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.t11 TTS g4377.t11 1727509 1727509
chr_2 g4377 g4377.t11 isoform g4377.t11 1727910 1729115
chr_2 g4377 g4377.t11 exon g4377.t11.exon1 1727910 1728173
chr_2 g4377 g4377.t11 cds g4377.t11.CDS1 1727910 1728173
chr_2 g4377 g4377.t11 exon g4377.t11.exon2 1728231 1728453
chr_2 g4377 g4377.t11 cds g4377.t11.CDS2 1728231 1728338
chr_2 g4377 g4377.t11 exon g4377.t11.exon3 1728565 1728663
chr_2 g4377 g4377.t11 exon g4377.t11.exon4 1728726 1728799
chr_2 g4377 g4377.t11 exon g4377.t11.exon5 1729058 1729115
chr_2 g4377 g4377.t11 TSS g4377.t11 1729348 1729348

Sequences

>g4377.t11 Gene=g4377 Length=718
ATGAGTGTTGGAGAAGCAGGTTTAGTTGGAAGTTTAGTTTGGCATAGTTCCCCAGTAGCA
ATATTATCTTTATTATAATGCCTCCAATTTTAATGTATTTATTTCGTGACTATGCAAGGA
AAGTTCATCCCGGCATTCATATAGTTTGGGGTCTACTTATTTTTGTTGGTCTTGCGTCTG
CATATTTTCATGCAACACTGTCTTTAATGGGTCAATTACTTGATGAATTGAAAATTTGCC
AAAAGTTTTTAAAAATCGAATTGTTTTCTCGGCACTTCTTCTTTTCATCAGTATTTTTGC
ATCGATTTTATCAGTTTGGCGACCATATGTGAATGCATTTGCCTTAATGACTTTGATAAT
ACCAACCGTATACTTGCTTTGTTGTGAACTTGATAGAGTTAAACACAAAGACCCTGAAGT
GTTTTCCCTCGGTATACGTTCTTTAGTATTGATGATATGCGCTGTCACTATATGGTTTAA
TGATAGAATGTTTTGTGACTTTTATACATCAATGCAGATCACATATTTGCATGCGATTTG
GCATGTTGCAATATTTCTCTCCAGCTACACGTGCTGTGTTCTTTTTGCATATTTCTATGT
TCAACTCGAAAGACCAAAGATACATTGTAAACTAGCTTATTTCCCAGAAAATACATTAAT
AAGTGCATTCGGAATTCCTTATGTCGATTTCAAGCAACGAAAATCAATTCATGATTAA

>g4377.t11 Gene=g4377 Length=123
MTLIIPTVYLLCCELDRVKHKDPEVFSLGIRSLVLMICAVTIWFNDRMFCDFYTSMQITY
LHAIWHVAIFLSSYTCCVLFAYFYVQLERPKIHCKLAYFPENTLISAFGIPYVDFKQRKS
IHD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g4377.t11 PANTHER PTHR46139:SF3 ALKALINE CERAMIDASE 1 119 9.3E-31
3 g4377.t11 PANTHER PTHR46139 ALKALINE CERAMIDASE 1 119 9.3E-31
1 g4377.t11 Pfam PF05875 Ceramidase 7 103 6.3E-14
7 g4377.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 24 -
10 g4377.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 25 44 -
8 g4377.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 45 63 -
9 g4377.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 64 85 -
6 g4377.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 86 123 -
4 g4377.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 25 43 -
5 g4377.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 63 85 -

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. There were no conditions that were differentially expressed