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SMPDL3A sphingomyelin phosphodiesterase acid like 3A [ Homo sapiens (human) ]

Gene ID: 10924, updated on 13-Mar-2020

Summary

Official Symbol
SMPDL3Aprovided by HGNC
Official Full Name
sphingomyelin phosphodiesterase acid like 3Aprovided by HGNC
Primary source
HGNC:HGNC:17389
See related
Ensembl:ENSG00000172594 MIM:610728
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
ASM3A; ASML3a; yR36GH4.1
Expression
Ubiquitous expression in colon (RPKM 18.5), small intestine (RPKM 18.4) and 25 other tissues See more
Orthologs

Genomic context

See SMPDL3A in Genome Data Viewer
Location:
6q22.31
Exon count:
9
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (122788456..122809720)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (123109601..123130865)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 564, pseudogene Neighboring gene fatty acid binding protein 7 Neighboring gene ATP synthase membrane subunit g pseudogene 2 Neighboring gene clavesin 2

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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ20177

Gene Ontology Provided by GOA

Function Evidence Code Pubs
phosphoric diester hydrolase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
phosphoric diester hydrolase activity IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
NOT sphingomyelin phosphodiesterase activity IDA
Inferred from Direct Assay
more info
PubMed 
zinc ion binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
nucleoside triphosphate catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
NOT sphingomyelin catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
extracellular exosome HDA PubMed 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
extracellular space IMP
Inferred from Mutant Phenotype
more info
PubMed 

General protein information

Preferred Names
acid sphingomyelinase-like phosphodiesterase 3a
Names
0610010C24Rik
ASM-like phosphodiesterase 3a
NP_001273067.1
NP_006705.1
XP_005266854.1
XP_005266855.1
XP_005266856.1
XP_005266858.1
XP_005266859.1
XP_016865692.1
XP_016865693.1

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_001286138.1NP_001273067.1  acid sphingomyelinase-like phosphodiesterase 3a isoform b

    See identical proteins and their annotated locations for NP_001273067.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon in the 5' coding region and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AK301365, DA510600, Y08136
    Consensus CDS
    CCDS69190.1
    UniProtKB/Swiss-Prot
    Q92484
    Related
    ENSP00000442152.1, ENST00000539041.5
    Conserved Domains (2) summary
    COG1409
    Location:13206
    CpdA; 3',5'-cyclic AMP phosphodiesterase CpdA [Signal transduction mechanisms]
    cd00842
    Location:1205
    MPP_ASMase; acid sphingomyelinase and related proteins, metallophosphatase domain
  2. NM_006714.5NP_006705.1  acid sphingomyelinase-like phosphodiesterase 3a isoform a precursor

    See identical proteins and their annotated locations for NP_006705.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    BC018999, DA510600, Y08136
    Consensus CDS
    CCDS5128.1
    UniProtKB/Swiss-Prot
    Q92484
    Related
    ENSP00000357425.4, ENST00000368440.5
    Conserved Domains (1) summary
    cd00842
    Location:40336
    MPP_ASMase; acid sphingomyelinase and related proteins, metallophosphatase domain

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_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    122788456..122809720
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017010204.2XP_016865693.1  acid sphingomyelinase-like phosphodiesterase 3a isoform X5

    Conserved Domains (2) summary
    COG1409
    Location:9119
    CpdA; 3',5'-cyclic AMP phosphodiesterase CpdA [Signal transduction mechanisms]
    cl13995
    Location:4118
    MPP_superfamily; metallophosphatase superfamily, metallophosphatase domain
  2. XM_005266798.3XP_005266855.1  acid sphingomyelinase-like phosphodiesterase 3a isoform X2

    See identical proteins and their annotated locations for XP_005266855.1

    Conserved Domains (1) summary
    cl13995
    Location:40247
    MPP_superfamily; metallophosphatase superfamily, metallophosphatase domain
  3. XM_017010203.2XP_016865692.1  acid sphingomyelinase-like phosphodiesterase 3a isoform X4

  4. XM_005266801.3XP_005266858.1  acid sphingomyelinase-like phosphodiesterase 3a isoform X5

    Conserved Domains (2) summary
    COG1409
    Location:9119
    CpdA; 3',5'-cyclic AMP phosphodiesterase CpdA [Signal transduction mechanisms]
    cl13995
    Location:4118
    MPP_superfamily; metallophosphatase superfamily, metallophosphatase domain
  5. XM_005266802.3XP_005266859.1  acid sphingomyelinase-like phosphodiesterase 3a isoform X6

    Conserved Domains (1) summary
    cl13995
    Location:1116
    MPP_superfamily; metallophosphatase superfamily, metallophosphatase domain
  6. XM_005266799.2XP_005266856.1  acid sphingomyelinase-like phosphodiesterase 3a isoform X3

    Conserved Domains (1) summary
    cd00842
    Location:40308
    MPP_ASMase; acid sphingomyelinase and related proteins, metallophosphatase domain
  7. XM_005266797.5XP_005266854.1  acid sphingomyelinase-like phosphodiesterase 3a isoform X1

    Conserved Domains (2) summary
    cd00842
    Location:14310
    MPP_ASMase; acid sphingomyelinase and related proteins, metallophosphatase domain
    pfam00149
    Location:50271
    Metallophos; Calcineurin-like phosphoesterase
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