Gene loci information

Transcript annotation

  • This transcript has been annotated as Alkaline ceramidase.

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_2 g4377 g4377.t7 TTS g4377.t7 1727509 1727509
chr_2 g4377 g4377.t7 isoform g4377.t7 1727745 1729115
chr_2 g4377 g4377.t7 exon g4377.t7.exon1 1727745 1728173
chr_2 g4377 g4377.t7 cds g4377.t7.CDS1 1727910 1728173
chr_2 g4377 g4377.t7 exon g4377.t7.exon2 1728231 1728491
chr_2 g4377 g4377.t7 cds g4377.t7.CDS2 1728231 1728491
chr_2 g4377 g4377.t7 exon g4377.t7.exon3 1728554 1728663
chr_2 g4377 g4377.t7 cds g4377.t7.CDS3 1728554 1728663
chr_2 g4377 g4377.t7 exon g4377.t7.exon4 1728726 1728804
chr_2 g4377 g4377.t7 cds g4377.t7.CDS4 1728726 1728804
chr_2 g4377 g4377.t7 exon g4377.t7.exon5 1728872 1728927
chr_2 g4377 g4377.t7 cds g4377.t7.CDS5 1728872 1728927
chr_2 g4377 g4377.t7 exon g4377.t7.exon6 1729085 1729115
chr_2 g4377 g4377.t7 cds g4377.t7.CDS6 1729085 1729115
chr_2 g4377 g4377.t7 TSS g4377.t7 1729348 1729348

Sequences

>g4377.t7 Gene=g4377 Length=966
ATGAGTGTTGGAGAAGCAGGTTTAGTTGGAAATTGGTGTGAAGGCAATTATGCGATAATA
TCAAGTATTGCCGAATTCTATAATACGTTCAGCAATATTATCTTTATTATAATGCCTCCA
ATTTTAATGTATTTATTTCGTGACTATGCAAGGAAAGTTCATCCCGGCATTCATATAGTT
TGGGGTCTACTTATTTTTGTTGGTCTTGCGTCTGCATATTTTCATGCAACACTGTCTTTA
ATGGGTCAATTACTTGATGAATTGAGTATTCTTTGGGTCTACTCACTTACAATGGCACTC
TTTTGTCCAAGAAGAAATTTGCCAAAAGTTTTTAAAAATCGAATTGTTTTCTCGGCACTT
CTTCTTTTCATCAGTATTTTTGCATCGATTTTATCAGTTTGGCGACCATATGTGAATGCA
TTTGCCTTAATGACTTTGATAATACCAACCGTATACTTGCTTTGTTGTGAACTTGATAGA
GTTAAACACAAAGACCCTGAAGTGTTTTCCCTCGGTATACGTTCTTTAGTATTGATGATA
TGCGCTGTCACTATATGGTTTAATGATAGAATGTTTTGTGACTTTTATACATCAATGCAG
ATCACATATTTGCATGCGATTTGGCATGTTGCAATATTTCTCTCCAGCTACACGTGCTGT
GTTCTTTTTGCATATTTCTATGTTCAACTCGAAAGACCAAAGATACATTGTAAACTAGCT
TATTTCCCAGAAAATACATTAATAAGTGCATTCGGAATTCCTTATGTCGATTTCAAGCAA
CGAAAATCAATTCATGATTAAAATAATGAATTAAGAATGAATAATATTTTATGTGTGATC
ATAGTGTAGTGATAGAAGTTTAAAACTAACTTTTGTGAACAAATCAATTCTTCCAATAGA
AATAGTGTATAATTTTTTTACATGAGAATGCTTTGATTGCTCGGTTTTTAATTTTAAATA
ATTACT

>g4377.t7 Gene=g4377 Length=266
MSVGEAGLVGNWCEGNYAIISSIAEFYNTFSNIIFIIMPPILMYLFRDYARKVHPGIHIV
WGLLIFVGLASAYFHATLSLMGQLLDELSILWVYSLTMALFCPRRNLPKVFKNRIVFSAL
LLFISIFASILSVWRPYVNAFALMTLIIPTVYLLCCELDRVKHKDPEVFSLGIRSLVLMI
CAVTIWFNDRMFCDFYTSMQITYLHAIWHVAIFLSSYTCCVLFAYFYVQLERPKIHCKLA
YFPENTLISAFGIPYVDFKQRKSIHD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g4377.t7 PANTHER PTHR46139:SF3 ALKALINE CERAMIDASE 11 262 9.8E-91
3 g4377.t7 PANTHER PTHR46139 ALKALINE CERAMIDASE 11 262 9.8E-91
1 g4377.t7 Pfam PF05875 Ceramidase 11 245 1.9E-49
18 g4377.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 25 -
25 g4377.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 26 46 -
11 g4377.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 47 57 -
24 g4377.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 58 76 -
17 g4377.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 77 87 -
23 g4377.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 88 103 -
13 g4377.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 104 114 -
22 g4377.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 115 134 -
16 g4377.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 135 139 -
21 g4377.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 140 156 -
12 g4377.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 157 167 -
20 g4377.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 168 187 -
15 g4377.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 188 206 -
19 g4377.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 207 228 -
14 g4377.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 229 266 -
8 g4377.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 24 46 -
9 g4377.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 59 78 -
6 g4377.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 88 102 -
10 g4377.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 115 134 -
7 g4377.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 138 155 -
5 g4377.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 168 186 -
4 g4377.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 206 228 -

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:0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides MF
GO:0016021 integral component of membrane CC
GO:0006672 ceramide metabolic process BP

KEGG

Orthology

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. There were no conditions that were differentially expressed