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.t4 TTS g4377.t4 1727509 1727509
chr_2 g4377 g4377.t4 isoform g4377.t4 1727745 1729115
chr_2 g4377 g4377.t4 exon g4377.t4.exon1 1727745 1728173
chr_2 g4377 g4377.t4 cds g4377.t4.CDS1 1727910 1728173
chr_2 g4377 g4377.t4 exon g4377.t4.exon2 1728231 1728491
chr_2 g4377 g4377.t4 cds g4377.t4.CDS2 1728231 1728491
chr_2 g4377 g4377.t4 exon g4377.t4.exon3 1728554 1728804
chr_2 g4377 g4377.t4 cds g4377.t4.CDS3 1728554 1728589
chr_2 g4377 g4377.t4 exon g4377.t4.exon4 1728872 1728927
chr_2 g4377 g4377.t4 exon g4377.t4.exon5 1729058 1729115
chr_2 g4377 g4377.t4 TSS g4377.t4 1729348 1729348

Sequences

>g4377.t4 Gene=g4377 Length=1055
ATGAGTGTTGGAGAAGCAGGTTTAGTTGGAAGTTTAGTTTGGCATAGTTCCCCAGTAGAT
TGGTGTGAAGGCAATTATGCGATAATATCAAGTATTGCCGAATTCTATAATACGTTCAGC
AATATTATCTTTATTATAATGCCTCCAATTTTAATGTATTTATTTCGTGACTATGCAAGG
AAAGTTCATCCCGGTCAGTCACTTTTCTTAAATATAAATTAATCTTTTAAATTAAATTGA
TATTATTGATTGTAGGCATTCATATAGTTTGGGGTCTACTTATTTTTGTTGGTCTTGCGT
CTGCATATTTTCATGCAACACTGTCTTTAATGGGTCAATTACTTGATGAATTGAGTATTC
TTTGGGTCTACTCACTTACAATGGCACTCTTTTGTCCAAGAAGAAATTTGCCAAAAGTTT
TTAAAAATCGAATTGTTTTCTCGGCACTTCTTCTTTTCATCAGTATTTTTGCATCGATTT
TATCAGTTTGGCGACCATATGTGAATGCATTTGCCTTAATGACTTTGATAATACCAACCG
TATACTTGCTTTGTTGTGAACTTGATAGAGTTAAACACAAAGACCCTGAAGTGTTTTCCC
TCGGTATACGTTCTTTAGTATTGATGATATGCGCTGTCACTATATGGTTTAATGATAGAA
TGTTTTGTGACTTTTATACATCAATGCAGATCACATATTTGCATGCGATTTGGCATGTTG
CAATATTTCTCTCCAGCTACACGTGCTGTGTTCTTTTTGCATATTTCTATGTTCAACTCG
AAAGACCAAAGATACATTGTAAACTAGCTTATTTCCCAGAAAATACATTAATAAGTGCAT
TCGGAATTCCTTATGTCGATTTCAAGCAACGAAAATCAATTCATGATTAAAATAATGAAT
TAAGAATGAATAATATTTTATGTGTGATCATAGTGTAGTGATAGAAGTTTAAAACTAACT
TTTGTGAACAAATCAATTCTTCCAATAGAAATAGTGTATAATTTTTTTACATGAGAATGC
TTTGATTGCTCGGTTTTTAATTTTAAATAATTACT

>g4377.t4 Gene=g4377 Length=186
MGQLLDELSILWVYSLTMALFCPRRNLPKVFKNRIVFSALLLFISIFASILSVWRPYVNA
FALMTLIIPTVYLLCCELDRVKHKDPEVFSLGIRSLVLMICAVTIWFNDRMFCDFYTSMQ
ITYLHAIWHVAIFLSSYTCCVLFAYFYVQLERPKIHCKLAYFPENTLISAFGIPYVDFKQ
RKSIHD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g4377.t4 PANTHER PTHR46139:SF3 ALKALINE CERAMIDASE 1 182 7.3E-52
3 g4377.t4 PANTHER PTHR46139 ALKALINE CERAMIDASE 1 182 7.3E-52
1 g4377.t4 Pfam PF05875 Ceramidase 2 165 2.2E-23
14 g4377.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
18 g4377.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 23 -
9 g4377.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 24 34 -
16 g4377.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 35 54 -
13 g4377.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 55 59 -
19 g4377.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 60 76 -
11 g4377.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 77 87 -
15 g4377.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 88 107 -
12 g4377.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 108 126 -
17 g4377.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 127 148 -
10 g4377.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 149 186 -
8 g4377.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 10 28 -
5 g4377.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 35 54 -
4 g4377.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 58 75 -
7 g4377.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 88 106 -
6 g4377.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 126 148 -

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