Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t4 isoform g11836.t4 18685526 18687152
chr_1 g11836 g11836.t4 exon g11836.t4.exon1 18685526 18685722
chr_1 g11836 g11836.t4 cds g11836.t4.CDS1 18685624 18685722
chr_1 g11836 g11836.t4 exon g11836.t4.exon2 18685783 18687152
chr_1 g11836 g11836.t4 cds g11836.t4.CDS2 18685783 18686409
chr_1 g11836 g11836.t4 TTS g11836.t4 18687146 18687146
chr_1 g11836 g11836.t4 TSS g11836.t4 NA NA

Sequences

>g11836.t4 Gene=g11836 Length=1567
ATCTATCTGAGCGTCAAATTGAAAGATGGTGGAGAAGGCGTAAAGCGCAAGATAAACCTA
CAACATTAAAAAAATTCTGTGAAAATGTATGGCGATGTATGTATTATACTTATAGTTTCA
TTTTCGGAGCCATAGTAATGTGGGATAAGCCATGGTTATGGGATATTAAGCAATGCTGGT
ATAACTATCCGCATCAGTCTATTCTAAATGACGTATGGTGGTACTATATGATCTCAATGG
CGTTTTATTGGTCATTAACTTTTTCGCAATGCTTCGACAATAAGCGCAAAGACTTTTGGC
AAATGTTCATTCATCATGTTTTGACTCTAGTATTGATATCTCTTAGTTGGATTTGCAATT
TACATCGTGTTGGTTCATTAGTATTAATTGTACATGATTTTGCTGACATATTTTTGGAAG
CTGCAAAGTTTTTGAAATATGCAAGTCTACAGAAAGCTTGCGATATTGTTTTTGGAGTTT
TCACAGTGTCTTGGCTTGTAACAAGATTAGGATTATATCCGAGAATAATTTATAGTTCTA
CAATAGAAGCACCGCAAATTTTACCAATGTATCCTGTTTATTACATATTTAATTCATTAC
TTATTATGCTTCTCGTGCTTCATCTCATATGGACTTATATGATCTTGCAAGTTGTAGTGC
AAACAATTAAAGCTGGACAAATGGAAGGCGATGTTCGTTCAAGTTCTGATGAAGTTTCTG
ATAGTTCTGAAAATCGCGATAAACCTATGCATAATGGGAATGCTGAATCACCTAAAAAAG
AAAATCATTCTTACAACAACACATCACCTAAAAAGATAAATTGATTTGTAAATAATCAAT
TATTCACATTTCTTCATTCCAAAATATTTTGGAGAATGATCATAACAAGATGGGTATTTC
ATTTCAATCAGTTTCGAAGATCTAATTTTACACTATCTAGAATTTTGATTATTAACTAAG
AGTTTCAAACAAAAAAGTCTCAGTTTTATTAAAAAGCAGTTAGAAAAGATCGAATAATTA
CGTATTTTAGGGAATTTGAAATGTTTAAAATGAATGAATGAAAGACTTTGATTCTCTAGT
GAAAGATATTTTTTTACCTATCTTTATTGGTAGATAAAACATTAAATGATGATTAACCTA
AGTGTAAAAACTAAAAAGATTTTACCAAGATATTACTGTTGTAGAAATCAATTTTTTTAA
TCATAAATCTCTTATATCCTAAAATACTAAATCTTTAAAAAGTAATGAGAAAATATTTTT
AGATTGCTTATTTGCAATTTAAAAGAAGAAAATGAGGCGACAAACAACAGAATGATTAAA
AACCATATCTACATTTGATTGTTTTATTAGTTTTTTTATCTGCTTTAAGAAACGAACCAA
ATTTATTGTTCTTAAGCTTATTTGTGACTTTCATTTGAAAGTTTTTGTTGATCAGTTATG
TATGTTAGTCTAATTAATTGATCTACTAATTCATTATTGCATTGAACAATTTTTATATTA
TTAAAATCATTAGAACTAATTAATGTGTCATTTTTTGGAATAAATATTTTTTGCTAAGTT
TAAACAA

>g11836.t4 Gene=g11836 Length=241
MYYTYSFIFGAIVMWDKPWLWDIKQCWYNYPHQSILNDVWWYYMISMAFYWSLTFSQCFD
NKRKDFWQMFIHHVLTLVLISLSWICNLHRVGSLVLIVHDFADIFLEAAKFLKYASLQKA
CDIVFGVFTVSWLVTRLGLYPRIIYSSTIEAPQILPMYPVYYIFNSLLIMLLVLHLIWTY
MILQVVVQTIKAGQMEGDVRSSSDEVSDSSENRDKPMHNGNAESPKKENHSYNNTSPKKI
N

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g11836.t4 MobiDBLite mobidb-lite consensus disorder prediction 198 241 -
22 g11836.t4 MobiDBLite mobidb-lite consensus disorder prediction 201 225 -
21 g11836.t4 MobiDBLite mobidb-lite consensus disorder prediction 226 241 -
2 g11836.t4 PANTHER PTHR12560 LONGEVITY ASSURANCE FACTOR 1 LAG1 1 228 2.9E-102
3 g11836.t4 PANTHER PTHR12560:SF56 LD18904P 1 228 2.9E-102
15 g11836.t4 PIRSF PIRSF005225 LAG1_LAC1 1 233 5.0E-78
1 g11836.t4 Pfam PF03798 TLC domain 2 183 9.6E-42
8 g11836.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 39 -
14 g11836.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 40 59 -
6 g11836.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 60 65 -
11 g11836.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 66 85 -
9 g11836.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 86 90 -
13 g11836.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 91 109 -
4 g11836.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 110 120 -
12 g11836.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 121 140 -
7 g11836.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 141 159 -
10 g11836.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 160 183 -
5 g11836.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 184 241 -
24 g11836.t4 ProSiteProfiles PS50922 TLC domain profile. 1 191 17.449
20 g11836.t4 SMART SM00724 lag1_27 1 191 2.1E-63
19 g11836.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 39 56 -
16 g11836.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 66 88 -
18 g11836.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 123 145 -
17 g11836.t4 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.

Raw TPM values