 250 | 260 | - |
| 16 | g11917.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 261 | 281 | - |
| 11 | g11917.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 282 | 300 | - |
| 15 | g11917.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 301 | 324 | - |
| 9 | g11917.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 325 | 378 | - |
| 30 | g11917.t1 | ProSiteProfiles | PS50922 | TLC domain profile. | 133 | 332 | 15.417 |
| 29 | g11917.t1 | SMART | SM00724 | lag1_27 | 133 | 332 | 5.4E-46 |
| 4 | g11917.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 82 | 144 | 1.41E-5 |
| 24 | g11917.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 39 | 61 | - |
| 26 | g11917.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 181 | 200 | - |
| 28 | g11917.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 210 | 232 | - |
| 27 | g11917.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 265 | 287 | - |
| 25 | g11917.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 302 | 324 | - |
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 K04709 (very-long-chain ceramide synthase)
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.
