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.t6 TTS g4377.t6 1727509 1727509
chr_2 g4377 g4377.t6 isoform g4377.t6 1727745 1729115
chr_2 g4377 g4377.t6 exon g4377.t6.exon1 1727745 1728173
chr_2 g4377 g4377.t6 cds g4377.t6.CDS1 1727910 1728173
chr_2 g4377 g4377.t6 exon g4377.t6.exon2 1728231 1728491
chr_2 g4377 g4377.t6 cds g4377.t6.CDS2 1728231 1728491
chr_2 g4377 g4377.t6 exon g4377.t6.exon3 1728554 1728663
chr_2 g4377 g4377.t6 cds g4377.t6.CDS3 1728554 1728663
chr_2 g4377 g4377.t6 exon g4377.t6.exon4 1728726 1728804
chr_2 g4377 g4377.t6 cds g4377.t6.CDS4 1728726 1728780
chr_2 g4377 g4377.t6 exon g4377.t6.exon5 1728872 1728927
chr_2 g4377 g4377.t6 exon g4377.t6.exon6 1729062 1729115
chr_2 g4377 g4377.t6 TSS g4377.t6 1729348 1729348

Sequences

>g4377.t6 Gene=g4377 Length=989
ATGAGTGTTGGAGAAGCAGGTTTAGTTGGAAGTTTAGTTTGGCATAGTTCCCCAATTGGT
GTGAAGGCAATTATGCGATAATATCAAGTATTGCCGAATTCTATAATACGTTCAGCAATA
TTATCTTTATTATAATGCCTCCAATTTTAATGTATTTATTTCGTGACTATGCAAGGAAAG
TTCATCCCGGCATTCATATAGTTTGGGGTCTACTTATTTTTGTTGGTCTTGCGTCTGCAT
ATTTTCATGCAACACTGTCTTTAATGGGTCAATTACTTGATGAATTGAGTATTCTTTGGG
TCTACTCACTTACAATGGCACTCTTTTGTCCAAGAAGAAATTTGCCAAAAGTTTTTAAAA
ATCGAATTGTTTTCTCGGCACTTCTTCTTTTCATCAGTATTTTTGCATCGATTTTATCAG
TTTGGCGACCATATGTGAATGCATTTGCCTTAATGACTTTGATAATACCAACCGTATACT
TGCTTTGTTGTGAACTTGATAGAGTTAAACACAAAGACCCTGAAGTGTTTTCCCTCGGTA
TACGTTCTTTAGTATTGATGATATGCGCTGTCACTATATGGTTTAATGATAGAATGTTTT
GTGACTTTTATACATCAATGCAGATCACATATTTGCATGCGATTTGGCATGTTGCAATAT
TTCTCTCCAGCTACACGTGCTGTGTTCTTTTTGCATATTTCTATGTTCAACTCGAAAGAC
CAAAGATACATTGTAAACTAGCTTATTTCCCAGAAAATACATTAATAAGTGCATTCGGAA
TTCCTTATGTCGATTTCAAGCAACGAAAATCAATTCATGATTAAAATAATGAATTAAGAA
TGAATAATATTTTATGTGTGATCATAGTGTAGTGATAGAAGTTTAAAACTAACTTTTGTG
AACAAATCAATTCTTCCAATAGAAATAGTGTATAATTTTTTTACATGAGAATGCTTTGAT
TGCTCGGTTTTTAATTTTAAATAATTACT

>g4377.t6 Gene=g4377 Length=229
MPPILMYLFRDYARKVHPGIHIVWGLLIFVGLASAYFHATLSLMGQLLDELSILWVYSLT
MALFCPRRNLPKVFKNRIVFSALLLFISIFASILSVWRPYVNAFALMTLIIPTVYLLCCE
LDRVKHKDPEVFSLGIRSLVLMICAVTIWFNDRMFCDFYTSMQITYLHAIWHVAIFLSSY
TCCVLFAYFYVQLERPKIHCKLAYFPENTLISAFGIPYVDFKQRKSIHD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g4377.t6 PANTHER PTHR46139:SF3 ALKALINE CERAMIDASE 1 225 5.0E-74
3 g4377.t6 PANTHER PTHR46139 ALKALINE CERAMIDASE 1 225 5.0E-74
1 g4377.t6 Pfam PF05875 Ceramidase 5 208 3.7E-34
11 g4377.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 20 -
22 g4377.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 21 39 -
16 g4377.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 40 50 -
18 g4377.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 51 66 -
12 g4377.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 67 77 -
21 g4377.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 78 97 -
14 g4377.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 98 102 -
19 g4377.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 103 119 -
10 g4377.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 120 130 -
20 g4377.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 131 150 -
15 g4377.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 151 169 -
17 g4377.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 170 191 -
13 g4377.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 192 229 -
4 g4377.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 20 42 -
9 g4377.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 52 71 -
7 g4377.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 78 97 -
5 g4377.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 101 118 -
8 g4377.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 131 149 -
6 g4377.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 169 191 -

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