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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SIGLEC16 Gene

pseudogene   GIFtS: 35
GCID: GC19P050473

Sialic Acid Binding Ig-Like Lectin 16 (Gene/Pseudogene)

(Previous names: sialic acid binding Ig-like lectin, pseudogene 16)
(Previous symbol: SIGLECP16)
  Search for SIGLEC16
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Sialic Acid Binding Ig-Like Lectin 16 (Gene/Pseudogene)1 2
SIGLECP161 2 3
Siglec-P162 3
Sialic Acid Binding Ig-Like Lectin, Pseudogene 161
Siglec-163

External Ids:    HGNC: 248511   Entrez Gene: 4007092   Ensembl: ENSG000001616437   UniProtKB: A6NMB13   
ORGUL members:         
NONCODE14:n405659 n387087 n383530      

Export aliases for SIGLEC16 gene to outside databases

Previous GC identifers: GC19P055168 GC19P046849


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for SIGLEC16 Gene: 
SIGLEC16 (sialic acid binding Ig-like lectin 16 (gene/pseudogene)) is a pseudogene, and is affiliated with the lncRNA class. Among its related super-pathways are Immune System and DAP12 signaling.

UniProtKB/Swiss-Prot: SIG16_HUMAN, A6NMB1
Function: Putative adhesion molecule that mediates sialic-acid dependent binding to cells (By similarity)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000019.9  NC_018930.2  NT_011109.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SIGLEC16 gene promoter:
         E2F-3a   E2F   E2F-1   FOXO1a   E2F-2   FOXO1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for SIGLEC16

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SIGLEC16


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19q13.33   Ensembl cytogenetic band:  19q13.33   HGNC cytogenetic band: 19q13.3

SIGLEC16 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SIGLEC16 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P050473:  view genomic region     (about GC identifiers)

Start:
50,472,857 bp from pter      End:
50,479,076 bp from pter
Size:
6,220 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for SIGLEC16

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: SIG16_HUMAN, A6NMB1 (See protein sequence)
Recommended Name: Sialic acid-binding Ig-like lectin 16 precursor  
Size: 481 amino acids; 52992 Da
Subcellular location: Membrane; Single-pass type I membrane protein
Caution: According to PubMed:18629938, the SIGLECP16 sequence, that was initially classified as a pseudogene, has
a 4 bp deletion when compared with the sequence shown in this entry. This deletion is a polymorphism with a
frequency of around 50% in the UK population. The frameshifted allele is non-functional whereas the sequence
displayed here seems to be functional. The functional allele has been named SIGLEC16 in PubMed:18629938

Explore the universe of human proteins at neXtProt for SIGLEC16: NX_A6NMB1

SIGLEC16 Protein expression data from MOPED1, PaxDb2 and MAXQB3 : --
Reactome Protein details: A6NMB1
Human Recombinant Protein Products for SIGLEC16: 

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Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005886plasma membrane TAS--
GO:0016021integral to membrane IEA--

SIGLEC16 for ontologies           About GeneDecksing



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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
HGNC Gene Families: 
SIGLEC: Sialic acid binding Ig-like lectins
C2SET: Immunoglobulin superfamily / C2-set domain containing
ISET: Immunoglobulin superfamily / I-set domain containing
VSET: Immunoglobulin superfamily / V-set domain containing

5/8 InterPro protein domains (see all 8):
 IPR003598 Ig_sub2
 IPR007110 Ig-like_dom
 IPR013162 CD80_C2-set
 IPR003006 Ig/MHC_CS
 IPR003599 Ig_sub

Graphical View of Domain Structure for InterPro Entry A6NMB1

ProtoNet protein and cluster: A6NMB1

UniProtKB/Swiss-Prot: SIG16_HUMAN, A6NMB1
Similarity: Belongs to the immunoglobulin superfamily. SIGLEC (sialic acid binding Ig-like lectin) family
Similarity: Contains 3 Ig-like C2-type (immunoglobulin-like) domains
Similarity: Contains 1 Ig-like V-type (immunoglobulin-like) domain


SIGLEC16 for domains           About GeneDecksing


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

Molecular Function:

     UniProtKB/Swiss-Prot Summary: SIG16_HUMAN, A6NMB1
Function: Putative adhesion molecule that mediates sialic-acid dependent binding to cells (By similarity)

Animal Models:

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(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
About This Section

SuperPaths for SIGLEC16 About                                                                                                See pathways by source

SuperPathContained pathways About
1Immune System
Immune System0.56
Innate Immune System0.50
2Signaling by FGFR
DAP12 interactions0.91

Pathways by source                                                                                                                                                                 See SuperPaths
Show all pathways


3        Reactome Pathways for SIGLEC16
    DAP12 interactions
Immune System
Innate Immune System



SIGLEC16 for pathways           About GeneDecksing

Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SIGLEC16

Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0007155cell adhesion IEA--
GO:0045087innate immune response TAS--

SIGLEC16 for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
Browse Small Molecules at EMD Millipore
Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for SIGLEC16 (SIG16)

Search CenterWatch for drugs/clinical trials and news about SIGLEC16

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

Unigene Clusters for SIGLEC16:

Sialic acid binding Ig-like lectin 16 (gene/pseudogene)
Hs.568076  [show with all ESTs], Hs.738007
Unigene Representative Sequences: AK301031, BC039008
4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000602139 ENST00000599858 ENST00000417280 ENST00000456956(uc002prf.3 uc010ybj.1 uc010ybk.1)

miRNA
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  QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SIGLEC16

Additional mRNA sequence: 

BC039008.1 EU330985.1 

1 DOTS entry:

DT.97792297 

3 AceView cDNA sequences:

BC030222 AI913240 BC039008 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

SIGLEC16 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
SIGLEC16 Expression
About this image


Genevestigator expression for SIGLEC16

SOURCE GeneReport for Unigene clusters: Hs.568076 Hs.738007

UniProtKB/Swiss-Prot: SIG16_HUMAN, A6NMB1
Tissue specificity: Expressed in bone marrow, fetal brain, fetal liver, lung and salivary gland. Detected in
brain, macrophage, cancerous esophagus and lung at protein level

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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SIGLEC16

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section
  --

ENSEMBL Gene Tree for SIGLEC16 (if available)
TreeFam Gene Tree for SIGLEC16 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
Paralogs for SIGLEC16 gene
11 SIMAP similar genes for SIGLEC16 using alignment to 2 protein entries:     SIG16_HUMAN (see all proteins):
SIGLEC11    SIGLEC10    CD33    SIGLEC14    SIGLEC12    CEA
SIGLEC9    SIGLEC7    SIGLEC8    SIGLEC5    SIGLEC6

SIGLEC16 for paralogs           About GeneDecksing



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/214 SNPs in SIGLEC16 are shown (see all 214)    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 19 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1459753721,2
--50470993(+) TGCTTA/GTCTTT 1 -- us2k10--------
rs789189081,2
F--50471051(+) AGTGTA/GTATGT 1 -- us2k11Minor allele frequency- G:0.01WA 118
rs621151631,2
C,F--50471178(+) AATTAC/AAAATA 1 -- us2k11Minor allele frequency- A:0.50NA 2
rs1916725371,2
--50471211(+) CATAAA/CACAAA 1 -- us2k10--------
rs43109771,2
C,F,A--50471300(+) tgcagT/Ggacgg 1 -- us2k18Minor allele frequency- G:0.24WA NA CSA EA 367
rs1415650941,2
--50471365(+) GTCTCC/GTGAGT 1 -- us2k10--------
rs1842648171,2
C--50471390(+) GTGAGC/TGCCAC 1 -- us2k10--------
rs1881112911,2
--50471431(+) GAGACA/GGGGTT 1 -- us2k10--------
rs355469221,2
C--50471710(+) AAAAA-/AGTGTA 1 -- us2k10--------
rs118806381,2
C,F,H--50471823(+) caagtA/Tcccat 1 -- us2k12Minor allele frequency- T:0.11NA WA 120

HapMap Linkage Disequilibrium report for SIGLEC16 (50472857 - 50479076 bp)

Structural Variations
     Database of Genomic Variants (DGV) 3 variations for SIGLEC16:    About this table     
Variant IDTypeSubtypePubMed ID
dgv54n68CNV Loss17160897
nsv9739CNV Gain+Loss18304495
nsv7309OTHER Inversion18451855


Human Gene Mutation Database (HGMD): SIGLEC16
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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

SIGLEC16 for disorders           About MalaCards

SIGLEC16 for disorders           About GeneDecksing


Export disorders for SIGLEC16 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
About This Section

PubMed articles for SIGLEC16 gene integrated from 9 sources:
(articles sorted by number of sources associating them with SIGLEC16)
    Utopia: connect your pdf to the dynamic
world of online information

  1. SIGLEC16 encodes a DAP12-associated receptor expressed in macrophages that evolved from its inhibitory counterpart SIGLEC11 and has functional and non-functional alleles in humans. (PubMed id 18629938)1, 2, 3 Cao H....Barrow A.D. (2008)
  2. Cloning and characterization of human Siglec-11. A recently evolved signaling molecule that can interact with SHP-1 and SHP-2 and is expressed by tissue macrophages, including brain microglia. (PubMed id 11986327)1, 2, 3 Angata T....Varki A. (2002)
  3. The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)1, 2 Grimwood J.... Lucas S.M. (2004)
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
  6. A second uniquely human mutation affecting sialic acid biology. (PubMed id 11546777)1 Angata T.... Varki A. (2001)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 400709 HGNC: 24851 AceView: LOC400709 Ensembl:ENSG00000161643 euGenes: HUgn400709
ECgene: SIGLEC16 H-InvDB: SIGLEC16

(According to HUGE)
About This Section
  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
NameDescription
PharmGKB entry for SIGLEC16 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for SIGLEC16 gene:
Search GeneIP for patents involving SIGLEC16

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
About This Section

 
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 inGenious Targeting Laboratory - Custom generated mouse model solutions for SIGLEC16
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GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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