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SMPDL3B sphingomyelin phosphodiesterase acid like 3B [ Homo sapiens (human) ]

Gene ID: 27293, updated on 13-Mar-2020

Summary

Official Symbol
SMPDL3Bprovided by HGNC
Official Full Name
sphingomyelin phosphodiesterase acid like 3Bprovided by HGNC
Primary source
HGNC:HGNC:21416
See related
Ensembl:ENSG00000130768 MIM:617737
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ASML3B
Expression
Biased expression in duodenum (RPKM 6.3), colon (RPKM 6.3) and 13 other tissues See more
Orthologs

Genomic context

See SMPDL3B in Genome Data Viewer
Location:
1p35.3
Exon count:
10
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (27934955..27959152)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (28261456..28285663)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene thymocyte selection associated family member 2 Neighboring gene replication protein A2 Neighboring gene XK related 8 Neighboring gene EYA transcriptional coactivator and phosphatase 3 Neighboring gene RNA, 7SL, cytoplasmic 559, pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
hydrolase activity, acting on glycosyl bonds IEA
Inferred from Electronic Annotation
more info
 
phosphoric diester hydrolase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
phosphoric diester hydrolase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
phosphoric diester hydrolase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
sphingomyelin phosphodiesterase activity IEA
Inferred from Electronic Annotation
more info
 
zinc ion binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
biological_process ND
No biological Data available
more info
 
inflammatory response IEA
Inferred from Electronic Annotation
more info
 
innate immune response IEA
Inferred from Electronic Annotation
more info
 
membrane lipid catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of inflammatory response ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of toll-like receptor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
sphingomyelin catabolic process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
anchored component of membrane IEA
Inferred from Electronic Annotation
more info
 
extracellular exosome HDA PubMed 
extracellular space HDA PubMed 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
acid sphingomyelinase-like phosphodiesterase 3b
Names
ASM-like phosphodiesterase 3b

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001009568.2NP_001009568.1  acid sphingomyelinase-like phosphodiesterase 3b isoform 2 precursor

    See identical proteins and their annotated locations for NP_001009568.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AL512288, BC014444, BP284513, DC370191
    Consensus CDS
    CCDS30656.1
    UniProtKB/Swiss-Prot
    Q92485
    Related
    ENSP00000362995.4, ENST00000373888.8
    Conserved Domains (1) summary
    cd00842
    Location:23323
    MPP_ASMase; acid sphingomyelinase and related proteins, metallophosphatase domain
  2. NM_001304579.2NP_001291508.1  acid sphingomyelinase-like phosphodiesterase 3b isoform 3

    See identical proteins and their annotated locations for NP_001291508.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate splice junction at the 5' end of an internal exon compared to variant 1, which causes translation initiation at a downstream start codon. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AK293566, AL512288, BP284513, CA425405
    UniProtKB/TrEMBL
    B4DEC6
    Conserved Domains (1) summary
    cl13995
    Location:3117
    MPP_superfamily; metallophosphatase superfamily, metallophosphatase domain
  3. NM_014474.4NP_055289.2  acid sphingomyelinase-like phosphodiesterase 3b isoform 1 precursor

    See identical proteins and their annotated locations for NP_055289.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AK301349, AK316500, AL512288, CA425405
    Consensus CDS
    CCDS30655.1
    UniProtKB/Swiss-Prot
    Q92485
    UniProtKB/TrEMBL
    B4DW34
    Related
    ENSP00000363001.3, ENST00000373894.8
    Conserved Domains (2) summary
    cd00842
    Location:23323
    MPP_ASMase; acid sphingomyelinase and related proteins, metallophosphatase domain
    pfam00149
    Location:82281
    Metallophos; Calcineurin-like phosphoesterase

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    27934955..27959152
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011541259.2XP_011539561.1  acid sphingomyelinase-like phosphodiesterase 3b isoform X1

    Conserved Domains (2) summary
    cd00842
    Location:53353
    MPP_ASMase; acid sphingomyelinase and related proteins, metallophosphatase domain
    pfam00149
    Location:112311
    Metallophos; Calcineurin-like phosphoesterase
  2. XM_011541260.2XP_011539562.1  acid sphingomyelinase-like phosphodiesterase 3b isoform X2

    Conserved Domains (2) summary
    cd00842
    Location:1246
    MPP_ASMase; acid sphingomyelinase and related proteins, metallophosphatase domain
    pfam00149
    Location:5204
    Metallophos; Calcineurin-like phosphoesterase
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