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.t5 TTS g4377.t5 1727509 1727509
chr_2 g4377 g4377.t5 isoform g4377.t5 1727745 1729115
chr_2 g4377 g4377.t5 exon g4377.t5.exon1 1727745 1728173
chr_2 g4377 g4377.t5 cds g4377.t5.CDS1 1727910 1728173
chr_2 g4377 g4377.t5 exon g4377.t5.exon2 1728231 1728491
chr_2 g4377 g4377.t5 cds g4377.t5.CDS2 1728231 1728491
chr_2 g4377 g4377.t5 exon g4377.t5.exon3 1728554 1728651
chr_2 g4377 g4377.t5 cds g4377.t5.CDS3 1728554 1728651
chr_2 g4377 g4377.t5 exon g4377.t5.exon4 1728726 1728832
chr_2 g4377 g4377.t5 cds g4377.t5.CDS4 1728726 1728780
chr_2 g4377 g4377.t5 exon g4377.t5.exon5 1729041 1729115
chr_2 g4377 g4377.t5 TSS g4377.t5 1729348 1729348

Sequences

>g4377.t5 Gene=g4377 Length=970
ATGAGTGTTGGAGAAGCAGGTTTAGTTGGAAGTTTAGTTTGGCATAGTTCCCCAGTAGGT
ACGTAAAATTTATAAAAATTAATGAAATTTTTTTTATTTATAGTTCAGCAATATTATCTT
TATTATAATGCCTCCAATTTTAATGTATTTATTTCGTGACTATGCAAGGAAAGTTCATCC
CGTTTGGGGTCTACTTATTTTTGTTGGTCTTGCGTCTGCATATTTTCATGCAACACTGTC
TTTAATGGGTCAATTACTTGATGAATTGAGTATTCTTTGGGTCTACTCACTTACAATGGC
ACTCTTTTGTCCAAGAAGAAATTTGCCAAAAGTTTTTAAAAATCGAATTGTTTTCTCGGC
ACTTCTTCTTTTCATCAGTATTTTTGCATCGATTTTATCAGTTTGGCGACCATATGTGAA
TGCATTTGCCTTAATGACTTTGATAATACCAACCGTATACTTGCTTTGTTGTGAACTTGA
TAGAGTTAAACACAAAGACCCTGAAGTGTTTTCCCTCGGTATACGTTCTTTAGTATTGAT
GATATGCGCTGTCACTATATGGTTTAATGATAGAATGTTTTGTGACTTTTATACATCAAT
GCAGATCACATATTTGCATGCGATTTGGCATGTTGCAATATTTCTCTCCAGCTACACGTG
CTGTGTTCTTTTTGCATATTTCTATGTTCAACTCGAAAGACCAAAGATACATTGTAAACT
AGCTTATTTCCCAGAAAATACATTAATAAGTGCATTCGGAATTCCTTATGTCGATTTCAA
GCAACGAAAATCAATTCATGATTAAAATAATGAATTAAGAATGAATAATATTTTATGTGT
GATCATAGTGTAGTGATAGAAGTTTAAAACTAACTTTTGTGAACAAATCAATTCTTCCAA
TAGAAATAGTGTATAATTTTTTTACATGAGAATGCTTTGATTGCTCGGTTTTTAATTTTA
AATAATTACT

>g4377.t5 Gene=g4377 Length=225
MPPILMYLFRDYARKVHPVWGLLIFVGLASAYFHATLSLMGQLLDELSILWVYSLTMALF
CPRRNLPKVFKNRIVFSALLLFISIFASILSVWRPYVNAFALMTLIIPTVYLLCCELDRV
KHKDPEVFSLGIRSLVLMICAVTIWFNDRMFCDFYTSMQITYLHAIWHVAIFLSSYTCCV
LFAYFYVQLERPKIHCKLAYFPENTLISAFGIPYVDFKQRKSIHD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g4377.t5 PANTHER PTHR46139:SF3 ALKALINE CERAMIDASE 1 221 1.6E-69
3 g4377.t5 PANTHER PTHR46139 ALKALINE CERAMIDASE 1 221 1.6E-69
1 g4377.t5 Pfam PF05875 Ceramidase 13 204 2.9E-33
10 g4377.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 19 -
19 g4377.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 20 37 -
15 g4377.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 38 42 -
18 g4377.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 43 62 -
13 g4377.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 63 73 -
22 g4377.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 74 93 -
14 g4377.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 94 98 -
20 g4377.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 99 115 -
12 g4377.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 116 126 -
21 g4377.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 127 146 -
16 g4377.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 147 165 -
17 g4377.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 166 187 -
11 g4377.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 188 225 -
6 g4377.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 20 37 -
9 g4377.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 47 61 -
8 g4377.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 74 93 -
4 g4377.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 97 114 -
5 g4377.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 127 145 -
7 g4377.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 165 187 -

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