SMPD5 (sphingomyelin phosphodiesterase 5) - Rat Genome Database

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Gene: SMPD5 (sphingomyelin phosphodiesterase 5) Sus scrofa
Analyze
Symbol: SMPD5
Name: sphingomyelin phosphodiesterase 5
RGD ID: 14249229
Description: ENCODES a protein that exhibits sphingomyelin phosphodiesterase activity (inferred); INVOLVED IN ceramide metabolic process (ortholog); FOUND IN endoplasmic reticulum membrane (inferred); extracellular region (inferred); membrane (inferred); INTERACTS WITH deoxynivalenol
Type: protein-coding
RefSeq Status: MODEL
Previously known as: sphingomyelin phosphodiesterase 5 (pseudogene); sphingomyelin phosphodiesterase 5, pseudogene
RGD Orthologs
Human
Mouse
Rat
Squirrel
Alliance Orthologs
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.14639,228 - 643,057 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24587,417 - 590,516 (+)NCBISscrofa10.2Sscrofa10.2susScr3
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
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
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
SMPD5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh388144,049,398 - 144,050,059 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl8144,049,079 - 144,051,203 (+)EnsemblGRCh38hg38GRCh38
GRCh378145,104,299 - 145,104,960 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 368145,176,011 - 145,178,536 (+)NCBINCBI36Build 36hg18NCBI36
Cytogenetic Map8q24.3NCBI
HuRef8140,378,671 - 140,381,988 (+)NCBIHuRef
CHM1_18145,143,113 - 145,146,430 (+)NCBICHM1_1
T2T-CHM13v2.08145,210,248 - 145,210,909 (+)NCBIT2T-CHM13v2.0
Smpd5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391576,178,478 - 76,181,096 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1576,178,548 - 76,181,096 (+)EnsemblGRCm39 Ensembl
GRCm381576,294,278 - 76,296,896 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1576,294,348 - 76,296,896 (+)EnsemblGRCm38mm10GRCm38
MGSCv371576,124,717 - 76,127,326 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361576,124,697 - 76,126,431 (+)NCBIMGSCv36mm8
Celera1577,794,347 - 77,796,956 (+)NCBICelera
Cytogenetic Map15D3NCBI
cM Map1535.67NCBI
Smpd5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87109,889,532 - 109,892,428 (+)NCBIGRCr8
mRatBN7.27108,009,182 - 108,011,767 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7108,009,173 - 108,011,763 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7109,752,870 - 109,755,411 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07111,976,554 - 111,979,095 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07111,935,104 - 111,937,643 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.07117,351,694 - 117,354,241 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7117,351,648 - 117,354,084 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07117,337,465 - 117,340,002 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47114,323,149 - 114,327,026 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049364708,139,207 - 8,142,061 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0

Variants

.
Variants in SMPD5
83 total Variants

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 hemolymphoid system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium
Low 1 3 2 1 1 2
Below cutoff 5 2 3 1 1 15 1 1

Sequence


Reference Sequences
RefSeq Acc Id: XM_021090358   ⟹   XP_020946017
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.14639,228 - 643,057 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_020946017 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSSCP00000006331
  ENSSSCP00000006331.4
  ENSSSCP00000067021.1
Reference Protein Sequences
RefSeq Acc Id: XP_020946017   ⟸   XM_021090358
- UniProtKB: F1RSL3 (UniProtKB/TrEMBL)
- Sequence:
Protein Domains
Endonuclease/exonuclease/phosphatase


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000005922 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000006502 ENTREZGENE
  ENSSSCT00000006502.5 UniProtKB/TrEMBL
  ENSSSCT00000085549.2 UniProtKB/TrEMBL
Gene3D-CATH 3.60.10.10 UniProtKB/TrEMBL
InterPro Endo/exonu/phosph_ase_sf UniProtKB/TrEMBL
  Endo/exonuclease/phosphatase UniProtKB/TrEMBL
  Sph/SMPD2-like UniProtKB/TrEMBL
  Sphingomyelinase/PLipase_C UniProtKB/TrEMBL
NCBI Gene SMPD5 ENTREZGENE
PANTHER SPHINGOMYELIN PHOSPHODIESTERASE 5 UniProtKB/TrEMBL
  SPHINGOMYELINASE FAMILY MEMBER UniProtKB/TrEMBL
Pfam Exo_endo_phos UniProtKB/TrEMBL
Superfamily-SCOP SSF56219 UniProtKB/TrEMBL
UniProt A0A5G2QYK0_PIG UniProtKB/TrEMBL
  F1RSL3 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:109161 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-08-04 SMPD5  sphingomyelin phosphodiesterase 5  SMPD5  sphingomyelin phosphodiesterase 5 (pseudogene)  Symbol and/or name change 5135510 APPROVED
2020-06-26 SMPD5  sphingomyelin phosphodiesterase 5 (pseudogene)  SMPD5  sphingomyelin phosphodiesterase 5, pseudogene  Symbol and/or name change 5135510 APPROVED
2019-08-13 SMPD5  sphingomyelin phosphodiesterase 5, pseudogene  SMPD5  sphingomyelin phosphodiesterase 5  Symbol and/or name change 5135510 APPROVED