Human Gene SIGLEC11 (ENST00000447370.6_8) from GENCODE V47lift37
  Description: sialic acid binding Ig like lectin 11, transcript variant 1 (from RefSeq NM_052884.3)
Gencode Transcript: ENST00000447370.6_8
Gencode Gene: ENSG00000161640.15_11
Transcript (Including UTRs)
   Position: hg19 chr19:50,452,242-50,464,429 Size: 12,188 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg19 chr19:50,453,227-50,464,338 Size: 11,112 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathways
Other NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:50,452,242-50,464,429)mRNA (may differ from genome)Protein (698 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SIG11_HUMAN
DESCRIPTION: RecName: Full=Sialic acid-binding Ig-like lectin 11; Short=Sialic acid-binding lectin 11; Short=Siglec-11; Flags: Precursor;
FUNCTION: Putative adhesion molecule that mediates sialic-acid dependent binding to cells. Preferentially binds to alpha-2,8- linked sialic acid. The sialic acid recognition site may be masked by cis interactions with sialic acids on the same cell surface. In the immune response, may act as an inhibitory receptor upon ligand induced tyrosine phosphorylation by recruiting cytoplasmic phosphatase(s) via their SH2 domain(s) that block signal transduction through dephosphorylation of signaling molecules.
SUBUNIT: Interacts with PTPN6/SHP-1 and PTPN11/SHP-2 upon phosphorylation.
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein.
TISSUE SPECIFICITY: Expressed by macrophages in various tissues including Kupffer cells. Also found in brain microglia.
DOMAIN: Contains 1 copy of a cytoplasmic motif that is referred to as the immunoreceptor tyrosine-based inhibitor motif (ITIM). This motif is involved in modulation of cellular responses. The phosphorylated ITIM motif can bind the SH2 domain of several SH2- containing phosphatases.
PTM: Phosphorylated on tyrosine residues.
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.
CAUTION: It is uncertain whether Met-1 or Met-13 is the initiator.
SEQUENCE CAUTION: Sequence=AAK72907.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=AAQ88502.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 35.06 RPKM in Ovary
Total median expression: 68.14 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -34.7091-0.381 Picture PostScript Text
3' UTR -467.40985-0.475 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR013162 - CD80_C2-set
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR003006 - Ig/MHC_CS
IPR013098 - Ig_I-set
IPR003599 - Ig_sub
IPR003598 - Ig_sub2
IPR013106 - Ig_V-set
IPR013151 - Immunoglobulin

Pfam Domains:
PF00047 - Immunoglobulin domain
PF07679 - Immunoglobulin I-set domain
PF07686 - Immunoglobulin V-set domain
PF13895 - Immunoglobulin domain
PF13927 - Immunoglobulin domain

SCOP Domains:
48726 - Immunoglobulin

ModBase Predicted Comparative 3D Structure on Q96RL6
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0019902 phosphatase binding
GO:0030246 carbohydrate binding
GO:0033691 sialic acid binding

Biological Process:
GO:0007155 cell adhesion
GO:0098740 multi organism cell adhesion
GO:1900425 negative regulation of defense response to bacterium

Cellular Component:
GO:0009986 cell surface
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AF337818 - Homo sapiens sialic acid-binding lectin 11 (SIGLEC11) mRNA, complete cds.
AY358135 - Homo sapiens clone DNA180628 SIGLEC11 (UNQ9222) mRNA, complete cds.
AB072038 - Homo sapiens mRNA for Sialic acid-binding Ig-like lectin Siglec-12, complete cds.
BC156822 - Synthetic construct Homo sapiens clone IMAGE:100062514, MGC:190535 sialic acid binding Ig-like lectin 11 (SIGLEC11) mRNA, encodes complete protein.
JD482623 - Sequence 463647 from Patent EP1572962.
JD351977 - Sequence 333001 from Patent EP1572962.
JD448420 - Sequence 429444 from Patent EP1572962.
JD332404 - Sequence 313428 from Patent EP1572962.
JD175943 - Sequence 156967 from Patent EP1572962.
JD138316 - Sequence 119340 from Patent EP1572962.
JD344705 - Sequence 325729 from Patent EP1572962.
JD447115 - Sequence 428139 from Patent EP1572962.
JD085875 - Sequence 66899 from Patent EP1572962.
JD047633 - Sequence 28657 from Patent EP1572962.
JD129975 - Sequence 110999 from Patent EP1572962.
JD217426 - Sequence 198450 from Patent EP1572962.
JD112323 - Sequence 93347 from Patent EP1572962.
JD482798 - Sequence 463822 from Patent EP1572962.
JD277691 - Sequence 258715 from Patent EP1572962.
JD425461 - Sequence 406485 from Patent EP1572962.
JD105893 - Sequence 86917 from Patent EP1572962.
JD117226 - Sequence 98250 from Patent EP1572962.
JD425460 - Sequence 406484 from Patent EP1572962.
JD522384 - Sequence 503408 from Patent EP1572962.
JD425459 - Sequence 406483 from Patent EP1572962.
JD319621 - Sequence 300645 from Patent EP1572962.
JD329199 - Sequence 310223 from Patent EP1572962.
JD294078 - Sequence 275102 from Patent EP1572962.
JD247032 - Sequence 228056 from Patent EP1572962.
JD413457 - Sequence 394481 from Patent EP1572962.
JD198149 - Sequence 179173 from Patent EP1572962.
JD212755 - Sequence 193779 from Patent EP1572962.
JD247031 - Sequence 228055 from Patent EP1572962.
JD043877 - Sequence 24901 from Patent EP1572962.
JD061905 - Sequence 42929 from Patent EP1572962.
JD202719 - Sequence 183743 from Patent EP1572962.
JD183143 - Sequence 164167 from Patent EP1572962.
JD173722 - Sequence 154746 from Patent EP1572962.
JD535083 - Sequence 516107 from Patent EP1572962.
JD220375 - Sequence 201399 from Patent EP1572962.
JD222398 - Sequence 203422 from Patent EP1572962.
JD081664 - Sequence 62688 from Patent EP1572962.
JD346350 - Sequence 327374 from Patent EP1572962.
JD311854 - Sequence 292878 from Patent EP1572962.
JD311855 - Sequence 292879 from Patent EP1572962.
JD425883 - Sequence 406907 from Patent EP1572962.
JD255740 - Sequence 236764 from Patent EP1572962.
JD297723 - Sequence 278747 from Patent EP1572962.
JD365008 - Sequence 346032 from Patent EP1572962.
JD504552 - Sequence 485576 from Patent EP1572962.
JD411123 - Sequence 392147 from Patent EP1572962.
JD203728 - Sequence 184752 from Patent EP1572962.
JD497968 - Sequence 478992 from Patent EP1572962.
JD466298 - Sequence 447322 from Patent EP1572962.
JD407689 - Sequence 388713 from Patent EP1572962.
JD258855 - Sequence 239879 from Patent EP1572962.
JD353140 - Sequence 334164 from Patent EP1572962.
JD077928 - Sequence 58952 from Patent EP1572962.
JD335709 - Sequence 316733 from Patent EP1572962.
JD343464 - Sequence 324488 from Patent EP1572962.
JD024895 - Sequence 5919 from Patent EP1572962.
JD029397 - Sequence 10421 from Patent EP1572962.
JD021663 - Sequence 2687 from Patent EP1572962.
JD036141 - Sequence 17165 from Patent EP1572962.
DQ576924 - Homo sapiens piRNA piR-45036, complete sequence.
JD316778 - Sequence 297802 from Patent EP1572962.
JD335215 - Sequence 316239 from Patent EP1572962.
JD408037 - Sequence 389061 from Patent EP1572962.
JD395318 - Sequence 376342 from Patent EP1572962.
JD394900 - Sequence 375924 from Patent EP1572962.
JD334818 - Sequence 315842 from Patent EP1572962.
JD465893 - Sequence 446917 from Patent EP1572962.
JD282679 - Sequence 263703 from Patent EP1572962.
JD180151 - Sequence 161175 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q96RL6 (Reactome details) participates in the following event(s):

R-HSA-5685607 Sialic acid binds SIGLEC
R-HSA-198933 Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
R-HSA-1280218 Adaptive Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000447370.1, ENST00000447370.2, ENST00000447370.3, ENST00000447370.4, ENST00000447370.5, NM_052884, Q96RL6, SIG11_HUMAN, uc320ozj.1, uc320ozj.2, UNQ9222/PRO28718
UCSC ID: ENST00000447370.6_8
RefSeq Accession: NM_052884.3
Protein: Q96RL6 (aka SIG11_HUMAN or SILB_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.