SMPD4: Difference between revisions

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{{Infobox_gene}}
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'''Sphingomyelin phosphodiesterase 4''' is an [[enzyme]] that in humans is encoded by the ''SMPD4'' [[gene]].<ref name="pmid16517606">{{cite journal | vauthors = Krut O, Wiegmann K, Kashkar H, Yazdanpanah B, Krönke M | title = Novel tumor necrosis factor-responsive mammalian neutral sphingomyelinase-3 is a C-tail-anchored protein | journal = The Journal of Biological Chemistry | volume = 281 | issue = 19 | pages = 13784–93 | date = May 2006 | pmid = 16517606 | pmc =  | doi = 10.1074/jbc.M511306200 }}</ref><ref name="entrez">{{cite web | title = Entrez Gene: SMPD4 sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)| url = https://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=55627| accessdate = }}</ref>
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== Model organisms ==
{{GNF_Protein_box
| image =
| image_source =
| PDB =  
| Name = Sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)
| HGNCid = 32949
| Symbol = SMPD4
| AltSymbols =; FLJ20297; FLJ20756; KIAA1418; NSMASE3; nSMase-3
| OMIM = 610457
| ECnumber = 
| Homologene = 9813
| MGIid = 1924876
| GeneAtlas_image1 = PBB_GE_SMPD4_207856_s_at_tn.png
| Function =
| Component =
| Process =
| Orthologs = {{GNF_Ortholog_box
    | Hs_EntrezGene = 55627
    | Hs_Ensembl = ENSG00000136699
    | Hs_RefseqProtein = NP_060221
    | Hs_RefseqmRNA = NM_017751
    | Hs_GenLoc_db = 
    | Hs_GenLoc_chr = 2
    | Hs_GenLoc_start = 130625452
    | Hs_GenLoc_end = 130650635
    | Hs_Uniprot = Q9NXE4
    | Mm_EntrezGene = 77626
    | Mm_Ensembl = ENSMUSG00000005899
    | Mm_RefseqmRNA = NM_029945
    | Mm_RefseqProtein = NP_084221
    | Mm_GenLoc_db = 
    | Mm_GenLoc_chr = 16
    | Mm_GenLoc_start = 17532920
    | Mm_GenLoc_end = 17558391
    | Mm_Uniprot = Q6ZPR5
  }}
}}
'''Sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)''', also known as '''SMPD4''', is a human [[gene]].<ref name="entrez">{{cite web | title = Entrez Gene: SMPD4 sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)| url = http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=55627| accessdate = }}</ref>


<!-- The PBB_Summary template is automatically maintained by Protein Box Bot. See Template:PBB_Controls to Stop updates. -->
[[Model organism]]s have been used in the study of SMPD4 function. A conditional [[knockout mouse]] line called ''Smpd4<sup>tm2b(KOMP)Wtsi</sup>'' was generated at the [[Wellcome Trust Sanger Institute]].<ref name="mgp_reference">{{cite journal |title=The Sanger Mouse Genetics Programme: high throughput characterisation of knockout mice |author=Gerdin AK |year=2010 |journal=Acta Ophthalmologica|volume=88 |pages=925–7|doi=10.1111/j.1755-3768.2010.4142.x }}</ref> Male and female animals underwent a standardized [[phenotypic screen]]<ref name="IMPCsearch_ref">{{cite web |url=http://www.mousephenotype.org/data/search?q=Smpd4#fq=*:*&facet=gene |title=International Mouse Phenotyping Consortium}}</ref> to determine the effects of deletion.<ref name="pmid21677750">{{cite journal | vauthors = Skarnes WC, Rosen B, West AP, Koutsourakis M, Bushell W, Iyer V, Mujica AO, Thomas M, Harrow J, Cox T, Jackson D, Severin J, Biggs P, Fu J, Nefedov M, de Jong PJ, Stewart AF, Bradley A | title = A conditional knockout resource for the genome-wide study of mouse gene function | journal = Nature | volume = 474 | issue = 7351 | pages = 337–42 | date = Jun 2011 | pmid = 21677750 | pmc = 3572410 | doi = 10.1038/nature10163 }}</ref><ref name="mouse_library">{{cite journal | vauthors = Dolgin E | title = Mouse library set to be knockout | journal = Nature | volume = 474 | issue = 7351 | pages = 262–3 | date = Jun 2011 | pmid = 21677718 | doi = 10.1038/474262a }}</ref><ref name="mouse_for_all_reasons">{{cite journal | vauthors = Collins FS, Rossant J, Wurst W | title = A mouse for all reasons | journal = Cell | volume = 128 | issue = 1 | pages = 9–13 | date = Jan 2007 | pmid = 17218247 | doi = 10.1016/j.cell.2006.12.018 }}</ref><ref name="pmid23870131">{{cite journal | vauthors = White JK, Gerdin AK, Karp NA, Ryder E, Buljan M, Bussell JN, Salisbury J, Clare S, Ingham NJ, Podrini C, Houghton R, Estabel J, Bottomley JR, Melvin DG, Sunter D, Adams NC, Tannahill D, Logan DW, Macarthur DG, Flint J, Mahajan VB, Tsang SH, Smyth I, Watt FM, Skarnes WC, Dougan G, Adams DJ, Ramirez-Solis R, Bradley A, Steel KP | title = Genome-wide generation and systematic phenotyping of knockout mice reveals new roles for many genes | journal = Cell | volume = 154 | issue = 2 | pages = 452–64 | date = Jul 2013 | pmid = 23870131 | pmc = 3717207 | doi = 10.1016/j.cell.2013.06.022 }}</ref> Additional screens performed:  - In-depth immunological phenotyping<ref name="iii_ref">{{cite web |url= http://www.immunophenotyping.org/data/search?keys=Smpd4&field_gene_construct_tid=All |title=Infection and Immunity Immunophenotyping (3i) Consortium}}</ref>
{{PBB_Summary
{| class="wikitable sortable collapsible collapsed" border="1" cellpadding="2" style="float: left;" |
| section_title =  
|+ ''Smpd4'' knockout mouse phenotype
| summary_text =  
|-
}}
! Characteristic!! Phenotype
|-
| colspan=2; style="text-align: center;" | All data available at.<ref name="IMPCsearch_ref"/><ref name="iii_ref" />
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| Insulin || bgcolor="#488ED3"|Normal


==References==
|-
{{reflist|2}}
| Homozygous viability at P14 || bgcolor="#C40000"|Abnormal
==Further reading==
 
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| [[Recessive]] lethal study || bgcolor="#488ED3"|Normal
 
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| Homozygous Fertility || bgcolor="#C40000"|Abnormal
 
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| [[Dual-energy X-ray absorptiometry|DEXA]] || bgcolor="#488ED3"|Normal
 
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| [[Radiography]] || bgcolor="#488ED3"|Normal
 
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| ''[[Haematology]]'' 16 Weeks || bgcolor="#488ED3"|Normal
 
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| Peripheral blood leukocytes 16 Weeks || bgcolor="#488ED3"|Normal
 
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== References ==
{{reflist}}
 
== Further reading ==
{{refbegin | 2}}
{{refbegin | 2}}
{{PBB_Further_reading
* {{cite journal | vauthors = Andersson B, Wentland MA, Ricafrente JY, Liu W, Gibbs RA | title = A "double adaptor" method for improved shotgun library construction | journal = Analytical Biochemistry | volume = 236 | issue = 1 | pages = 107–13 | date = Apr 1996 | pmid = 8619474 | doi = 10.1006/abio.1996.0138 }}
| citations =
* {{cite journal | vauthors = Hillier LD, Lennon G, Becker M, Bonaldo MF, Chiapelli B, Chissoe S, Dietrich N, DuBuque T, Favello A, Gish W, Hawkins M, Hultman M, Kucaba T, Lacy M, Le M, Le N, Mardis E, Moore B, Morris M, Parsons J, Prange C, Rifkin L, Rohlfing T, Schellenberg K, Bento Soares M, Tan F, Thierry-Meg J, Trevaskis E, Underwood K, Wohldman P, Waterston R, Wilson R, Marra M | title = Generation and analysis of 280,000 human expressed sequence tags | journal = Genome Research | volume = 6 | issue = 9 | pages = 807–28 | date = Sep 1996 | pmid = 8889549 | doi = 10.1101/gr.6.9.807 }}
*{{cite journal | author=Andersson B, Wentland MA, Ricafrente JY, ''et al.'' |title=A "double adaptor" method for improved shotgun library construction. |journal=Anal. Biochem. |volume=236 |issue= 1 |pages= 107-13 |year= 1996 |pmid= 8619474 |doi= 10.1006/abio.1996.0138 }}
* {{cite journal | vauthors = Yu W, Andersson B, Worley KC, Muzny DM, Ding Y, Liu W, Ricafrente JY, Wentland MA, Lennon G, Gibbs RA | title = Large-scale concatenation cDNA sequencing | journal = Genome Research | volume = 7 | issue = 4 | pages = 353–8 | date = Apr 1997 | pmid = 9110174 | pmc = 139146 | doi = 10.1101/gr.7.4.353 }}
*{{cite journal | author=Hillier LD, Lennon G, Becker M, ''et al.'' |title=Generation and analysis of 280,000 human expressed sequence tags. |journal=Genome Res. |volume=6 |issue= 9 |pages= 807-28 |year= 1997 |pmid= 8889549 |doi= }}
* {{cite journal | vauthors = Nagase T, Kikuno R, Ishikawa KI, Hirosawa M, Ohara O | title = Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro | journal = DNA Research | volume = 7 | issue = 1 | pages = 65–73 | date = Feb 2000 | pmid = 10718198 | doi = 10.1093/dnares/7.1.65 }}
*{{cite journal | author=Yu W, Andersson B, Worley KC, ''et al.'' |title=Large-scale concatenation cDNA sequencing. |journal=Genome Res. |volume=7 |issue= 4 |pages= 353-8 |year= 1997 |pmid= 9110174 |doi= }}
* {{cite journal | vauthors = Wiemann S, Weil B, Wellenreuther R, Gassenhuber J, Glassl S, Ansorge W, Böcher M, Blöcker H, Bauersachs S, Blum H, Lauber J, Düsterhöft A, Beyer A, Köhrer K, Strack N, Mewes HW, Ottenwälder B, Obermaier B, Tampe J, Heubner D, Wambutt R, Korn B, Klein M, Poustka A | title = Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs | journal = Genome Research | volume = 11 | issue = 3 | pages = 422–35 | date = Mar 2001 | pmid = 11230166 | pmc = 311072 | doi = 10.1101/gr.GR1547R }}
*{{cite journal | author=Nagase T, Kikuno R, Ishikawa KI, ''et al.'' |title=Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro. |journal=DNA Res. |volume=7 |issue= 1 |pages= 65-73 |year= 2000 |pmid= 10718198 |doi= }}
* {{cite journal | vauthors = Lehner B, Sanderson CM | title = A protein interaction framework for human mRNA degradation | journal = Genome Research | volume = 14 | issue = 7 | pages = 1315–23 | date = Jul 2004 | pmid = 15231747 | pmc = 442147 | doi = 10.1101/gr.2122004 }}
*{{cite journal | author=Wiemann S, Weil B, Wellenreuther R, ''et al.'' |title=Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. |journal=Genome Res. |volume=11 |issue= 3 |pages= 422-35 |year= 2001 |pmid= 11230166 |doi= 10.1101/gr.154701 }}
* {{cite journal | vauthors = Jana A, Pahan K | title = Human immunodeficiency virus type 1 gp120 induces apoptosis in human primary neurons through redox-regulated activation of neutral sphingomyelinase | journal = The Journal of Neuroscience | volume = 24 | issue = 43 | pages = 9531–40 | date = Oct 2004 | pmid = 15509740 | pmc = 1955476 | doi = 10.1523/JNEUROSCI.3085-04.2004 }}
*{{cite journal  | author=Strausberg RL, Feingold EA, Grouse LH, ''et al.'' |title=Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=99 |issue= 26 |pages= 16899-903 |year= 2003 |pmid= 12477932 |doi= 10.1073/pnas.242603899 }}
* {{cite journal | vauthors = Kimura K, Wakamatsu A, Suzuki Y, Ota T, Nishikawa T, Yamashita R, Yamamoto J, Sekine M, Tsuritani K, Wakaguri H, Ishii S, Sugiyama T, Saito K, Isono Y, Irie R, Kushida N, Yoneyama T, Otsuka R, Kanda K, Yokoi T, Kondo H, Wagatsuma M, Murakawa K, Ishida S, Ishibashi T, Takahashi-Fujii A, Tanase T, Nagai K, Kikuchi H, Nakai K, Isogai T, Sugano S | title = Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes | journal = Genome Research | volume = 16 | issue = 1 | pages = 55–65 | date = Jan 2006 | pmid = 16344560 | pmc = 1356129 | doi = 10.1101/gr.4039406 }}
*{{cite journal  | author=Ota T, Suzuki Y, Nishikawa T, ''et al.'' |title=Complete sequencing and characterization of 21,243 full-length human cDNAs. |journal=Nat. Genet. |volume=36 |issue= 1 |pages= 40-5 |year= 2004 |pmid= 14702039 |doi= 10.1038/ng1285 }}
* {{cite journal | vauthors = Ewing RM, Chu P, Elisma F, Li H, Taylor P, Climie S, McBroom-Cerajewski L, Robinson MD, O'Connor L, Li M, Taylor R, Dharsee M, Ho Y, Heilbut A, Moore L, Zhang S, Ornatsky O, Bukhman YV, Ethier M, Sheng Y, Vasilescu J, Abu-Farha M, Lambert JP, Duewel HS, Stewart II, Kuehl B, Hogue K, Colwill K, Gladwish K, Muskat B, Kinach R, Adams SL, Moran MF, Morin GB, Topaloglou T, Figeys D | title = Large-scale mapping of human protein-protein interactions by mass spectrometry | journal = Molecular Systems Biology | volume = 3 | issue = 1 | pages = 89 | year = 2007 | pmid = 17353931 | pmc = 1847948 | doi = 10.1038/msb4100134 }}
*{{cite journal | author=Lehner B, Sanderson CM |title=A protein interaction framework for human mRNA degradation. |journal=Genome Res. |volume=14 |issue= 7 |pages= 1315-23 |year= 2004 |pmid= 15231747 |doi= 10.1101/gr.2122004 }}
*{{cite journal  | author=Gerhard DS, Wagner L, Feingold EA, ''et al.'' |title=The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). |journal=Genome Res. |volume=14 |issue= 10B |pages= 2121-7 |year= 2004 |pmid= 15489334 |doi= 10.1101/gr.2596504 }}
*{{cite journal | author=Jana A, Pahan K |title=Human immunodeficiency virus type 1 gp120 induces apoptosis in human primary neurons through redox-regulated activation of neutral sphingomyelinase. |journal=J. Neurosci. |volume=24 |issue= 43 |pages= 9531-40 |year= 2005 |pmid= 15509740 |doi= 10.1523/JNEUROSCI.3085-04.2004 }}
*{{cite journal | author=Hillier LW, Graves TA, Fulton RS, ''et al.'' |title=Generation and annotation of the DNA sequences of human chromosomes 2 and 4. |journal=Nature |volume=434 |issue= 7034 |pages= 724-31 |year= 2005 |pmid= 15815621 |doi= 10.1038/nature03466 }}
*{{cite journal  | author=Kimura K, Wakamatsu A, Suzuki Y, ''et al.'' |title=Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. |journal=Genome Res. |volume=16 |issue= 1 |pages= 55-65 |year= 2006 |pmid= 16344560 |doi= 10.1101/gr.4039406 }}
*{{cite journal | author=Krut O, Wiegmann K, Kashkar H, ''et al.'' |title=Novel tumor necrosis factor-responsive mammalian neutral sphingomyelinase-3 is a C-tail-anchored protein. |journal=J. Biol. Chem. |volume=281 |issue= 19 |pages= 13784-93 |year= 2006 |pmid= 16517606 |doi= 10.1074/jbc.M511306200 }}
*{{cite journal  | author=Ewing RM, Chu P, Elisma F, ''et al.'' |title=Large-scale mapping of human protein-protein interactions by mass spectrometry. |journal=Mol. Syst. Biol. |volume=3 |issue= |pages= 89 |year= 2007 |pmid= 17353931 |doi= 10.1038/msb4100134 }}
}}
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Latest revision as of 06:42, 11 September 2017

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Identifiers
Aliases
External IDsGeneCards: [1]
Orthologs
SpeciesHumanMouse
Entrez

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Ensembl

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UniProt

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RefSeq (mRNA)

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RefSeq (protein)

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Location (UCSC)n/an/a
PubMed searchn/an/a
Wikidata
View/Edit Human

Sphingomyelin phosphodiesterase 4 is an enzyme that in humans is encoded by the SMPD4 gene.[1][2]

Model organisms

Model organisms have been used in the study of SMPD4 function. A conditional knockout mouse line called Smpd4tm2b(KOMP)Wtsi was generated at the Wellcome Trust Sanger Institute.[3] Male and female animals underwent a standardized phenotypic screen[4] to determine the effects of deletion.[5][6][7][8] Additional screens performed: - In-depth immunological phenotyping[9]

References

  1. ↑ Krut O, Wiegmann K, Kashkar H, Yazdanpanah B, Krönke M (May 2006). "Novel tumor necrosis factor-responsive mammalian neutral sphingomyelinase-3 is a C-tail-anchored protein". The Journal of Biological Chemistry. 281 (19): 13784–93. doi:10.1074/jbc.M511306200. PMID 16517606.
  2. ↑ "Entrez Gene: SMPD4 sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)".
  3. ↑ Gerdin AK (2010). "The Sanger Mouse Genetics Programme: high throughput characterisation of knockout mice". Acta Ophthalmologica. 88: 925–7. doi:10.1111/j.1755-3768.2010.4142.x.
  4. ↑ 4.0 4.1 "International Mouse Phenotyping Consortium".
  5. ↑ Skarnes WC, Rosen B, West AP, Koutsourakis M, Bushell W, Iyer V, Mujica AO, Thomas M, Harrow J, Cox T, Jackson D, Severin J, Biggs P, Fu J, Nefedov M, de Jong PJ, Stewart AF, Bradley A (Jun 2011). "A conditional knockout resource for the genome-wide study of mouse gene function". Nature. 474 (7351): 337–42. doi:10.1038/nature10163. PMC 3572410. PMID 21677750.
  6. ↑ Dolgin E (Jun 2011). "Mouse library set to be knockout". Nature. 474 (7351): 262–3. doi:10.1038/474262a. PMID 21677718.
  7. ↑ Collins FS, Rossant J, Wurst W (Jan 2007). "A mouse for all reasons". Cell. 128 (1): 9–13. doi:10.1016/j.cell.2006.12.018. PMID 17218247.
  8. ↑ White JK, Gerdin AK, Karp NA, Ryder E, Buljan M, Bussell JN, Salisbury J, Clare S, Ingham NJ, Podrini C, Houghton R, Estabel J, Bottomley JR, Melvin DG, Sunter D, Adams NC, Tannahill D, Logan DW, Macarthur DG, Flint J, Mahajan VB, Tsang SH, Smyth I, Watt FM, Skarnes WC, Dougan G, Adams DJ, Ramirez-Solis R, Bradley A, Steel KP (Jul 2013). "Genome-wide generation and systematic phenotyping of knockout mice reveals new roles for many genes". Cell. 154 (2): 452–64. doi:10.1016/j.cell.2013.06.022. PMC 3717207. PMID 23870131.
  9. ↑ 9.0 9.1 "Infection and Immunity Immunophenotyping (3i) Consortium".

Further reading

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