Gene loci information

Transcript annotation

  • This transcript has been annotated as Ceramide synthase 6.

Parent gene

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.t2 TSS g11836.t2 18683882 18683882
chr_1 g11836 g11836.t2 isoform g11836.t2 18684219 18686409
chr_1 g11836 g11836.t2 exon g11836.t2.exon1 18684219 18684358
chr_1 g11836 g11836.t2 cds g11836.t2.CDS1 18684318 18684358
chr_1 g11836 g11836.t2 exon g11836.t2.exon2 18685054 18685174
chr_1 g11836 g11836.t2 cds g11836.t2.CDS2 18685054 18685174
chr_1 g11836 g11836.t2 exon g11836.t2.exon3 18685501 18685722
chr_1 g11836 g11836.t2 cds g11836.t2.CDS3 18685501 18685722
chr_1 g11836 g11836.t2 exon g11836.t2.exon4 18685783 18686409
chr_1 g11836 g11836.t2 cds g11836.t2.CDS4 18685783 18686409
chr_1 g11836 g11836.t2 TTS g11836.t2 18687146 18687146

Sequences

>g11836.t2 Gene=g11836 Length=1110
GTTTGGCTTCCACCGAATATTACATGGAAAGATATTGATCCTCGAAATAGCAATGAAATT
GTGTATACTGATTATAGGCATCTTCTGTGGCCGATCCCTATGTCATTTGTCATTATATTG
TTGCGATTTATTATTGAAAGATATTGGATAACACCAATTGGTCGATCATTGGGTATCAAG
GCAACAAAAGCAAAAGCACCACTGTCAAATACAGTTTTGGAAGCGACTTATTCGAAACAT
TCAAAACTCAATCATAAAATAATTGTTCCATTGACAAAACAATTAGATCTATCTGAGCGT
CAAATTGAAAGATGGTGGAGAAGGCGTAAAGCGCAAGATAAACCTACAACATTAAAAAAA
TTCTGTGAAAATGTATGGCGATGTATGTATTATACTTATAGTTTCATTTTCGGAGCCATA
GTAATGTGGGATAAGCCATGGTTATGGGATATTAAGCAATGCTGGTATAACTATCCGCAT
CAGTCTATTCTAAATGACGTATGGTGGTACTATATGATCTCAATGGCGTTTTATTGGTCA
TTAACTTTTTCGCAATGCTTCGACAATAAGCGCAAAGACTTTTGGCAAATGTTCATTCAT
CATGTTTTGACTCTAGTATTGATATCTCTTAGTTGGATTTGCAATTTACATCGTGTTGGT
TCATTAGTATTAATTGTACATGATTTTGCTGACATATTTTTGGAAGCTGCAAAGTTTTTG
AAATATGCAAGTCTACAGAAAGCTTGCGATATTGTTTTTGGAGTTTTCACAGTGTCTTGG
CTTGTAACAAGATTAGGATTATATCCGAGAATAATTTATAGTTCTACAATAGAAGCACCG
CAAATTTTACCAATGTATCCTGTTTATTACATATTTAATTCATTACTTATTATGCTTCTC
GTGCTTCATCTCATATGGACTTATATGATCTTGCAAGTTGTAGTGCAAACAATTAAAGCT
GGACAAATGGAAGGCGATGTTCGTTCAAGTTCTGATGAAGTTTCTGATAGTTCTGAAAAT
CGCGATAAACCTATGCATAATGGGAATGCTGAATCACCTAAAAAAGAAAATCATTCTTAC
AACAACACATCACCTAAAAAGATAAATTGA

>g11836.t2 Gene=g11836 Length=336
MSFVIILLRFIIERYWITPIGRSLGIKATKAKAPLSNTVLEATYSKHSKLNHKIIVPLTK
QLDLSERQIERWWRRRKAQDKPTTLKKFCENVWRCMYYTYSFIFGAIVMWDKPWLWDIKQ
CWYNYPHQSILNDVWWYYMISMAFYWSLTFSQCFDNKRKDFWQMFIHHVLTLVLISLSWI
CNLHRVGSLVLIVHDFADIFLEAAKFLKYASLQKACDIVFGVFTVSWLVTRLGLYPRIIY
SSTIEAPQILPMYPVYYIFNSLLIMLLVLHLIWTYMILQVVVQTIKAGQMEGDVRSSSDE
VSDSSENRDKPMHNGNAESPKKENHSYNNTSPKKIN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
21 g11836.t2 CDD cd00086 homeodomain 39 83 3.59848E-4
6 g11836.t2 Gene3D G3DSA:1.10.10.60 - 34 83 6.6E-14
30 g11836.t2 MobiDBLite mobidb-lite consensus disorder prediction 293 336 -
29 g11836.t2 MobiDBLite mobidb-lite consensus disorder prediction 296 320 -
28 g11836.t2 MobiDBLite mobidb-lite consensus disorder prediction 321 336 -
3 g11836.t2 PANTHER PTHR12560 LONGEVITY ASSURANCE FACTOR 1 LAG1 1 323 1.6E-139
4 g11836.t2 PANTHER PTHR12560:SF56 LD18904P 1 323 1.6E-139
20 g11836.t2 PIRSF PIRSF005225 LAG1_LAC1 6 328 2.0E-90
1 g11836.t2 Pfam PF00046 Homeodomain 38 81 2.7E-6
2 g11836.t2 Pfam PF03798 TLC domain 87 278 7.7E-45
8 g11836.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 94 -
19 g11836.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 95 115 -
12 g11836.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 116 134 -
15 g11836.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 135 154 -
9 g11836.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 155 160 -
18 g11836.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 161 180 -
13 g11836.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 181 185 -
14 g11836.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 186 204 -
10 g11836.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 205 215 -
17 g11836.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 216 235 -
11 g11836.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 236 254 -
16 g11836.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 255 278 -
7 g11836.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 279 336 -
32 g11836.t2 ProSiteProfiles PS50071 ‘Homeobox’ domain profile. 40 83 8.697
31 g11836.t2 ProSiteProfiles PS50922 TLC domain profile. 86 286 17.728
27 g11836.t2 SMART SM00724 lag1_27 86 286 3.7E-75
5 g11836.t2 SUPERFAMILY SSF46689 Homeodomain-like 33 88 2.31E-7
22 g11836.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 91 110 -
24 g11836.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 134 151 -
26 g11836.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 164 186 -
25 g11836.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 218 235 -
23 g11836.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 255 277 -

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 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.

Raw TPM values