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    Siglec1 sialic acid binding Ig like lectin 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 311426, updated on 19-Apr-2019

    Summary

    Official Symbol
    Siglec1provided by RGD
    Official Full Name
    sialic acid binding Ig like lectin 1provided by RGD
    Primary source
    RGD:1311953
    See related
    Ensembl:ENSRNOG00000021243
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Sn
    Expression
    Biased expression in Spleen (RPKM 104.6), Thymus (RPKM 19.5) and 6 other tissues See more
    Orthologs

    Genomic context

    See Siglec1 in Genome Data Viewer
    Location:
    3q36
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    106 current Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (123612067..123631718, complement)
    104 previous assembly Rnor_5.0 (GCF_000001895.4) 3 NC_005102.3 (130111340..130130084, complement)

    Chromosome 3 - NC_005102.4Genomic Context describing neighboring genes Neighboring gene GDNF family receptor alpha 4 Neighboring gene ADAM metallopeptidase domain 33 Neighboring gene similar to 60S ribosomal protein L12 Neighboring gene heat shock protein family A (Hsp70) member 12B Neighboring gene similar to RIKEN cDNA 1700037H04

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Pathways from BioSystems

    • Cell adhesion molecules (CAMs), organism-specific biosystem (from KEGG)
      Cell adhesion molecules (CAMs), organism-specific biosystemCell adhesion molecules are (glyco)proteins expressed on the cell surface and play a critical role in a wide array of biologic processes that include hemostasis, the immune response, inflammation, em...
    • Cell adhesion molecules (CAMs), conserved biosystem (from KEGG)
      Cell adhesion molecules (CAMs), conserved biosystemCell adhesion molecules are (glyco)proteins expressed on the cell surface and play a critical role in a wide array of biologic processes that include hemostasis, the immune response, inflammation, em...

    General gene information

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    carbohydrate binding IEA
    Inferred from Electronic Annotation
    more info
     
    virion binding ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    Process Evidence Code Pubs
    clathrin-dependent endocytosis ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    clathrin-dependent endocytosis of virus by host cell ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    negative regulation of phagocytosis ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of T cell apoptotic process ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of extrinsic apoptotic signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    viral entry into host cell ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    Component Evidence Code Pubs
    early endosome ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    endocytic vesicle ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    late endosome ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    NOT lysosome ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    NOT plasma membrane raft ISO
    Inferred from Sequence Orthology
    more info
    PubMed 

    General protein information

    Preferred Names
    sialoadhesin
    Names
    sialic acid binding Ig-like lectin 1, sialoadhesin

    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_001107777.1NP_001101247.1  sialoadhesin precursor

      See identical proteins and their annotated locations for NP_001101247.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473949
      UniProtKB/TrEMBL
      D3ZVM6
      Related
      ENSRNOP00000028855.6, ENSRNOT00000028855.7
      Conserved Domains (7) summary
      cd00096
      Location:431504
      Ig; Immunoglobulin domain
      smart00408
      Location:255313
      IGc2; Immunoglobulin C-2 Type
      smart00409
      Location:625702
      IG; Immunoglobulin
      smart00410
      Location:255324
      IG_like; Immunoglobulin like
      pfam07679
      Location:808883
      I-set; Immunoglobulin I-set domain
      pfam13895
      Location:339409
      Ig_2; Immunoglobulin domain
      cl11960
      Location:21136
      Ig; Immunoglobulin domain

    RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

    Reference Rnor_6.0 Primary Assembly

    Genomic

    1. NC_005102.4 Reference Rnor_6.0 Primary Assembly

      Range
      123612067..123631718 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006235024.3XP_006235086.1  sialoadhesin isoform X3

      Conserved Domains (7) summary
      cd00096
      Location:431504
      Ig; Immunoglobulin domain
      smart00408
      Location:255313
      IGc2; Immunoglobulin C-2 Type
      smart00409
      Location:711788
      IG; Immunoglobulin
      smart00410
      Location:255324
      IG_like; Immunoglobulin like
      pfam07679
      Location:894969
      I-set; Immunoglobulin I-set domain
      pfam13895
      Location:515595
      Ig_2; Immunoglobulin domain
      cl11960
      Location:21136
      Ig; Immunoglobulin domain
    2. XM_017591748.1XP_017447237.1  sialoadhesin isoform X4

      UniProtKB/TrEMBL
      A0A0G2K320
      Related
      ENSRNOP00000072470.1, ENSRNOT00000091493.1
    3. XM_017591746.1XP_017447235.1  sialoadhesin isoform X1

    4. XM_017591749.1XP_017447238.1  sialoadhesin isoform X5

    5. XM_017591747.1XP_017447236.1  sialoadhesin isoform X2

    Alternate Rn_Celera

    Genomic

    1. AC_000071.1 Alternate Rn_Celera

      Range
      117098468..117117016 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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