General information for g13841.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Sphingomyelin phosphodiesterase 4.
Parent gene
- The parent gene g13841 is located on chr_1: 32745106..32747426 (+ 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_1 | g13841 | g13841.t1 | TSS | g13841.t1 | 32745036 | 32745036 |
| chr_1 | g13841 | g13841.t1 | isoform | g13841.t1 | 32745106 | 32747426 |
| chr_1 | g13841 | g13841.t1 | exon | g13841.t1.exon1 | 32745106 | 32745517 |
| chr_1 | g13841 | g13841.t1 | cds | g13841.t1.CDS1 | 32745106 | 32745517 |
| chr_1 | g13841 | g13841.t1 | exon | g13841.t1.exon2 | 32745577 | 32747426 |
| chr_1 | g13841 | g13841.t1 | cds | g13841.t1.CDS2 | 32745577 | 32747426 |
| chr_1 | g13841 | g13841.t1 | TTS | g13841.t1 | 32747555 | 32747555 |
Sequences
>g13841.t1 Gene=g13841 Length=2262
ATGTATCAATTACAAACTCGTATAAACGATATTCTTAATTATCCATTAGTGGAACGTATC
AATCAGTTGCGGTTTTGCATCGAAACAGCTCCTATCAAAGATTTACAAGCATTTTATCCA
ACATTAGTTTCAAACATTTTCGGCATTAATCAAAATCAGATCGGATGGGGCTTGAGAACA
GTAACACAAGCAAGTGCAGAATATTACCTACTTTACAACTTTTTCAATCCTCACGAAATA
TTTTTTCGACTAATTTATCGCCTTCAATCTTGCGGGTTTGTGAATAAATATGAAATTCCA
TTTCCTGAACTTCCGAAATATTTTATTCGAATGTTGGAAAGCGGAAGAGTTGATGGATTT
TATACAAAACTCATAAGTACTGAGCATTTTCAACCTAAAATGCTTTCATTGAATGCTTTT
GACTACTTCATTCTACATTTTGCTATTCATGGAGTAAAAAACTTACACAAAATATCACCT
GCTGCAATGGCTGTCAACAATGAGAACACAATGACTGTATATTTCAGCCTTGCTGCTGAT
TACTTATGCAATTTTCTTCCAAATGATCCAAATTCAATTGTCTATCCGCAAATTGATTTG
TCTCCAGTAAAAAATACAGCTCCCGTTCAAATTCCAATGGCACCGATCCGACAACCTAAA
TATTTGCTTCTTTCATCACTCTCTCATCAAATTCAAAATCCATCAAATCCTCCTAGAGAT
ATTCGATTTCAAGAAGCAGCAACAAGTAGAAGCTCAAGCAATTGGCGTAGTGAAACTATT
TTAATGTTTTTTATTGATTGCTGGCTAAGATATGACATGGATGAATGCTATGAAGTGCCA
TCTAACGAGTTTATTCGTATTCTTCGAATTCTTGTTAAACAGCTGCATTACTTTGGAAAT
TGCGCAGAACAGGACACTACGTCTCTTGCCATCTTACGAAAACAATCACACAGTCTTTTA
AATTCACGGATGTATGGATTTCTCAAGTCTGTCATGTCACGCTGGCCCATCGATACAACT
TTTCTGAACGTCCTAGAATTGTGGCTCTCTTACATTCAACCATGGCGTTATGTTTATAAT
CGCAACATTCAAAATTTAAATAGTGAAACAATCGAAATACCAAAACGCTTCAAGACATTT
ATTAATGAAAATTTACTCAGTTATACACAAATTTTTGTTCGACTCATTCCACGTTTCATG
AAAATGGATTTAAGTTTAAGTAAAAATGCTTTCATGCTATTTCGCATGTTGAAAGTTTTT
AAACAATCAAGTGAGATTCTTCGTGAAATGGAAAGGATTTTGATGAGTAATACAACAGGA
ATTCGTTCACATCACTCTTCGATGCACGAAAATTCAATTCATTCGCCACGATCAGCAAAT
AACTCAATGAATCGTTCAGGTGGAGAACGTCTTTCATTTCATCGTTATGCAAGTCAGTCA
GCATTATTTGATGATAGCACTTATATTTGTATGTTCAGCGATGAGGTAACTATGCAAATT
TACGAACTTATGCAACGTGCATATGCTGCTAAACTTAAAACAAATTATGAAGTTAATTTG
ATGGAGAAGCAATTGAAACAAAACATAACTTTATGGGAAAGATTTTTACAATTTATTGGT
TGGTTGAGTTCATTCAATTTCTCATTCACGCAAGCACTAGAGGAGAAGAAAAAAGCACCA
TTCTATTTGGATTTCATTCTTGATGTTCTTTCACCAATGTATAATATTCCGATTGAAGAC
ACAACTGCTGATTTCACTGCAAACGAAAATATTCTTGAAAACAGTGATAAAGAAAACCAT
GATAAATCAAATTTAAATATTACACCGAGTTTTATGAAGAGTCAATTGAGTCAAATATCA
TATACAGGAGATCCCGAGCTTTTACCCATTATGACGAGTGAAATTAAATTCCTAGTTCGA
TTTTTCTATCAAATTTCAAAAAAATTGAATGAAATGTTTGAGGATGAATTCAATTCGATT
TATAATCGCAATGATGTTTATGGACGTGTTTCAAGACAAATCTTATCGCCTCCTATTGAA
ACGAGAATTTTTGATAAATCTGCTGGTTATGCAGAATTGCAAGTAAATAACATTGGACCA
CGTTTAAGTTTGAGGAAATTTGCAAGCAAAACTGTCATCTTTTTGCTTCTCATGTCATTT
ATTTTTGGTAGAATATTTTTTGGAGCATCAAGTGTAGGTTTCCTAACTTTCATTCTAATA
AGTACTCTGTATCTTTTTATCAAAGCATTAATTTCTCCATAA
>g13841.t1 Gene=g13841 Length=753
MYQLQTRINDILNYPLVERINQLRFCIETAPIKDLQAFYPTLVSNIFGINQNQIGWGLRT
VTQASAEYYLLYNFFNPHEIFFRLIYRLQSCGFVNKYEIPFPELPKYFIRMLESGRVDGF
YTKLISTEHFQPKMLSLNAFDYFILHFAIHGVKNLHKISPAAMAVNNENTMTVYFSLAAD
YLCNFLPNDPNSIVYPQIDLSPVKNTAPVQIPMAPIRQPKYLLLSSLSHQIQNPSNPPRD
IRFQEAATSRSSSNWRSETILMFFIDCWLRYDMDECYEVPSNEFIRILRILVKQLHYFGN
CAEQDTTSLAILRKQSHSLLNSRMYGFLKSVMSRWPIDTTFLNVLELWLSYIQPWRYVYN
RNIQNLNSETIEIPKRFKTFINENLLSYTQIFVRLIPRFMKMDLSLSKNAFMLFRMLKVF
KQSSEILREMERILMSNTTGIRSHHSSMHENSIHSPRSANNSMNRSGGERLSFHRYASQS
ALFDDSTYICMFSDEVTMQIYELMQRAYAAKLKTNYEVNLMEKQLKQNITLWERFLQFIG
WLSSFNFSFTQALEEKKKAPFYLDFILDVLSPMYNIPIEDTTADFTANENILENSDKENH
DKSNLNITPSFMKSQLSQISYTGDPELLPIMTSEIKFLVRFFYQISKKLNEMFEDEFNSI
YNRNDVYGRVSRQILSPPIETRIFDKSAGYAELQVNNIGPRLSLRKFASKTVIFLLLMSF
IFGRIFFGASSVGFLTFILISTLYLFIKALISP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g13841.t1 | PANTHER | PTHR12988 | SPHINGOMYELIN PHOSPHODIESTERASE 4 | 2 | 751 | 3.2E-108 |
| 2 | g13841.t1 | Pfam | PF14724 | Mitochondrial-associated sphingomyelin phosphodiesterase | 6 | 276 | 2.6E-25 |
| 1 | g13841.t1 | Pfam | PF14724 | Mitochondrial-associated sphingomyelin phosphodiesterase | 279 | 705 | 1.1E-45 |
| 6 | g13841.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 706 | - |
| 9 | g13841.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 707 | 727 | - |
| 7 | g13841.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 728 | 732 | - |
| 8 | g13841.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 733 | 751 | - |
| 5 | g13841.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 752 | 753 | - |
| 4 | g13841.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 725 | 747 | - |
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:0050290 | sphingomyelin phosphodiesterase D activity | MF |
KEGG
Orthology
- This transcript has been annotated with K12353 (sphingomyelin phosphodiesterase 4)
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.
