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.t12 TTS g4377.t12 1727509 1727509
chr_2 g4377 g4377.t12 isoform g4377.t12 1727910 1729115
chr_2 g4377 g4377.t12 exon g4377.t12.exon1 1727910 1728173
chr_2 g4377 g4377.t12 cds g4377.t12.CDS1 1727910 1728173
chr_2 g4377 g4377.t12 exon g4377.t12.exon2 1728231 1728491
chr_2 g4377 g4377.t12 cds g4377.t12.CDS2 1728231 1728491
chr_2 g4377 g4377.t12 exon g4377.t12.exon3 1728554 1728663
chr_2 g4377 g4377.t12 cds g4377.t12.CDS3 1728554 1728663
chr_2 g4377 g4377.t12 exon g4377.t12.exon4 1728722 1728927
chr_2 g4377 g4377.t12 cds g4377.t12.CDS4 1728722 1728746
chr_2 g4377 g4377.t12 exon g4377.t12.exon5 1729058 1729115
chr_2 g4377 g4377.t12 TSS g4377.t12 1729348 1729348

Sequences

>g4377.t12 Gene=g4377 Length=899
ATGAGTGTTGGAGAAGCAGGTTTAGTTGGAAGTTTAGTTTGGCATAGTTCCCCAGTAGAT
TGGTGTGAAGGCAATTATGCGATAATATCAAGTATTGCCGAATTCTATAATACGGTAATC
TTTTTTAAATTTTTAGGAAATTACCTATTTCAGAAATTAATGAAATTTTTTTTATTTATA
GTTCAGCAATATTATCTTTATTATAATGCCTCCAATTTTAATGTATTTATTTCGTGACTA
TGCAAGGAAAGTTCATCCCGGTCAGCATTCATATAGTTTGGGGTCTACTTATTTTTGTTG
GTCTTGCGTCTGCATATTTTCATGCAACACTGTCTTTAATGGGTCAATTACTTGATGAAT
TGAGTATTCTTTGGGTCTACTCACTTACAATGGCACTCTTTTGTCCAAGAAGAAATTTGC
CAAAAGTTTTTAAAAATCGAATTGTTTTCTCGGCACTTCTTCTTTTCATCAGTATTTTTG
CATCGATTTTATCAGTTTGGCGACCATATGTGAATGCATTTGCCTTAATGACTTTGATAA
TACCAACCGTATACTTGCTTTGTTGTGAACTTGATAGAGTTAAACACAAAGACCCTGAAG
TGTTTTCCCTCGGTATACGTTCTTTAGTATTGATGATATGCGCTGTCACTATATGGTTTA
ATGATAGAATGTTTTGTGACTTTTATACATCAATGCAGATCACATATTTGCATGCGATTT
GGCATGTTGCAATATTTCTCTCCAGCTACACGTGCTGTGTTCTTTTTGCATATTTCTATG
TTCAACTCGAAAGACCAAAGATACATTGTAAACTAGCTTATTTCCCAGAAAATACATTAA
TAAGTGCATTCGGAATTCCTTATGTCGATTTCAAGCAACGAAAATCAATTCATGATTAA

>g4377.t12 Gene=g4377 Length=219
MQGKFIPVSIHIVWGLLIFVGLASAYFHATLSLMGQLLDELSILWVYSLTMALFCPRRNL
PKVFKNRIVFSALLLFISIFASILSVWRPYVNAFALMTLIIPTVYLLCCELDRVKHKDPE
VFSLGIRSLVLMICAVTIWFNDRMFCDFYTSMQITYLHAIWHVAIFLSSYTCCVLFAYFY
VQLERPKIHCKLAYFPENTLISAFGIPYVDFKQRKSIHD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g4377.t12 PANTHER PTHR46139:SF3 ALKALINE CERAMIDASE 6 215 1.8E-66
3 g4377.t12 PANTHER PTHR46139 ALKALINE CERAMIDASE 6 215 1.8E-66
1 g4377.t12 Pfam PF05875 Ceramidase 9 198 4.4E-33
10 g4377.t12 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
21 g4377.t12 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 31 -
14 g4377.t12 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 32 36 -
22 g4377.t12 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 37 56 -
13 g4377.t12 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 57 67 -
20 g4377.t12 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 68 87 -
16 g4377.t12 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 88 92 -
17 g4377.t12 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 93 109 -
12 g4377.t12 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 110 120 -
18 g4377.t12 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 121 140 -
15 g4377.t12 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 141 159 -
19 g4377.t12 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 160 181 -
11 g4377.t12 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 182 219 -
9 g4377.t12 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 5 27 -
8 g4377.t12 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 37 56 -
7 g4377.t12 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 68 87 -
6 g4377.t12 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 91 108 -
5 g4377.t12 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 121 139 -
4 g4377.t12 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 159 181 -

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