SMPD4BP (sphingomyelin phosphodiesterase 4B, pseudogene) - Rat Genome Database

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Gene: SMPD4BP (sphingomyelin phosphodiesterase 4B, pseudogene) Homo sapiens
Analyze
Symbol: SMPD4BP
Name: sphingomyelin phosphodiesterase 4B, pseudogene
RGD ID: 14988266
HGNC Page HGNC:24761
Description: INTERACTS WITH aristolochic acid A; sunitinib
Type: pseudo (Ensembl: transcribed_processed_pseudogene)
RefSeq Status: VALIDATED
Related Functional Gene: SMPD4  
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382131,492,813 - 131,521,576 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2131,492,813 - 131,520,421 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p14 Ensembl2131,492,813 - 131,521,573 (+)EnsemblGRCh38hg38GRCh38
GRCh372132,250,386 - 132,279,149 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map2q21.1NCBI
HuRef2124,243,848 - 124,272,640 (+)NCBIHuRef
CHM1_12132,254,007 - 132,282,771 (+)NCBICHM1_1
T2T-CHM13v2.02131,927,581 - 131,956,350 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:12477932   PMID:15146197   PMID:16344560  


Genomics

Variants

.
Variants in SMPD4BP
1 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:2587
Count of miRNA genes:780
Interacting mature miRNAs:943
Transcripts:ENST00000415574, ENST00000416745, ENST00000426369, ENST00000438378, ENST00000536977, ENST00000538598, ENST00000543513
Prediction methods:Microtar, 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 2256 2162 1452 386 1137 232 3854 1576 2999 224 1386 1501 165 1165 2346 3
Low 176 822 270 235 811 231 501 617 709 194 62 107 5 39 442 1
Below cutoff 1 1 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NR_026922 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC073869 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC093838 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC104778 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK123346 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK293811 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK300337 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK303293 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK304811 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK308371 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC093080 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BF222164 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CN337607 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CN337608 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068276 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DA277444 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DC407534 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KF456710 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000415574
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2131,492,813 - 131,520,421 (+)Ensembl
RefSeq Acc Id: ENST00000438378
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2131,492,813 - 131,521,573 (+)Ensembl
RefSeq Acc Id: ENST00000685161
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2131,493,076 - 131,501,852 (+)Ensembl
RefSeq Acc Id: ENST00000685795
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2131,493,062 - 131,501,852 (+)Ensembl
RefSeq Acc Id: ENST00000687223
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2131,493,062 - 131,501,852 (+)Ensembl
RefSeq Acc Id: ENST00000692700
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2131,492,902 - 131,506,919 (+)Ensembl
RefSeq Acc Id: NR_026922
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382131,492,813 - 131,521,576 (+)NCBI
T2T-CHM13v2.02131,927,581 - 131,956,350 (+)NCBI
Sequence:
Protein Sequences
GenBank Protein BAC85587 (Get FASTA)   NCBI Sequence Viewer  
  BAG57217 (Get FASTA)   NCBI Sequence Viewer  
  BAG62082 (Get FASTA)   NCBI Sequence Viewer  
  BAG64368 (Get FASTA)   NCBI Sequence Viewer  
  BAG65561 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences


Additional Information

Database Acc Id Source(s)
COSMIC SMPD4BP COSMIC
Ensembl Genes ENSG00000152117 Ensembl
  ENSG00000293311 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000438378 ENTREZGENE
GTEx ENSG00000152117 GTEx
  ENSG00000293311 GTEx
HGNC ID HGNC:24761 ENTREZGENE
Human Proteome Map SMPD4BP Human Proteome Map
NCBI Gene SMPD4BP ENTREZGENE