General information for g4377.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Alkaline ceramidase.
Parent gene
- The parent gene g4377 is located on chr_2: 1728882..1729115 (- strand)
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.t1 | TTS | g4377.t1 | 1727509 | 1727509 |
| chr_2 | g4377 | g4377.t1 | isoform | g4377.t1 | 1727910 | 1729115 |
| chr_2 | g4377 | g4377.t1 | exon | g4377.t1.exon1 | 1727910 | 1728173 |
| chr_2 | g4377 | g4377.t1 | cds | g4377.t1.CDS1 | 1727910 | 1728173 |
| chr_2 | g4377 | g4377.t1 | exon | g4377.t1.exon2 | 1728231 | 1728491 |
| chr_2 | g4377 | g4377.t1 | cds | g4377.t1.CDS2 | 1728231 | 1728491 |
| chr_2 | g4377 | g4377.t1 | exon | g4377.t1.exon3 | 1728554 | 1728663 |
| chr_2 | g4377 | g4377.t1 | cds | g4377.t1.CDS3 | 1728554 | 1728663 |
| chr_2 | g4377 | g4377.t1 | exon | g4377.t1.exon4 | 1728726 | 1728804 |
| chr_2 | g4377 | g4377.t1 | cds | g4377.t1.CDS4 | 1728726 | 1728804 |
| chr_2 | g4377 | g4377.t1 | exon | g4377.t1.exon5 | 1728872 | 1728927 |
| chr_2 | g4377 | g4377.t1 | cds | g4377.t1.CDS5 | 1728872 | 1728927 |
| chr_2 | g4377 | g4377.t1 | exon | g4377.t1.exon6 | 1729058 | 1729115 |
| chr_2 | g4377 | g4377.t1 | cds | g4377.t1.CDS6 | 1729058 | 1729115 |
| chr_2 | g4377 | g4377.t1 | TSS | g4377.t1 | 1729348 | 1729348 |
Sequences
>g4377.t1 Gene=g4377 Length=828
ATGAGTGTTGGAGAAGCAGGTTTAGTTGGAAGTTTAGTTTGGCATAGTTCCCCAGTAGAT
TGGTGTGAAGGCAATTATGCGATAATATCAAGTATTGCCGAATTCTATAATACGTTCAGC
AATATTATCTTTATTATAATGCCTCCAATTTTAATGTATTTATTTCGTGACTATGCAAGG
AAAGTTCATCCCGGCATTCATATAGTTTGGGGTCTACTTATTTTTGTTGGTCTTGCGTCT
GCATATTTTCATGCAACACTGTCTTTAATGGGTCAATTACTTGATGAATTGAGTATTCTT
TGGGTCTACTCACTTACAATGGCACTCTTTTGTCCAAGAAGAAATTTGCCAAAAGTTTTT
AAAAATCGAATTGTTTTCTCGGCACTTCTTCTTTTCATCAGTATTTTTGCATCGATTTTA
TCAGTTTGGCGACCATATGTGAATGCATTTGCCTTAATGACTTTGATAATACCAACCGTA
TACTTGCTTTGTTGTGAACTTGATAGAGTTAAACACAAAGACCCTGAAGTGTTTTCCCTC
GGTATACGTTCTTTAGTATTGATGATATGCGCTGTCACTATATGGTTTAATGATAGAATG
TTTTGTGACTTTTATACATCAATGCAGATCACATATTTGCATGCGATTTGGCATGTTGCA
ATATTTCTCTCCAGCTACACGTGCTGTGTTCTTTTTGCATATTTCTATGTTCAACTCGAA
AGACCAAAGATACATTGTAAACTAGCTTATTTCCCAGAAAATACATTAATAAGTGCATTC
GGAATTCCTTATGTCGATTTCAAGCAACGAAAATCAATTCATGATTAA
>g4377.t1 Gene=g4377 Length=275
MSVGEAGLVGSLVWHSSPVDWCEGNYAIISSIAEFYNTFSNIIFIIMPPILMYLFRDYAR
KVHPGIHIVWGLLIFVGLASAYFHATLSLMGQLLDELSILWVYSLTMALFCPRRNLPKVF
KNRIVFSALLLFISIFASILSVWRPYVNAFALMTLIIPTVYLLCCELDRVKHKDPEVFSL
GIRSLVLMICAVTIWFNDRMFCDFYTSMQITYLHAIWHVAIFLSSYTCCVLFAYFYVQLE
RPKIHCKLAYFPENTLISAFGIPYVDFKQRKSIHD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g4377.t1 | PANTHER | PTHR46139:SF3 | ALKALINE CERAMIDASE | 12 | 271 | 7.9E-94 |
| 3 | g4377.t1 | PANTHER | PTHR46139 | ALKALINE CERAMIDASE | 12 | 271 | 7.9E-94 |
| 1 | g4377.t1 | Pfam | PF05875 | Ceramidase | 15 | 254 | 2.9E-51 |
| 15 | g4377.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 34 | - |
| 20 | g4377.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 35 | 55 | - |
| 11 | g4377.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 56 | 66 | - |
| 25 | g4377.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 67 | 85 | - |
| 16 | g4377.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 86 | 96 | - |
| 24 | g4377.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 97 | 112 | - |
| 13 | g4377.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 113 | 123 | - |
| 19 | g4377.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 124 | 143 | - |
| 18 | g4377.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 144 | 148 | - |
| 23 | g4377.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 149 | 165 | - |
| 14 | g4377.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 166 | 176 | - |
| 21 | g4377.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 177 | 196 | - |
| 17 | g4377.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 197 | 215 | - |
| 22 | g4377.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 216 | 237 | - |
| 12 | g4377.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 238 | 275 | - |
| 10 | g4377.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 33 | 55 | - |
| 8 | g4377.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 68 | 87 | - |
| 7 | g4377.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 97 | 111 | - |
| 5 | g4377.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 124 | 143 | - |
| 4 | g4377.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 147 | 164 | - |
| 6 | g4377.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 177 | 195 | - |
| 9 | g4377.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 215 | 237 | - |
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 transcript has been annotated with K01441 (alkaline ceramidase)
Pathway
- This transcript belongs to the following pathways
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.
