SMPD5 (sphingomyelin phosphodiesterase 5 (pseudogene)) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: SMPD5 (sphingomyelin phosphodiesterase 5 (pseudogene)) Homo sapiens
Analyze
Symbol: SMPD5
Name: sphingomyelin phosphodiesterase 5 (pseudogene)
RGD ID: 10449059
HGNC Page HGNC
Description: Predicted to have sphingomyelin phosphodiesterase activity. Predicted to be involved in ceramide biosynthetic process and sphingomyelin catabolic process. Predicted to localize to endoplasmic reticulum membrane and mitochondrial membrane; INTERACTS WITH propanal; 6-propyl-2-thiouracil (ortholog); bisphenol A (ortholog).
Type: pseudo
RefSeq Status: VALIDATED
Also known as: CTD-3065J16.6; MA-nSMase; mitochondria-associated nSMase; sphingomyelin phosphodiesterase 3; sphingomyelin phosphodiesterase 5; sphingomyelin phosphodiesterase 5, pseudogene; uncharacterized protein SMPD5
RGD Orthologs
Mouse
Rat
Squirrel
Pig
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl8144,049,079 - 144,051,522 (+)EnsemblGRCh38hg38GRCh38
GRCh388144,049,398 - 144,050,059 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh378145,104,299 - 145,104,960 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 368145,176,011 - 145,178,536 (+)NCBINCBI36hg18NCBI36
Cytogenetic Map8q24.3NCBI
HuRef8140,378,671 - 140,381,988 (+)NCBIHuRef
CHM1_18145,143,838 - 145,146,381 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Biological Process

Cellular Component

Molecular Function

References

References - curated
1. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:23579449  


Genomics

Comparative Map Data
SMPD5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl8144,049,079 - 144,051,522 (+)EnsemblGRCh38hg38GRCh38
GRCh388144,049,398 - 144,050,059 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh378145,104,299 - 145,104,960 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 368145,176,011 - 145,178,536 (+)NCBINCBI36hg18NCBI36
Cytogenetic Map8q24.3NCBI
HuRef8140,378,671 - 140,381,988 (+)NCBIHuRef
CHM1_18145,143,838 - 145,146,381 (+)NCBICHM1_1
Smpd5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391576,178,478 - 76,181,096 (+)NCBIGRCm39mm39
GRCm39 Ensembl1576,178,548 - 76,181,096 (+)Ensembl
GRCm381576,294,278 - 76,296,896 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1576,294,348 - 76,296,896 (+)EnsemblGRCm38mm10GRCm38
MGSCv371576,124,717 - 76,127,326 (+)NCBIGRCm37mm9NCBIm37
MGSCv361576,124,697 - 76,126,431 (+)NCBImm8
Celera1577,794,347 - 77,796,956 (+)NCBICelera
Cytogenetic Map15D3NCBI
Smpd5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27108,009,182 - 108,011,767 (+)NCBI
Rnor_6.0 Ensembl7117,351,648 - 117,354,084 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07117,351,694 - 117,354,241 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07117,337,465 - 117,340,002 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47114,323,149 - 114,327,026 (+)NCBIRGSC3.4rn4RGSC3.4
Celera7104,361,922 - 104,364,461 (+)NCBICelera
Cytogenetic Map7q34NCBI
LOC101955719
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303713,106 - 715,902 (-)NCBI
SpeTri2.0NW_0049364708,139,207 - 8,142,061 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMPD5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.14639,228 - 643,057 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24587,417 - 590,516 (+)NCBISscrofa10.2Sscrofa10.2susScr3

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:762
Count of miRNA genes:511
Interacting mature miRNAs:574
Transcripts:ENST00000528912, ENST00000561181
Prediction methods:Miranda, Rnahybrid
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 sensory system adipose tissue appendage entire extraembryonic component
High
Medium 1 93 114 13 8 3 3 8 23
Low 375 910 299 161 1203 142 1007 178 1055 103 804 675 27 266 402 1
Below cutoff 1950 1803 1350 439 388 303 3111 1903 2580 267 596 846 140 918 2208 3

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000528912
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8144,049,557 - 144,051,522 (+)Ensembl
RefSeq Acc Id: ENST00000639008
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8144,049,079 - 144,051,203 (+)Ensembl
RefSeq Acc Id: NR_158554
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh388144,049,398 - 144,050,059 (+)NCBI

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 8q22.1-24.3(chr8:95606052-145054775)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053677]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053677]|See cases [RCV000053677] Chr8:95606052..145054775 [GRCh38]
Chr8:96618280..146280161 [GRCh37]
Chr8:96687456..146250965 [NCBI36]
Chr8:8q22.1-24.3
pathogenic
GRCh38/hg38 8q24.3(chr8:139447227-145054775)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053701]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053701]|See cases [RCV000053701] Chr8:139447227..145054775 [GRCh38]
Chr8:140459470..146280161 [GRCh37]
Chr8:140528652..146250965 [NCBI36]
Chr8:8q24.3
pathogenic
GRCh38/hg38 8q24.3(chr8:144002671-145054634)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053702]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053702]|See cases [RCV000053702] Chr8:144002671..145054634 [GRCh38]
Chr8:145076839..146280020 [GRCh37]
Chr8:145148827..146250824 [NCBI36]
Chr8:8q24.3
pathogenic
GRCh38/hg38 8q24.3(chr8:144002471-145054775)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000054311]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000054311]|See cases [RCV000054311] Chr8:144002471..145054775 [GRCh38]
Chr8:145076639..146280161 [GRCh37]
Chr8:145148627..146250965 [NCBI36]
Chr8:8q24.3
pathogenic
GRCh38/hg38 8q24.13-24.3(chr8:124514090-145054634)x3 copy number gain See cases [RCV000148117] Chr8:124514090..145054634 [GRCh38]
Chr8:125526331..146280020 [GRCh37]
Chr8:125595512..146250824 [NCBI36]
Chr8:8q24.13-24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:244417-145054775)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053604]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053604]|See cases [RCV000053604] Chr8:244417..145054775 [GRCh38]
Chr8:194417..146280161 [GRCh37]
Chr8:184417..146250965 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145054634)x3 copy number gain See cases [RCV000148092] Chr8:241530..145054634 [GRCh38]
Chr8:191530..146280020 [GRCh37]
Chr8:181530..146250824 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:52275 AgrOrtholog
COSMIC SMPD5 COSMIC
Ensembl Genes ENSG00000204791 Ensembl
GTEx ENSG00000204791 GTEx
HGNC ID HGNC:52275 ENTREZGENE
Human Proteome Map SMPD5 Human Proteome Map
NCBI Gene SMPD5 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-06-22 SMPD5  sphingomyelin phosphodiesterase 5 (pseudogene)  SMPD5  sphingomyelin phosphodiesterase 5, pseudogene  Symbol and/or name change 19259463 PROVISIONAL
2019-07-02 SMPD5  sphingomyelin phosphodiesterase 5, pseudogene  SMPD5  sphingomyelin phosphodiesterase 5  Symbol and/or name change 5135510 APPROVED