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 have 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 localize to 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 6-propyl-2-thiouracil; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Also 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: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21183,362,534 - 83,386,257 (-)NCBI
Rnor_6.0 Ensembl1187,522,971 - 87,546,687 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01187,522,971 - 87,546,687 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01190,575,599 - 90,599,309 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41185,352,180 - 85,375,918 (-)NCBIRGSC3.4rn4RGSC3.4
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


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

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 (-)NCBI
Rnor_6.0 Ensembl1187,522,971 - 87,546,687 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01187,522,971 - 87,546,687 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01190,575,599 - 90,599,309 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41185,352,180 - 85,375,918 (-)NCBIRGSC3.4rn4RGSC3.4
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
GRCh38.p13 Ensembl2130,151,392 - 130,182,750 (-)EnsemblGRCh38hg38GRCh38
GRCh382130,151,392 - 130,181,757 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372130,908,965 - 130,939,330 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362130,625,450 - 130,656,164 (-)NCBINCBI36hg18NCBI36
Celera2124,183,727 - 124,215,108 (-)NCBI
Cytogenetic Map2q21.1NCBI
HuRef2123,204,890 - 123,236,080 (-)NCBIHuRef
CHM1_12130,912,697 - 130,944,055 (-)NCBICHM1_1
Smpd4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391617,437,218 - 17,462,694 (+)NCBIGRCm39mm39
GRCm39 Ensembl1617,437,218 - 17,462,692 (+)Ensembl
GRCm381617,619,354 - 17,644,830 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1617,619,354 - 17,644,828 (+)EnsemblGRCm38mm10GRCm38
MGSCv371617,619,447 - 17,644,923 (+)NCBIGRCm37mm9NCBIm37
MGSCv361617,532,917 - 17,556,946 (+)NCBImm8
Celera1618,192,592 - 18,218,068 (+)NCBICelera
Cytogenetic Map16A3NCBI
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 (-)NCBI
ROS_Cfam_1.02631,806,536 - 31,827,917 (-)NCBI
UMICH_Zoey_3.12629,852,373 - 29,873,768 (-)NCBI
UNSW_CanFamBas_1.02629,476,170 - 29,497,990 (-)NCBI
UU_Cfam_GSD_1.02630,565,815 - 30,587,424 (-)NCBI
Smpd4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118140,077,691 - 140,106,127 (-)NCBI
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 - 50,689,353 (+)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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110131,882 - 162,244 (+)NCBI
ChlSab1.1 Ensembl10136,784 - 163,555 (+)Ensembl
Smpd4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624945566,203 - 592,254 (-)NCBI

Position Markers
RH134498  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21183,362,751 - 83,362,964 (-)MAPPER
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


QTLs in Region (Rnor_6.0)
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)111901627290463843Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115785881090463843Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115994302390463843Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116449467190463843Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116964970890463843Rat

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.


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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1187,522,971 - 87,546,687 (+)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
RefSeq Status:
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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21183,362,534 - 83,386,257 (-)NCBI
RefSeq Acc Id: XM_039088265   ⟹   XP_038944193
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21183,362,534 - 83,386,257 (-)NCBI
RefSeq Acc Id: XM_039088266   ⟹   XP_038944194
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21183,362,534 - 83,370,440 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001161278   ⟸   NM_001167806
- Sequence:
RefSeq Acc Id: XP_008767100   ⟸   XM_008768878
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000047410   ⟸   ENSRNOT00000043545
RefSeq Acc Id: XP_038944193   ⟸   XM_039088265
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038944192   ⟸   XM_039088264
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038944194   ⟸   XM_039088266
- Peptide Label: isoform X4

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
11 87529033 87529034 T A snv ACI/N (MCW), BN/SsN (MCW), Buf/N (MCW), WN/N (MCW), M520/N (MCW), MR/N (MCW), WKY/N (MCW), F344/NRrrc (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310674 AgrOrtholog
Ensembl Genes ENSRNOG00000001875 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000047410 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000043545 ENTREZGENE, UniProtKB/TrEMBL
InterPro Sphingomy_SMPD4 UniProtKB/TrEMBL
NCBI Gene 303790 ENTREZGENE
PANTHER PTHR12988 UniProtKB/TrEMBL
Pfam mit_SMPDase UniProtKB/TrEMBL
PhenoGen Smpd4 PhenoGen
UniProt F1MAK9_RAT 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