General information for g1883.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Sphingomyelin phosphodiesterase.
Parent gene
- The parent gene g1883 is located on chr_3: 13643439..13644848 (+ 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_3 | g1883 | g1883.t2 | isoform | g1883.t2 | 13642779 | 13644442 |
| chr_3 | g1883 | g1883.t2 | exon | g1883.t2.exon1 | 13642779 | 13642856 |
| chr_3 | g1883 | g1883.t2 | cds | g1883.t2.CDS1 | 13642779 | 13642856 |
| chr_3 | g1883 | g1883.t2 | exon | g1883.t2.exon2 | 13642932 | 13643446 |
| chr_3 | g1883 | g1883.t2 | cds | g1883.t2.CDS2 | 13642932 | 13643446 |
| chr_3 | g1883 | g1883.t2 | exon | g1883.t2.exon3 | 13643504 | 13643739 |
| chr_3 | g1883 | g1883.t2 | cds | g1883.t2.CDS3 | 13643504 | 13643739 |
| chr_3 | g1883 | g1883.t2 | exon | g1883.t2.exon4 | 13643798 | 13644008 |
| chr_3 | g1883 | g1883.t2 | cds | g1883.t2.CDS4 | 13643798 | 13644008 |
| chr_3 | g1883 | g1883.t2 | exon | g1883.t2.exon5 | 13644061 | 13644243 |
| chr_3 | g1883 | g1883.t2 | cds | g1883.t2.CDS5 | 13644061 | 13644243 |
| chr_3 | g1883 | g1883.t2 | exon | g1883.t2.exon6 | 13644424 | 13644442 |
| chr_3 | g1883 | g1883.t2 | cds | g1883.t2.CDS6 | 13644424 | 13644442 |
| chr_3 | g1883 | g1883.t2 | TTS | g1883.t2 | 13644869 | 13644869 |
| chr_3 | g1883 | g1883.t2 | TSS | g1883.t2 | NA | NA |
Sequences
>g1883.t2 Gene=g1883 Length=1242
ATGCAAATTTCTCTAAAGAAAGCTTTACAACAAATAAAATATTTTCAGGGTGACTATAGA
AAATGCGATAGCCCAAAACGTATGATAGATCACATGTACAAACATATTGCTGAAACGCAT
TCAGATATTGATTATATTTTATGGACCGGTGATCTTCCTCCACATGACATTTGGAATCAA
ACTAAAGAAGAAAATTTAAAAGTTCTTAAAGAAACTGTGAAGCAAATGGCTGAAGTATTT
CCTGGAATTCCAATTTTTCCAGCTCTTGGTAATCATGAAAGTGCGCCAGTTAATAGCTTT
CCACCACCATATGTTCAACAAGTTGATAGTTCAATAGCTTGGCTCTATGATGCTTTGGCA
GAAGAATGGCAAAAATGGTTACCACCATCTGTCTCATATACAATCAAAAGAGGAGCTTTT
TATTCAGTACTTGTTCGACCTGGCTTTAGGATCATTTCTATCAATATGAATTATTGTAAT
AACAAAAATTGGTGGCTGCTTCTTAATTCAACTGATCCAGCTACTCAATTACAATGGATT
ATTTATGAACTTCAAAGTGCTGAATTTTCAAACGAAAAAGTTCATATTATTGGTCATATT
CCTCCAGGACATGCAGATTGTTTAAAGATTTGGAGTAGAAATTATTATAAAATCGTTCAG
CGATATGAGAGCACAATTACTGCTCAATTCTTCGGTCATACACATTTTGATGAATTTGAA
GTCTTCTATGACTCAAATGATGTATCTCGTCCCACAAATATTGCTTATATTGGACCCAGT
GTGACTCCATATTATGATTTAAATCCTGGATATCGAATCTATTATATTGATGGTGATCAT
GATGCAACCACAAGATTAGTAATTGATCATGAAACTTGGATTATGAATCTCAAAGAAGCG
AATCTCTATGATTTTCCAATTTATTATAAACTTTATTCAACTCGTGCTGCATACAATCTT
AAAGCACTTAGACCATCTGATTGGGATGAATTAATTAATTCAATGACTGATGATCAAGAT
AAATTTGATCTTTATTATAAACATTATTGGAAAGCATCACCAGTAAGACCAGCATGTGAT
GCAGATTGCAGAAAACGAATATTATGCGATGCAAAAAGTGGCAGAAGTCACGATCGAAAA
TATTTCTGTGCAGAAGTTGAATCTAAATTGGATTCATCGAACGGAAGTTGGAGATCGTGG
ATTTATCGCGGAATTTCATTTTCCTTATCAATTATTAACTAA
>g1883.t2 Gene=g1883 Length=413
MQISLKKALQQIKYFQGDYRKCDSPKRMIDHMYKHIAETHSDIDYILWTGDLPPHDIWNQ
TKEENLKVLKETVKQMAEVFPGIPIFPALGNHESAPVNSFPPPYVQQVDSSIAWLYDALA
EEWQKWLPPSVSYTIKRGAFYSVLVRPGFRIISINMNYCNNKNWWLLLNSTDPATQLQWI
IYELQSAEFSNEKVHIIGHIPPGHADCLKIWSRNYYKIVQRYESTITAQFFGHTHFDEFE
VFYDSNDVSRPTNIAYIGPSVTPYYDLNPGYRIYYIDGDHDATTRLVIDHETWIMNLKEA
NLYDFPIYYKLYSTRAAYNLKALRPSDWDELINSMTDDQDKFDLYYKHYWKASPVRPACD
ADCRKRILCDAKSGRSHDRKYFCAEVESKLDSSNGSWRSWIYRGISFSLSIIN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g1883.t2 | CDD | cd00842 | MPP_ASMase | 17 | 272 | 5.96664E-122 |
| 6 | g1883.t2 | Coils | Coil | Coil | 59 | 79 | - |
| 5 | g1883.t2 | Gene3D | G3DSA:3.60.21.10 | - | 11 | 264 | 1.0E-8 |
| 2 | g1883.t2 | PANTHER | PTHR10340 | SPHINGOMYELIN PHOSPHODIESTERASE | 17 | 391 | 3.6E-185 |
| 3 | g1883.t2 | PANTHER | PTHR10340:SF34 | SPHINGOMYELIN PHOSPHODIESTERASE | 17 | 391 | 3.6E-185 |
| 1 | g1883.t2 | Pfam | PF00149 | Calcineurin-like phosphoesterase | 21 | 235 | 3.0E-20 |
| 4 | g1883.t2 | SUPERFAMILY | SSF56300 | Metallo-dependent phosphatases | 16 | 300 | 3.45E-52 |
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:0016787 | hydrolase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K12350 (sphingomyelin phosphodiesterase)
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.
