Smpd4 (sphingomyelin phosphodiesterase 4) - Rat Genome Database

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Gene: Smpd4 (sphingomyelin phosphodiesterase 4) Rattus norvegicus
Analyze
Symbol: Smpd4
Name: sphingomyelin phosphodiesterase 4
RGD ID: 1310674
Description: Predicted to enable sphingomyelin phosphodiesterase D activity and sphingomyelin phosphodiesterase activity. Predicted to be involved in several processes, including cellular response to tumor necrosis factor; ceramide biosynthetic process; and phospholipid catabolic process. Predicted to act upstream of or within in utero embryonic development. Predicted to be located in several cellular components, including nuclear outer membrane; sarcolemma; and trans-Golgi network. Orthologous to human SMPD4 (sphingomyelin phosphodiesterase 4); PARTICIPATES IN sphingolipid metabolic pathway; INTERACTS WITH 3-chloropropane-1,2-diol; 6-propyl-2-thiouracil; acrylamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC303790; RGD1310674; similar to RIKEN cDNA 4122402O22; sphingomyelin phosphodiesterase 4, neutral membrane
RGD Orthologs
Human
Mouse
Chinchilla
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21183,362,534 - 83,386,257 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1183,362,534 - 83,386,250 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1192,090,000 - 92,113,844 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01184,751,160 - 84,775,004 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01183,804,775 - 83,828,619 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01187,522,971 - 87,546,687 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1187,522,971 - 87,546,687 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01190,575,599 - 90,599,309 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41185,352,180 - 85,375,918 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15169,511,693 - 169,512,094 (+)NCBI
Celera1182,134,192 - 82,157,831 (-)NCBICelera
Cytogenetic Map11q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:16517606   PMID:18505924   PMID:27996060   PMID:31142202   PMID:31495489  


Genomics

Comparative Map Data
Smpd4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21183,362,534 - 83,386,257 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1183,362,534 - 83,386,250 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1192,090,000 - 92,113,844 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01184,751,160 - 84,775,004 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01183,804,775 - 83,828,619 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01187,522,971 - 87,546,687 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1187,522,971 - 87,546,687 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01190,575,599 - 90,599,309 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41185,352,180 - 85,375,918 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15169,511,693 - 169,512,094 (+)NCBI
Celera1182,134,192 - 82,157,831 (-)NCBICelera
Cytogenetic Map11q23NCBI
SMPD4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382130,151,392 - 130,181,757 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2130,151,392 - 130,182,750 (-)EnsemblGRCh38hg38GRCh38
GRCh372130,908,965 - 130,939,330 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362130,625,450 - 130,656,164 (-)NCBINCBI36Build 36hg18NCBI36
Celera2124,183,727 - 124,215,108 (-)NCBICelera
Cytogenetic Map2q21.1NCBI
HuRef2123,204,890 - 123,236,080 (-)NCBIHuRef
CHM1_12130,912,697 - 130,944,055 (-)NCBICHM1_1
T2T-CHM13v2.02130,585,291 - 130,615,727 (-)NCBIT2T-CHM13v2.0
Smpd4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391617,437,218 - 17,462,694 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1617,437,218 - 17,462,692 (+)EnsemblGRCm39 Ensembl
GRCm381617,619,354 - 17,644,830 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1617,619,354 - 17,644,828 (+)EnsemblGRCm38mm10GRCm38
MGSCv371617,619,447 - 17,644,923 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361617,532,917 - 17,556,946 (+)NCBIMGSCv36mm8
Celera1618,192,592 - 18,218,068 (+)NCBICelera
Cytogenetic Map16A3NCBI
cM Map1610.92NCBI
Smpd4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544219,184,794 - 19,210,999 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495544219,184,794 - 19,210,999 (-)NCBIChiLan1.0ChiLan1.0
SMPD4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12630,397,687 - 30,419,072 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2630,398,768 - 30,418,979 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2630,356,382 - 30,377,775 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02631,806,536 - 31,827,917 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2631,806,545 - 31,827,885 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12629,852,373 - 29,873,768 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02629,476,170 - 29,497,990 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02630,565,815 - 30,587,424 (-)NCBIUU_Cfam_GSD_1.0
Smpd4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118140,077,691 - 140,106,127 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366192,647,967 - 2,676,488 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049366192,647,880 - 2,676,371 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMPD4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1450,663,608 - 50,689,352 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11450,663,488 - 50,689,355 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21454,226,485 - 54,252,793 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SMPD4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110131,882 - 162,244 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl10136,784 - 163,555 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660585,555,408 - 5,586,699 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Smpd4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624945566,203 - 592,254 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Smpd4
105 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:254
Count of miRNA genes:171
Interacting mature miRNAs:191
Transcripts:ENSRNOT00000043545
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115635142486241447Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116034659086241447Rat
634339Niddm50Non-insulin dependent diabetes mellitus QTL 503.32blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)116642214886241447Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116642214886241447Rat
2302043Pia27Pristane induced arthritis QTL 2718.60.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)118256654583440803Rat

Markers in Region
RH134498  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21183,362,751 - 83,362,964 (-)MAPPERmRatBN7.2
Rnor_6.01187,546,257 - 87,546,469NCBIRnor6.0
Rnor_5.01190,598,879 - 90,599,091UniSTSRnor5.0
RGSC_v3.41185,352,398 - 85,352,610UniSTSRGSC3.4
Celera1182,134,410 - 82,134,622UniSTS
RH 3.4 Map11707.7UniSTS
Cytogenetic Map11q23UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 34 44 31 16 31 66 29 41 11
Low 9 13 10 3 10 8 11 8 6 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000043545   ⟹   ENSRNOP00000047410
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1183,362,534 - 83,386,250 (-)Ensembl
Rnor_6.0 Ensembl1187,522,971 - 87,546,687 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000102059   ⟹   ENSRNOP00000090299
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1183,362,534 - 83,386,250 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000102536   ⟹   ENSRNOP00000089916
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1183,362,534 - 83,386,250 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000104577   ⟹   ENSRNOP00000082466
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1183,363,395 - 83,386,250 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000107761   ⟹   ENSRNOP00000096822
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1183,362,534 - 83,386,178 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000110966   ⟹   ENSRNOP00000096298
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1183,362,534 - 83,382,348 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000114247   ⟹   ENSRNOP00000080381
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1183,362,534 - 83,386,250 (-)Ensembl
RefSeq Acc Id: NM_001167806   ⟹   NP_001161278
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21183,362,534 - 83,386,250 (-)NCBI
Rnor_6.01187,522,971 - 87,546,687 (+)NCBI
Rnor_5.01190,575,599 - 90,599,309 (+)NCBI
RGSC_v3.41185,352,180 - 85,375,918 (-)RGD
Celera1182,134,192 - 82,157,831 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008768878   ⟹   XP_008767100
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21183,362,534 - 83,386,132 (-)NCBI
Rnor_6.01187,523,062 - 87,546,685 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039088264   ⟹   XP_038944192
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21183,362,534 - 83,386,257 (-)NCBI
RefSeq Acc Id: XM_039088265   ⟹   XP_038944193
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21183,362,534 - 83,386,257 (-)NCBI
RefSeq Acc Id: XM_039088266   ⟹   XP_038944194
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21183,362,534 - 83,370,440 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001161278   ⟸   NM_001167806
- UniProtKB: A6JSK9 (UniProtKB/TrEMBL),   F1MAK9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008767100   ⟸   XM_008768878
- Peptide Label: isoform X1
- UniProtKB: A0A8I6B4V4 (UniProtKB/TrEMBL),   F1MAK9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000047410   ⟸   ENSRNOT00000043545
RefSeq Acc Id: XP_038944193   ⟸   XM_039088265
- Peptide Label: isoform X3
- UniProtKB: F1MAK9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038944192   ⟸   XM_039088264
- Peptide Label: isoform X2
- UniProtKB: F1MAK9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038944194   ⟸   XM_039088266
- Peptide Label: isoform X4
- UniProtKB: A0A8I5ZPX8 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000089916   ⟸   ENSRNOT00000102536
RefSeq Acc Id: ENSRNOP00000080381   ⟸   ENSRNOT00000114247
RefSeq Acc Id: ENSRNOP00000082466   ⟸   ENSRNOT00000104577
RefSeq Acc Id: ENSRNOP00000096298   ⟸   ENSRNOT00000110966
RefSeq Acc Id: ENSRNOP00000090299   ⟸   ENSRNOT00000102059
RefSeq Acc Id: ENSRNOP00000096822   ⟸   ENSRNOT00000107761

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1MAK9-F1-model_v2 AlphaFold F1MAK9 1-824 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13698322
Promoter ID:EPDNEW_R8846
Type:multiple initiation site
Name:Smpd4_1
Description:sphingomyelin phosphodiesterase 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01187,522,971 - 87,523,031EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310674 AgrOrtholog
BioCyc Gene G2FUF-20602 BioCyc
BioCyc Pathway PWY3DJ-11281 [sphingomyelin metabolism] BioCyc
Ensembl Genes ENSRNOG00000001875 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000043545 ENTREZGENE
  ENSRNOT00000043545.6 UniProtKB/TrEMBL
  ENSRNOT00000102059.1 UniProtKB/TrEMBL
  ENSRNOT00000102536 ENTREZGENE
  ENSRNOT00000102536.1 UniProtKB/TrEMBL
  ENSRNOT00000104577.1 UniProtKB/TrEMBL
  ENSRNOT00000107761 ENTREZGENE
  ENSRNOT00000107761.1 UniProtKB/TrEMBL
  ENSRNOT00000110966.1 UniProtKB/TrEMBL
  ENSRNOT00000114247 ENTREZGENE
  ENSRNOT00000114247.1 UniProtKB/TrEMBL
InterPro Sphingomy_SMPD4 UniProtKB/TrEMBL
NCBI Gene 303790 ENTREZGENE
PANTHER PTHR12988 UniProtKB/TrEMBL
  SPHINGOMYELIN PHOSPHODIESTERASE 4 UniProtKB/TrEMBL
Pfam mit_SMPDase UniProtKB/TrEMBL
PhenoGen Smpd4 PhenoGen
RatGTEx ENSRNOG00000001875 RatGTEx
UniProt A0A8I5ZPX8 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZXZ7_RAT UniProtKB/TrEMBL
  A0A8I6ADG7_RAT UniProtKB/TrEMBL
  A0A8I6B4V4 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GIS3_RAT UniProtKB/TrEMBL
  A0A8I6GLJ2_RAT UniProtKB/TrEMBL
  A6JSK9 ENTREZGENE, UniProtKB/TrEMBL
  F1MAK9 ENTREZGENE, UniProtKB/TrEMBL
  Q5U2Q9_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-16 Smpd4  sphingomyelin phosphodiesterase 4  Smpd4  sphingomyelin phosphodiesterase 4, neutral membrane  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-27 Smpd4  sphingomyelin phosphodiesterase 4  RGD1310674  similar to RIKEN cDNA 4122402O22  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1310674  similar to RIKEN cDNA 4122402O22  RGD1310674_predicted  similar to RIKEN cDNA 4122402O22 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1310674_predicted  similar to RIKEN cDNA 4122402O22 (predicted)  LOC303790_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC303790_predicted  similar to RIKEN cDNA 4122402O22 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL