Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t14 TTS g4377.t14 1727509 1727509
chr_2 g4377 g4377.t14 isoform g4377.t14 1728245 1729115
chr_2 g4377 g4377.t14 exon g4377.t14.exon1 1728245 1728491
chr_2 g4377 g4377.t14 cds g4377.t14.CDS1 1728246 1728491
chr_2 g4377 g4377.t14 exon g4377.t14.exon2 1728554 1728663
chr_2 g4377 g4377.t14 cds g4377.t14.CDS2 1728554 1728663
chr_2 g4377 g4377.t14 exon g4377.t14.exon3 1728726 1728804
chr_2 g4377 g4377.t14 cds g4377.t14.CDS3 1728726 1728804
chr_2 g4377 g4377.t14 exon g4377.t14.exon4 1728872 1728927
chr_2 g4377 g4377.t14 cds g4377.t14.CDS4 1728872 1728927
chr_2 g4377 g4377.t14 exon g4377.t14.exon5 1729058 1729115
chr_2 g4377 g4377.t14 cds g4377.t14.CDS5 1729058 1729115
chr_2 g4377 g4377.t14 TSS g4377.t14 1729348 1729348

Sequences

>g4377.t14 Gene=g4377 Length=550
ATGAGTGTTGGAGAAGCAGGTTTAGTTGGAAGTTTAGTTTGGCATAGTTCCCCAGTAGAT
TGGTGTGAAGGCAATTATGCGATAATATCAAGTATTGCCGAATTCTATAATACGTTCAGC
AATATTATCTTTATTATAATGCCTCCAATTTTAATGTATTTATTTCGTGACTATGCAAGG
AAAGTTCATCCCGGCATTCATATAGTTTGGGGTCTACTTATTTTTGTTGGTCTTGCGTCT
GCATATTTTCATGCAACACTGTCTTTAATGGGTCAATTACTTGATGAATTGAGTATTCTT
TGGGTCTACTCACTTACAATGGCACTCTTTTGTCCAAGAAGAAATTTGCCAAAAGTTTTT
AAAAATCGAATTGTTTTCTCGGCACTTCTTCTTTTCATCAGTATTTTTGCATCGATTTTA
TCAGTTTGGCGACCATATGTGAATGCATTTGCCTTAATGACTTTGATAATACCAACCGTA
TACTTGCTTTGTTGTGAACTTGATAGAGTTAAACACAAAGACCCTGAAGTGTTTTCCCTC
GGTATACGTT

>g4377.t14 Gene=g4377 Length=183
MSVGEAGLVGSLVWHSSPVDWCEGNYAIISSIAEFYNTFSNIIFIIMPPILMYLFRDYAR
KVHPGIHIVWGLLIFVGLASAYFHATLSLMGQLLDELSILWVYSLTMALFCPRRNLPKVF
KNRIVFSALLLFISIFASILSVWRPYVNAFALMTLIIPTVYLLCCELDRVKHKDPEVFSL
GIR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g4377.t14 PANTHER PTHR46139:SF3 ALKALINE CERAMIDASE 12 181 8.2E-62
3 g4377.t14 PANTHER PTHR46139 ALKALINE CERAMIDASE 12 181 8.2E-62
1 g4377.t14 Pfam PF05875 Ceramidase 15 174 1.3E-37
12 g4377.t14 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 34 -
16 g4377.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 35 55 -
10 g4377.t14 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 56 66 -
18 g4377.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 67 85 -
13 g4377.t14 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 86 96 -
17 g4377.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 97 112 -
11 g4377.t14 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 113 123 -
15 g4377.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 124 143 -
14 g4377.t14 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 144 148 -
19 g4377.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 149 167 -
9 g4377.t14 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 168 183 -
8 g4377.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 33 55 -
7 g4377.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 68 87 -
6 g4377.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 97 111 -
5 g4377.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 124 143 -
4 g4377.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 147 164 -

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

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