General information for g6630.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative neutral sphingomyelinase.
Parent gene
- The parent gene g6630 is located on chr_2: 17873718..17876635 (+ 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 | g6630 | g6630.t1 | TSS | g6630.t1 | 17872119 | 17872119 |
| chr_2 | g6630 | g6630.t1 | isoform | g6630.t1 | 17872175 | 17873718 |
| chr_2 | g6630 | g6630.t1 | exon | g6630.t1.exon1 | 17872175 | 17872240 |
| chr_2 | g6630 | g6630.t1 | cds | g6630.t1.CDS1 | 17872175 | 17872240 |
| chr_2 | g6630 | g6630.t1 | exon | g6630.t1.exon2 | 17872513 | 17872783 |
| chr_2 | g6630 | g6630.t1 | cds | g6630.t1.CDS2 | 17872513 | 17872783 |
| chr_2 | g6630 | g6630.t1 | exon | g6630.t1.exon3 | 17872847 | 17873718 |
| chr_2 | g6630 | g6630.t1 | cds | g6630.t1.CDS3 | 17872847 | 17873718 |
| chr_2 | g6630 | g6630.t1 | TTS | g6630.t1 | 17874568 | 17874568 |
Sequences
>g6630.t1 Gene=g6630 Length=1209
ATGGTTTTGACAATTTCTGTTTTAACAATGAACGTTTGGGGAATACCTTTCATATCCGCG
GACAAGGATATCAGAATCGAAAAAATTTCAGAGCATCTTGTCACAAGTGAATATGATGTA
ATTTCATTACAAGAAGTTTGGAGTGAATATGACTTTCAAAAAATTCGTGACAAGCTTTCC
AAAAAGTATCCATATGCACATTATTTTTATAGTGGTGTCTTTGGAAGCGGTTTATGTGTA
TTTTCAAAACATCAAATAATATCAGTGTTTTTCCATCATTGGGCACTCAACGGCTATGTG
CATAAAATACAACATGCAGATTGGTTTGGAGGCAAAGGAGTAGGACTTTGCCGGCTCAAA
GTAAATGATAAAATTGTTAATTTTTATACAGCACATCTTCATGCAGAATATGATAAATTA
CGTGATGATTATGTGACACATCGTATTATTCAAGCATTTGATACAGCGCAATTTTTAGAA
AATACTCGTGGAAATTGTTCATTACAAATTTTAGCTGGTGATTTAAACACTGAACCTAAC
GATTTGGCATATAGAATTTTATTATCGGTTTCCGGTATGAAAGATTCATTTGTACAGAAT
ACTGAAGTTCAACCATATTTCGCAACTTCAGATTACATTAACAACAGTTACACAAAAGTA
AAAAATGCAAATGGAAAAGAGGGAGTTCGTATTGATTATGTTCTTTATCGAGAAGGAAAT
GATTCTGTATCTAATGTAGAAAAATACGAAATGCCGTTACTTGAAAAAATTCCTGATTAT
AATATAAGTTATTCTGATCACGAAGCTGTGCATGCAAAAATTATAATAATTCCAAAGAAA
GAAAATGAATTATTTTCAAGCGGAGTTGATCAAATTCTTACTATTCAAAATAATATTAAA
AACTTGAAAGAATGTATTGCCACATGCAATCAAAGTTTAAAGACAATTGAATCTCATCGT
TGTAGTTATTCATTGATGGCTATAGGTCTTTTAGTTATACTTTTAAATATATTAGAAATA
AGTCCTTCGTATGGTTTTAAAACAGTTTACCTAATTATTAAATTCCTTATAATCAGTTTG
ATACTTTTTCTCATATTTATGGCAACAATTTGGAATGTTATGGAGAAGCATGGAATTCTT
TCTGGAAAGTTAGCAATGCAAATAACATTGAAAAATAGTGAAATTATCATGGAAAATATT
AATAATTAA
>g6630.t1 Gene=g6630 Length=402
MVLTISVLTMNVWGIPFISADKDIRIEKISEHLVTSEYDVISLQEVWSEYDFQKIRDKLS
KKYPYAHYFYSGVFGSGLCVFSKHQIISVFFHHWALNGYVHKIQHADWFGGKGVGLCRLK
VNDKIVNFYTAHLHAEYDKLRDDYVTHRIIQAFDTAQFLENTRGNCSLQILAGDLNTEPN
DLAYRILLSVSGMKDSFVQNTEVQPYFATSDYINNSYTKVKNANGKEGVRIDYVLYREGN
DSVSNVEKYEMPLLEKIPDYNISYSDHEAVHAKIIIIPKKENELFSSGVDQILTIQNNIK
NLKECIATCNQSLKTIESHRCSYSLMAIGLLVILLNILEISPSYGFKTVYLIIKFLIISL
ILFLIFMATIWNVMEKHGILSGKLAMQITLKNSEIIMENINN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g6630.t1 | Gene3D | G3DSA:3.60.10.10 | - | 3 | 273 | 7.8E-56 |
| 2 | g6630.t1 | PANTHER | PTHR12393:SF7 | SPHINGOMYELIN PHOSPHODIESTERASE 2 | 3 | 392 | 2.2E-97 |
| 3 | g6630.t1 | PANTHER | PTHR12393 | SPHINGOMYELIN PHOSPHODIESTERASE RELATED | 3 | 392 | 2.2E-97 |
| 1 | g6630.t1 | Pfam | PF03372 | Endonuclease/Exonuclease/phosphatase family | 8 | 267 | 4.0E-14 |
| 11 | g6630.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 14 | - |
| 12 | g6630.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 1 | - |
| 13 | g6630.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 2 | 10 | - |
| 16 | g6630.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 11 | 14 | - |
| 9 | g6630.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 15 | 321 | - |
| 14 | g6630.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 322 | 338 | - |
| 8 | g6630.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 339 | 349 | - |
| 15 | g6630.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 350 | 374 | - |
| 10 | g6630.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 375 | 402 | - |
| 6 | g6630.t1 | SUPERFAMILY | SSF56219 | DNase I-like | 4 | 273 | 2.02E-51 |
| 5 | g6630.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 323 | 342 | - |
| 4 | g6630.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 349 | 371 | - |
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:0004767 | sphingomyelin phosphodiesterase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K12351 (sphingomyelin phosphodiesterase 2)
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.
