General information for g1883.t3
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.t3 | isoform | g1883.t3 | 13643063 | 13644848 |
| chr_3 | g1883 | g1883.t3 | exon | g1883.t3.exon1 | 13643063 | 13643446 |
| chr_3 | g1883 | g1883.t3 | cds | g1883.t3.CDS1 | 13643079 | 13643446 |
| chr_3 | g1883 | g1883.t3 | exon | g1883.t3.exon2 | 13643504 | 13643739 |
| chr_3 | g1883 | g1883.t3 | cds | g1883.t3.CDS2 | 13643504 | 13643739 |
| chr_3 | g1883 | g1883.t3 | exon | g1883.t3.exon3 | 13643798 | 13644008 |
| chr_3 | g1883 | g1883.t3 | cds | g1883.t3.CDS3 | 13643798 | 13644008 |
| chr_3 | g1883 | g1883.t3 | exon | g1883.t3.exon4 | 13644061 | 13644243 |
| chr_3 | g1883 | g1883.t3 | cds | g1883.t3.CDS4 | 13644061 | 13644243 |
| chr_3 | g1883 | g1883.t3 | exon | g1883.t3.exon5 | 13644398 | 13644652 |
| chr_3 | g1883 | g1883.t3 | cds | g1883.t3.CDS5 | 13644398 | 13644461 |
| chr_3 | g1883 | g1883.t3 | exon | g1883.t3.exon6 | 13644724 | 13644848 |
| chr_3 | g1883 | g1883.t3 | TTS | g1883.t3 | 13644869 | 13644869 |
| chr_3 | g1883 | g1883.t3 | TSS | g1883.t3 | NA | NA |
Sequences
>g1883.t3 Gene=g1883 Length=1394
AGAAACTGTGAAGCAAATGGCTGAAGTATTTCCTGGAATTCCAATTTTTCCAGCTCTTGG
TAATCATGAAAGTGCGCCAGTTAATAGCTTTCCACCACCATATGTTCAACAAGTTGATAG
TTCAATAGCTTGGCTCTATGATGCTTTGGCAGAAGAATGGCAAAAATGGTTACCACCATC
TGTCTCATATACAATCAAAAGAGGAGCTTTTTATTCAGTACTTGTTCGACCTGGCTTTAG
GATCATTTCTATCAATATGAATTATTGTAATAACAAAAATTGGTGGCTGCTTCTTAATTC
AACTGATCCAGCTACTCAATTACAATGGATTATTTATGAACTTCAAAGTGCTGAATTTTC
AAACGAAAAAGTTCATATTATTGGTCATATTCCTCCAGGACATGCAGATTGTTTAAAGAT
TTGGAGTAGAAATTATTATAAAATCGTTCAGCGATATGAGAGCACAATTACTGCTCAATT
CTTCGGTCATACACATTTTGATGAATTTGAAGTCTTCTATGACTCAAATGATGTATCTCG
TCCCACAAATATTGCTTATATTGGACCCAGTGTGACTCCATATTATGATTTAAATCCTGG
ATATCGAATCTATTATATTGATGGTGATCATGATGCAACCACAAGATTAGTAATTGATCA
TGAAACTTGGATTATGAATCTCAAAGAAGCGAATCTCTATGATTTTCCAATTTATTATAA
ACTTTATTCAACTCGTGCTGCATACAATCTTAAAGCACTTAGACCATCTGATTGGGATGA
ATTAATTAATTCAATGACTGATGATCAAGATAAATTTGATCTTTATTATAAACATTATTG
GAAAGCATCACCAGTAAGACCAGCATGTGATGCAGATTGCAGAAAACGAATATTATGCGA
TGCAAAAAGTGGCAGAAGTCACGATCGAAAATATTTCTGTGCAGAAGTTGAATCTAAATT
GGATTCATCGAACGGAAGTTGGAGATCGTGGATTTATCGCGGAATTTCATTTTCTAATAA
AACAATGTCTAATAATACAGCTTATCAATTATTAACTAATGAAGTTGGTGATCCTTAAAC
ATTCACACACAAAAAATCAAAATCAAAATCAGACCCCTCATGGATACTCGACATACAAAA
TACATTGTGTAAATACAAAAATTATACAATCTAATTTAAGAACAAAAATATTATTGTAAA
TATAAATGAAACATGTGTACAAAATGCTTATTGGTGGATTTGGTCAAAAAAATGAGTTGG
AAGTACAAGATTCAACGCTCTATACTCAGTGACTTCAAAAATTCCTAGCTATGTCATGAG
CTTTGGTTAATTAGAACAAAAGCAATTTACGTGATAAAAAGAAAGAGAAAATTATTGTAA
CATGCAAGAGAATA
>g1883.t3 Gene=g1883 Length=353
MAEVFPGIPIFPALGNHESAPVNSFPPPYVQQVDSSIAWLYDALAEEWQKWLPPSVSYTI
KRGAFYSVLVRPGFRIISINMNYCNNKNWWLLLNSTDPATQLQWIIYELQSAEFSNEKVH
IIGHIPPGHADCLKIWSRNYYKIVQRYESTITAQFFGHTHFDEFEVFYDSNDVSRPTNIA
YIGPSVTPYYDLNPGYRIYYIDGDHDATTRLVIDHETWIMNLKEANLYDFPIYYKLYSTR
AAYNLKALRPSDWDELINSMTDDQDKFDLYYKHYWKASPVRPACDADCRKRILCDAKSGR
SHDRKYFCAEVESKLDSSNGSWRSWIYRGISFSNKTMSNNTAYQLLTNEVGDP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g1883.t3 | CDD | cd00842 | MPP_ASMase | 1 | 197 | 0.0e+00 |
| 5 | g1883.t3 | Gene3D | G3DSA:3.60.21.10 | - | 77 | 182 | 8.6e-06 |
| 2 | g1883.t3 | PANTHER | PTHR10340 | SPHINGOMYELIN PHOSPHODIESTERASE | 1 | 316 | 0.0e+00 |
| 3 | g1883.t3 | PANTHER | PTHR10340:SF34 | SPHINGOMYELIN PHOSPHODIESTERASE | 1 | 316 | 0.0e+00 |
| 1 | g1883.t3 | Pfam | PF00149 | Calcineurin-like phosphoesterase | 7 | 160 | 0.0e+00 |
| 4 | g1883.t3 | SUPERFAMILY | SSF56300 | Metallo-dependent phosphatases | 7 | 225 | 0.0e+00 |
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 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.
