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    COL11A1 collagen, type XI, alpha 1 [ Homo sapiens (human) ]

    Gene ID: 1301, updated on 11-May-2013
    Official Symbol
    COL11A1provided by HGNC
    Official Full Name
    collagen, type XI, alpha 1provided by HGNC
    Primary source
    HGNC:2186
    See related
    Ensembl:ENSG00000060718; HPRD:00375; MIM:120280; Vega:OTTHUMG00000010872
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    STL2; COLL6; CO11A1
    Summary
    This gene encodes one of the two alpha chains of type XI collagen, a minor fibrillar collagen. Type XI collagen is a heterotrimer but the third alpha chain is a post-translationally modified alpha 1 type II chain. Mutations in this gene are associated with type II Stickler syndrome and with Marshall syndrome. A single-nucleotide polymorphism in this gene is also associated with susceptibility to lumbar disc herniation. Multiple transcript variants have been identified for this gene. [provided by RefSeq, Nov 2009]
    Location :
    1p21
    Sequence :
    Chromosome: 1; NC_000001.10 (103342023..103574052, complement)
    See COL11A1 in Epigenomics, MapViewer

    Chromosome 1 - NC_000001.10Genomic Context describing neighboring genes Neighboring gene ribosomal protein SA pseudogene 19 Neighboring gene DnaJ (Hsp40) homolog, subfamily A, member 1 pseudogene 5 Neighboring gene olfactomedin 3 Neighboring gene superoxide dismutase 2, mitochondrial pseudogene 1 Neighboring gene actin, gamma 1 pseudogene 4 Neighboring gene RNA-binding region (RNP1, RRM) containing 3 Neighboring gene amylase, alpha 2B (pancreatic)

    Go to nucleotideGraphics FASTA GenBank

    Go to reference sequence details

    Related articles in PubMed

    1. F-box protein FBXL19-mediated ubiquitination and degradation of the receptor for IL-33 limits pulmonary inflammation. Zhao J, et al. Nat Immunol, 2012 Jun 3. PMID 22660580.
    2. COL11A1 gene is associated with limbus vertebra in gymnasts. Koyama K, et al. Int J Sports Med, 2012 Jul. PMID 22510797.
    3. Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. Estrada K, et al. Nat Genet, 2012 Apr 15. PMID 22504420.
    4. A recessive form of Marshall syndrome is caused by a mutation in the COL11A1 gene. Khalifa O, et al. J Med Genet, 2012 Apr. PMID 22499343.
    5. Characterization of a novel mouse monoclonal antibody, clone 1E8.33, highly specific for human procollagen 11A1, a tumor-associated stromal component. García-Ocaña M, et al. Int J Oncol, 2012 May. PMID 22322826.

    See all (53) citations in PubMed

    See citations in PubMed for homologs of this gene provided by HomoloGene

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    1. a TT genotype of COL11A1 polymorphism may be a significant risk factor for limbus vertebra in Japanese collegiate gymnasts.
      Title: COL11A1 gene is associated with limbus vertebra in gymnasts.
    2. our data shall improve the overall understanding of fibrochondrogenesis especially in surviving homozygous patients and, at least partly, explain the phenotypic variability associated with COL11A1 gene mutations.
      Title: Clinical and molecular analysis of UAE fibrochondrogenesis patients expands the phenotype and reveals two COL11A1 homozygous null mutations.
    3. study reports the first evidence that adds COL11A1 defect as a cause of Marshall syndrome with a recessive mode of inheritance
      Title: A recessive form of Marshall syndrome is caused by a mutation in the COL11A1 gene.
    4. variants detected in COL11A1 in patients with Stickler syndrome
      Title: Splicing analysis of unclassified variants in COL2A1 and COL11A1 identifies deep intronic pathogenic mutations.
    5. Characterize mouse monoclonal antibody specific for human procollagen 11A1 and report its use for immunohistochemistry in human breast tumor tissue.
      Title: Characterization of a novel mouse monoclonal antibody, clone 1E8.33, highly specific for human procollagen 11A1, a tumor-associated stromal component.
    6. Common polymorphisms in four candidate genes (COL11A1, COL18A1, FBN1 and PLOD1) were unlikely to play important roles in the genetic susceptibility to high myopia.
      Title: A DNA pooling-based case-control study of myopia candidate genes COL11A1, COL18A1, FBN1, and PLOD1 in a Chinese population.
    7. These findings identify COL11A1 as a locus for fibrochondrogenesis and indicate that there might be phenotypic manifestations among carriers.
      Title: Fibrochondrogenesis results from mutations in the COL11A1 type XI collagen gene.
    8. Study identified 57 novel mutations including missense changes in both COL2A1 and COL11A1.
      Title: Stickler syndrome and the vitreous phenotype: mutations in COL2A1 and COL11A1.
    9. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    10. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Genome-wide analysis of chromosomal alterations in patients with esophageal squamous cell carcinoma exposed to tobacco and betel quid from high-risk area in India.
    Submit: New GeneRIF Correction See all (19)

    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Stickler syndrome, type 2

    Summary from GeneReviews: Stickler Syndrome Go to GeneReviews

    Disease Characteristics
    Stickler syndrome is a connective tissue disorder that can include ocular findings of myopia, cataract, and retinal detachment; hearing loss that is both conductive and sensorineural; midfacial underdevelopment and cleft palate (either alone or as part of the Robin sequence); and mild spondyloepiphyseal dysplasia and/or precocious arthritis. Variable phenotypic expression of Stickler syndrome occurs both within and among families; interfamilial variability is in part explained by locus and allelic heterogeneity.
    Diagnosis Testing
    The diagnosis of Stickler syndrome is clinically based. At present, no consensus minimal clinical diagnostic criteria exist. Mutations affecting one of five genes (COL2A1, COL9A1, COL9A2, COL11A1, and COL11A2) have been associated with Stickler syndrome; because a few families with features of Stickler syndrome are not linked to any of these four loci, mutations in other genes may also cause the disorder. Molecular genetic testing for COL2A1, COL9A1, COL9A2, COL11A1, and COL11A2 is available in clinical laboratories.
    Genetic Counseling
    Stickler syndrome caused by mutations in COL2A1, COL11A1, or COL11A2 is inherited in an autosomal dominant manner; Stickler syndrome caused by mutations in COL9A1 or COL9A2 is inherited in an autosomal recessive manner. In families with autosomal dominant inheritance, affected individuals have a 50% chance of passing on the mutation to each offspring. In families with autosomal recessive inheritance, each sib of an affected individual has a 25% chance of being affected, a 50% chance of being an asymptomatic carrier, and a 25% chance of being unaffected and not a carrier. Prenatal testing is possible in pregnancies at increased risk if the disease-causing mutation(s) in the family are known.
    References
    Products Interactant Other Gene Complex Source Pubs Description
    P12107 Q08345 DDR1    HPRD  PubMed  
    BioGRID:107698 BioGRID:120078 FBXL19    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:107698 BioGRID:113164 UBC    BioGRID  PubMed Affinity Capture-Western 
    • Amoebiasis, organism-specific biosystem (from KEGG)
      Amoebiasis, organism-specific biosystemEntamoeba histolytica, an extracellular protozoan parasite is a human pathogen that invades the intestinal epithelium. Infection occurs on ingestion of contaminated water and food. The pathogenesis o...
    • Amoebiasis, conserved biosystem (from KEGG)
      Amoebiasis, conserved biosystemEntamoeba histolytica, an extracellular protozoan parasite is a human pathogen that invades the intestinal epithelium. Infection occurs on ingestion of contaminated water and food. The pathogenesis o...
    • Assembly of collagen fibrils and other multimeric structures, organism-specific biosystem (from REACTOME)
      Assembly of collagen fibrils and other multimeric structures, organism-specific biosystemCollagen trimers in triple-helical form, referred to as procollagen or collagen molecules, are exported from the ER and trafficked through the Golgi network before secretion into the extracellular sp...
    • Collagen biosynthesis and modifying enzymes, organism-specific biosystem (from REACTOME)
      Collagen biosynthesis and modifying enzymes, organism-specific biosystemThe biosynthesis of collagen is a multistep process. Collagen propeptides are cotranslationally translocated into the ER lumen. Propeptides undergo a number of post-translational modifications. Proli...
    • Collagen formation, organism-specific biosystem (from REACTOME)
      Collagen formation, organism-specific biosystemCollagen is a family of at least 29 structural proteins derived from over 40 human genes (Myllyharju & Kivirikko 2004). It is the main component of connective tissue, and the most abundant protein in...
    • ECM-receptor interaction, organism-specific biosystem (from KEGG)
      ECM-receptor interaction, organism-specific biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
    • ECM-receptor interaction, conserved biosystem (from KEGG)
      ECM-receptor interaction, conserved biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
    • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
      Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin, fibronectin and laminin embedded in a viscoelastic gel of ani...
    • Focal Adhesion, organism-specific biosystem (from WikiPathways)
      Focal Adhesion, organism-specific biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
    • Focal adhesion, organism-specific biosystem (from KEGG)
      Focal adhesion, organism-specific biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
    • Focal adhesion, conserved biosystem (from KEGG)
      Focal adhesion, conserved biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
    • PI3K-Akt signaling pathway, organism-specific biosystem (from KEGG)
      PI3K-Akt signaling pathway, organism-specific biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
    • PI3K-Akt signaling pathway, conserved biosystem (from KEGG)
      PI3K-Akt signaling pathway, conserved biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
    • Protein digestion and absorption, organism-specific biosystem (from KEGG)
      Protein digestion and absorption, organism-specific biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
    • Protein digestion and absorption, conserved biosystem (from KEGG)
      Protein digestion and absorption, conserved biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...

    Markers

    Genotypes

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    extracellular matrix binding NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    extracellular matrix structural constituent NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    protein binding, bridging NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    cartilage condensation IEA
    Inferred from Electronic Annotation
    more info
    		  
    chondrocyte development IEA
    Inferred from Electronic Annotation
    more info
    		  
    collagen catabolic process TAS
    Traceable Author Statement
    more info
    		  
    collagen fibril organization NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    detection of mechanical stimulus involved in sensory perception of sound IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    embryonic skeletal system morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    extracellular matrix disassembly TAS
    Traceable Author Statement
    more info
    		  
    extracellular matrix organization NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    extracellular matrix organization TAS
    Traceable Author Statement
    more info
    		  
    inner ear morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    proteoglycan metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    sensory perception of sound IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    ventricular cardiac muscle tissue morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    visual perception IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    collagen type XI IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    collagen type XI NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
    		  
    extracellular region TAS
    Traceable Author Statement
    more info
    		  
    Preferred Names
    collagen alpha-1(XI) chain
    Names
    collagen alpha-1(XI) chain
    collagen XI, alpha-1 polypeptide

    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.

    Genomic

    1. NG_008033.1 RefSeqGene

      Range
      5001..237030
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001190709.1 → NP_001177638.1  collagen alpha-1(XI) chain isoform E preproprotein

      Status: REVIEWED

      Description
      Transcript Variant: This variant (E, previously referred to as C) does not utilize either alternate exon 6A or 6B. The encoded isoform (E, previously referred to as C) is shorter than isoform A. There are no publicly available transcripts representing this variant; it is supported by mRNA annotation on DNA accession AF101112.1, protein AAF04724.1, submitted by the authors of PMID:10486316.
      Source sequence(s)
      AB208844, AC093150, AC099567, BU159588, BX476821, CA448616, J04177
      Consensus CDS
      CCDS53348.1
      UniProtKB/Swiss-Prot
      P12107
      UniProtKB/TrEMBL
      Q59HB5
      Related
      ENSP00000302551, ENST00000353414
      Conserved Domains (3) summary
      cd00110
      Location:73 – 225
      Blast Score: 108
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
      pfam01410
      Location:1554 – 1765
      Blast Score: 870
      COLFI; Fibrillar collagen C-terminal domain
      pfam01391
      Location:772 – 831
      Blast Score: 137
      Collagen; Collagen triple helix repeat (20 copies)

    2. NM_001854.3 → NP_001845.3  collagen alpha-1(XI) chain isoform A preproprotein

      Status: REVIEWED

      Description
      Transcript Variant: This variant (A) utilizes alternate exon 6, designated exon 6A. The encoded isoform (A) has a 39 aa region specified by exon 6A, that differs from the corresponding 51 aa region encoded by exon 6B in isoform B.
      Source sequence(s)
      AB208844, AC093150, AC099567, BU159588, BX476821, J04177
      Consensus CDS
      CCDS778.1
      UniProtKB/Swiss-Prot
      P12107
      UniProtKB/TrEMBL
      Q59HB5
      Related
      ENSP00000359114, OTTHUMP00000012567, ENST00000370096, OTTHUMT00000029997
      Conserved Domains (3) summary
      cd00110
      Location:73 – 225
      Blast Score: 108
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
      pfam01410
      Location:1593 – 1804
      Blast Score: 870
      COLFI; Fibrillar collagen C-terminal domain
      pfam01391
      Location:811 – 870
      Blast Score: 137
      Collagen; Collagen triple helix repeat (20 copies)

    3. NM_080629.2 → NP_542196.2  collagen alpha-1(XI) chain isoform B preproprotein

      Status: REVIEWED

      Description
      Transcript Variant: This variant (B) utilizes alternate exon 6, designated exon 6B, and encodes the longest isoform (B). There are no publicly available transcripts representing this variant; it is supported by mRNA annotation on DNA accession AF101112.1, protein AAF04726.1, submitted by the authors of PMID:10486316.
      Source sequence(s)
      AB208844, AC093150, AC099567, BU159588, BX476821, J04177
      UniProtKB/Swiss-Prot
      P12107
      UniProtKB/TrEMBL
      Q59HB5
      Related
      ENSP00000351163, ENST00000358392
      Conserved Domains (3) summary
      cd00110
      Location:73 – 225
      Blast Score: 109
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
      pfam01410
      Location:1605 – 1816
      Blast Score: 871
      COLFI; Fibrillar collagen C-terminal domain
      pfam01391
      Location:823 – 882
      Blast Score: 139
      Collagen; Collagen triple helix repeat (20 copies)

    4. NM_080630.3 → NP_542197.3  collagen alpha-1(XI) chain isoform C preproprotein

      Status: REVIEWED

      Description
      Transcript Variant: This variant (C, previously referred to as D) includes alternate exon 6A but lacks two other alternate exons, resulting in the loss of an in-frame segment in the coding region, compared to variant A. The encoded isoform (C, previously referred to as D) is shorter than isoform A.
      Source sequence(s)
      AC093150, AC099567, BC117697, CA448616
      Consensus CDS
      CCDS780.2
      UniProtKB/Swiss-Prot
      P12107
      Conserved Domains (3) summary
      cd00110
      Location:73 – 225
      Blast Score: 108
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
      pfam01410
      Location:1477 – 1688
      Blast Score: 871
      COLFI; Fibrillar collagen C-terminal domain
      pfam01391
      Location:695 – 754
      Blast Score: 133
      Collagen; Collagen triple helix repeat (20 copies)

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

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

    Reference GRCh37.p10 Primary Assembly

    Genomic

    1. NC_000001.10 Reference GRCh37.p10 Primary Assembly

      Range
      103342023..103574052, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000133.1 Alternate HuRef

      Range
      101474202..101706091, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.0

    Genomic

    1. NC_018912.1 Alternate CHM1_1.0

      Range
      103364160..103596258, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    genomic ABBA01045414.1 (11485..21941) None
    genomic ABBA01045415.1 None
    genomic ABBA01045416.1 None
    genomic ABBA01045417.1 None
    genomic ABBA01045418.1 None
    genomic AC093150.4 (2001..113390) None
    genomic AC099567.2 (117096..171400) None
    genomic AF017809.1 None
    genomic AF101112.1 AAF04724.1
      AAF04725.1
      AAF04726.1
    genomic AL627203.7 (2001..68335) None
    genomic AMYH01000833.1 (125968..127982) None
    genomic AMYH01000834.1 None
    genomic AMYH01000835.1 None
    genomic AY705366.1 AAW47652.1
    genomic AY705367.1 AAW47653.1
    genomic AY705368.1 AAW47654.1
    genomic AY705369.1 AAW47655.1
    genomic AY705370.1 AAW47656.1
    genomic AY744914.2 AAU88421.2
    genomic AY870934.1 AAW65382.1
    genomic AY870935.1 AAW65383.1
    genomic AY870936.1 AAW65384.1
    genomic AY870937.1 AAW65385.1
    genomic AY870938.1 AAW65386.1
    genomic AY870939.1 AAW65387.1
    genomic AY870940.1 AAW65388.1
    genomic AY870941.1 AAW65389.1
    genomic AY870942.1 AAW65390.1
    genomic CH471097.2 EAW72908.1
      EAW72909.1
      EAW72910.1
      EAW72911.1
      EAW72912.1
      EAW72913.1
    genomic DQ097164.1 AAZ06348.1
    genomic L38956.1 AAA79171.1
    genomic U12139.1 AAN86608.1
    mRNA AB208844.1 BAD92081.1
    mRNA AK299025.1 BAG61102.1
    mRNA AU118365.1 None
    mRNA BC117697.1 AAI17698.1
    mRNA BU159588.1 None
    mRNA BX476821.1 None
    mRNA CA448616.1 None
    mRNA J04177.1 AAA51891.1
    Protein Accession Links
    GenPept Link UniProtKB Link
    P12107.4 GenPept UniProtKB/Swiss-Prot:P12107

    Additional Links

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Medical
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous

      Supplemental Content

      Table of contents

      Related information

      • Order cDNA clone
        Order cDNA clone
      • BioAssay
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        BioSystems
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      • CCDS
        Links from Gene to CCDS are established if a gene encodes a protein sequence that is a member of a Consensus CDS (CCDS).
      • ClinVar
        Related medical variations
      • Conserved Domains
        Conserved Domain Database Links between Entrez Gene and Conserved Domain Database (CDD) are calculated from the domains annotated by the CDD group on Reference Sequence proteins.
      • dbVar
        Link from Gene to dbVar
      • EST
        Link to related EST entry
      • Full text in PMC
        PMC links
      • Full text in PMC_nucleotide
        Full text in PubMedCentral identified from shared sequence links
      • GAP
        GAP Links
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        Genome records having the gene annotated on corresponding genomic reference sequence.
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        GTR associated with a gene
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        Related information in MedGen
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        Link to related Nucleotide entry
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        Links between OMIM and Gene are calculated by Gene based on MIM numbers included in the summary and phenotype sections of the Gene record.
      • Probe
        Related Probe entry
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        Link to related protein entry
      • PubChem Compound
        PubChem Compounds
      • PubChem Substance
        PubChem Substances
      • PubMed
        Links between Gene and PubMed are the result of the following: 1. Manual curation within NCBI. Part of the process of generating a REVIEWED RefSeq is an analysis of the current literature. Papers that are seminal in defining the gene, its sequence, and its function are added to the record at that time. Alert users point out gaps or errors in papers associated with a Gene record. These messages are reviewed and implemented as required. 2. Integration of information from other public databases. Gene integrates gene-citation from resources external to NCBI such as model organism-specific databases, Gene Ontology (GO), groups curating interactions, and sequence databases. The assumption in using these source is that they report citations specific to a gene in a known species. Gene does not process citations from OMIM automatically, because many of citations in OMIM refer to studies of genes in species other than human.
      • PubMed (GeneRIF)
        GeneRIF -- Gene Reference Into Function Staff of the Index Section in the National Library of Medicine review the current literature. When they find articles focused on the structure and function of a gene, they write a brief summary of the impact of the paper and make the connection between the citation (PubMed) and Gene. An interface exists for interested users to submit such data as well. http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html
      • PubMed (OMIM)
        Links are provided when Gene has a link to a record in OMIM, and OMIM explicitly cites these publications in PubMed.
      • PubMed(nucleotide/PMC)
        Citations in PubMed identified from shared sequence and PMC links.
      • RefSeq Proteins
        Link to Protein RefSeqs
      • RefSeq RNAs
        Link to Nucleotide RefSeq RNAs
      • RefSeqGene
        Link to Nucleotide RefSeqGenes
      • SNP
        Related SNP records
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        Related Clinical SNP
      • Taxonomy
        Link to related taxonomy entry
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        Links are provided between Gene and UniGene when both databases calculate links to the same mRNA record (gi).
      • UniSTS
        Related UniSTS records

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