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.t2 isoform g4377.t2 1727256 1728481
chr_2 g4377 g4377.t2 exon g4377.t2.exon1 1727256 1728173
chr_2 g4377 g4377.t2 cds g4377.t2.CDS1 1727910 1728173
chr_2 g4377 g4377.t2 exon g4377.t2.exon2 1728231 1728481
chr_2 g4377 g4377.t2 cds g4377.t2.CDS2 1728231 1728476
chr_2 g4377 g4377.t2 TSS g4377.t2 1729348 1729348
chr_2 g4377 g4377.t2 TTS g4377.t2 NA NA

Sequences

>g4377.t2 Gene=g4377 Length=1169
TTACAATGGCACTCTTTTGTCCAAGAAGAAATTTGCCAAAAGTTTTTAAAAATCGAATTG
TTTTCTCGGCACTTCTTCTTTTCATCAGTATTTTTGCATCGATTTTATCAGTTTGGCGAC
CATATGTGAATGCATTTGCCTTAATGACTTTGATAATACCAACCGTATACTTGCTTTGTT
GTGAACTTGATAGAGTTAAACACAAAGACCCTGAAGTGTTTTCCCTCGGTATACGTTCTT
TAGTATTGATGATATGCGCTGTCACTATATGGTTTAATGATAGAATGTTTTGTGACTTTT
ATACATCAATGCAGATCACATATTTGCATGCGATTTGGCATGTTGCAATATTTCTCTCCA
GCTACACGTGCTGTGTTCTTTTTGCATATTTCTATGTTCAACTCGAAAGACCAAAGATAC
ATTGTAAACTAGCTTATTTCCCAGAAAATACATTAATAAGTGCATTCGGAATTCCTTATG
TCGATTTCAAGCAACGAAAATCAATTCATGATTAAAATAATGAATTAAGAATGAATAATA
TTTTATGTGTGATCATAGTGTAGTGATAGAAGTTTAAAACTAACTTTTGTGAACAAATCA
ATTCTTCCAATAGAAATAGTGTATAATTTTTTTACATGAGAATGCTTTGATTGCTCGGTT
TTTAATTTTAAATAATTACTTAAATAATAGGTTTAAAGAATTTATTTTTCGTTTGTATGT
GATAGATGATAATACACTTTACCTTGAGTCAATATTTGTAACACAGCATCAAAATATTTA
ATACGTAGATACATACATCACTGACAGGATTTTGAAATGAAAAGTGACTTTAGAGGTGAT
AAGAAAATTAACGCTTAAATGCATTCTTTTTATTTAAAGAATCAGAAATAAAAAGCAAAT
AAAAATTTTATAAAGTATTTTTTAGTTTTATTTTATCGATTAATATAATTATATAAGAGA
TTACAGATGTGCAACAGTATAAATTGCAATATAAGCATTAAACAAGTATATAGAATGTAA
TTTTAAAATATAAATAATCACACGCGACCTTTGACGTGACGTGATAGTCATAAATTTTAC
CAGATTCGCAATTCGTTTTATTAACGTGATTATGATTACTAAATTTAGATGTGCTGATAA
CATATTCATTCATCAGAAAATTAAATGAT

>g4377.t2 Gene=g4377 Length=169
MALFCPRRNLPKVFKNRIVFSALLLFISIFASILSVWRPYVNAFALMTLIIPTVYLLCCE
LDRVKHKDPEVFSLGIRSLVLMICAVTIWFNDRMFCDFYTSMQITYLHAIWHVAIFLSSY
TCCVLFAYFYVQLERPKIHCKLAYFPENTLISAFGIPYVDFKQRKSIHD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g4377.t2 PANTHER PTHR46139:SF3 ALKALINE CERAMIDASE 1 165 6.4E-43
3 g4377.t2 PANTHER PTHR46139 ALKALINE CERAMIDASE 1 165 6.4E-43
1 g4377.t2 Pfam PF05875 Ceramidase 13 148 1.1E-17
10 g4377.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 17 -
15 g4377.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 18 37 -
11 g4377.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 38 42 -
16 g4377.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 43 59 -
9 g4377.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 60 70 -
14 g4377.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 71 90 -
12 g4377.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 91 109 -
13 g4377.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 110 131 -
8 g4377.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 132 169 -
4 g4377.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 35 -
6 g4377.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 40 59 -
7 g4377.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 71 89 -
5 g4377.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 109 131 -

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