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CILP2 Gene

protein-coding   GIFtS: 49
GCID: GC19P019649

Cartilage Intermediate Layer Protein 2

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Cartilage Intermediate Layer Protein 21 2
CILP-22 3
CLIP-22
Cartilage Intermediate Layer Protein-Like Protein 22

External Ids:    HGNC: 242131   Entrez Gene: 1481132   Ensembl: ENSG000001601617   OMIM: 6124195   UniProtKB: Q8IUL83   

Export aliases for CILP2 gene to outside databases

Previous GC identifers: GC19P019473 GC19P019511 GC19P019211


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for CILP2 Gene:
CILP2 (cartilage intermediate layer protein 2) is a protein-coding gene. GO annotations related to this gene include nucleotide diphosphatase activity and alkaline phosphatase activity. An important paralog of this gene is CILP.

UniProtKB/Swiss-Prot: CILP2_HUMAN, Q8IUL8
Function: May play a role in cartilage scaffolding (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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000019.9  NC_018930.2  NT_011295.12  
Regulatory elements:
   Regulatory transcription factor binding sites in the CILP2 gene promoter:
         HSF1 (long)   CUTL1   E47   Egr-2   E2F-1   CP2   E2F   HSF1short   ATF6   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): CILP2 promoter sequence
   Search Chromatin IP Primers for CILP2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CILP2


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

Entrez Gene cytogenetic band: 19p13.11   Ensembl cytogenetic band:  19p13.11   HGNC cytogenetic band: 19p13.11

CILP2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CILP2 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P019649:  view genomic region     (about GC identifiers)

Start:
19,649,057 bp from pter      End:
19,657,468 bp from pter
Size:
8,412 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: CILP2_HUMAN, Q8IUL8 (See protein sequence)
Recommended Name: Cartilage intermediate layer protein 2 precursor  
Size: 1156 amino acids; 126291 Da
Secondary accessions: Q6NV88 Q8N4A6 Q8WV21

Explore the universe of human proteins at neXtProt for CILP2: NX_Q8IUL8

Explore proteomics data for CILP2 at MOPED

Post-translational modifications: 

  • May be cleaved into 2 chains possibly by a furin-like protease upon or preceding secretion (By similarity)1
  • Glycosylation2 at Thr236, Asn276, Asn308, Asn329
  • Modification sites at PhosphoSitePlus

  • See CILP2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_694953.2  
    ENSEMBL proteins: 
     ENSP00000467413   ENSP00000291495  

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    Cloud-Clone Corp. Proteins for CILP2

     
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    antibodies-online peptides for CILP2

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    IGD: Immunoglobulin superfamily / Immunoglobulin-like domain containing

    Selected InterPro protein domains (see all 6):
     IPR003598 Ig_sub2
     IPR000884 Thrombospondin_1_rpt
     IPR008969 CarboxyPept-like_regulatory
     IPR013783 Ig-like_fold
     IPR007110 Ig-like_dom

    Graphical View of Domain Structure for InterPro Entry Q8IUL8

    ProtoNet protein and cluster: Q8IUL8

    3 Blocks protein domains:
    IPB003598 Immunoglobulin C-2 type
    IPB003599 Immunoglobulin subtype
    IPB008085 Thrombospondin type 1 repeat signature


    UniProtKB/Swiss-Prot: CILP2_HUMAN, Q8IUL8
    Similarity: Contains 1 Ig-like C2-type (immunoglobulin-like) domain
    Similarity: Contains 1 TSP type-1 domain


    Find genes that share domains with CILP2           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: CILP2_HUMAN, Q8IUL8
    Function: May play a role in cartilage scaffolding (By similarity)

         Gene Ontology (GO): 4 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004035NOT alkaline phosphatase activity IDA12746903
    GO:0004551NOT nucleotide diphosphatase activity IDA12746903
    GO:0005515protein binding ----
    GO:0030246carbohydrate binding ----
         
    Find genes that share ontologies with CILP2           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for CILP2:
     Increased HPV18 LCR reporter a 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for CILP2

    miRNA
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    hsa-miR-29c hsa-miR-29a hsa-miR-486-3p hsa-miR-29b
    SwitchGear 3'UTR luciferase reporter plasmidCILP2 3' UTR sequence
    Inhib. RNA
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    CILP2_HUMAN, Q8IUL8: Secreted, extracellular space, extracellular matrix (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular3
    plasma membrane2
    cytosol1
    endoplasmic reticulum1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005578proteinaceous extracellular matrix IEA--

    Find genes that share ontologies with CILP2           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for CILP2
    Interactions:

        Search GeneGlobe Interaction Network for CILP2

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for CILP2



    (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,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for CILP2 gene: 
    NM_153221.2  

    Unigene Cluster for CILP2:

    Cartilage intermediate layer protein 2
    Hs.279574  [show with all ESTs]
    Unigene Representative Sequence: AK127735
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000586018 ENST00000291495(uc002nmv.4 uc002nmw.4) ENST00000588333

    miRNA
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    hsa-miR-29c hsa-miR-29a hsa-miR-486-3p hsa-miR-29b
    SwitchGear 3'UTR luciferase reporter plasmidCILP2 3' UTR sequence
    Inhib. RNA
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      QuantiFast Probe-based Assays in human, mouse, rat CILP2

    Additional mRNA sequence: 

    AF542080.1 AK127735.1 AK314213.1 BC018939.2 BC034926.1 BC068256.1 

    3 DOTS entries:

    DT.100031141  DT.101976170  DT.97844737 

    Selected AceView cDNA sequences (see all 27):

    BC018939 BC034926 BQ181405 BQ181948 AK127735 BI196652 NM_153221 BQ181998 
    BC068256 CN479743 BX280777 BX112879 BQ181896 AF542080 BQ181874 BG929309 
    BQ182788 BG928970 AI073387 BF313161 BF353731 BI559947 AA861752 BF310577 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for CILP2    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b · 9c ^ 10a · 10b
    SP1:                                -                 -                                             
    SP2:                    -           -                 -                                             
    SP3:                                                                                                
    SP4:                                                                                -               


    ECgene alternative splicing isoforms for CILP2

    (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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    CILP2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CGGGGGAGGC
    CILP2 Expression
    About this image


    CILP2 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Bone (Muscoskeletal System)    fully expand to see all 9 entries
             Micromass-induced chondrocytes
     
     Cartilage (Muscoskeletal System)    fully expand to see all 9 entries
             Micromass-induced chondrocytes
             fetal cartilage   
    CILP2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CILP2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.279574

    UniProtKB/Swiss-Prot: CILP2_HUMAN, Q8IUL8
    Tissue specificity: Expressed in articular chondrocytes but not in knee meniscal cartilage cells

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    In Situ
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    (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)
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    This gene was present in the common ancestor of chordates.

    Orthologs for CILP2 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Cilp21 , 5 cartilage intermediate layer protein 21, 5 77.64(n)1
    80.09(a)1
      8 (34.01 cM)5
    687091  NM_026818.21  NP_081094.21 
     698803695 
    chicken
    (Gallus gallus)
    Aves CILP21 cartilage intermediate layer protein 2 69.99(n)
    65.41(a)
      430666  XM_003643398.2  XP_003643446.2 
    lizard
    (Anolis carolinensis)
    Reptilia CILP26
    cartilage intermediate layer protein 2
    62(a)
    1 ↔ 1
    GL344325.1(35082-43874)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia cilp21 cartilage intermediate layer protein 2 56.8(n)
    56.85(a)
      100491609  XM_002936334.2  XP_002936380.2 
    zebrafish
    (Danio rerio)
    Actinopterygii cilp21 cartilage intermediate layer protein 2 57.06(n)
    57(a)
      557778  XM_680899.4  XP_685991.4 


    ENSEMBL Gene Tree for CILP2 (if available)
    TreeFam Gene Tree for CILP2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CILP2 gene
    CILP2  
    1 SIMAP similar gene for CILP2 using alignment to 2 protein entries:     CILP2_HUMAN (see all proteins):
    CILP

    Find genes that share paralogs with CILP2           About GenesLikeMe



    (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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for CILP2 (see all 266)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs104018221,2
    C,F--19649007(+) AGGGCC/TAGGGG 1 -- us2k11Minor allele frequency- T:0.22WA 118
    rs1807227181,2
    --19649086(+) GCGGCA/CGCCAG 1 -- ut510--------
    rs1997193161,2
    C--19649127(+) GGAGCC/GCGGAC 1 -- ut510--------
    rs1500966341,2
    C--19649269(+) CGAGGA/GCCTGG 1 -- int10--------
    rs116707611,2
    C,F,H--19649327(+) CACGCG/CCTTCC 1 -- int16Minor allele frequency- C:0.18NA WA 426
    rs1389319891,2
    --19649475(+) ATCACC/TGGCCA 1 -- int10--------
    rs286753331,2
    C--19649484(+) CAGGTC/TTCCCA 1 -- int12Minor allele frequency- T:0.00NA 4
    rs116707751,2
    C,F,A,H--19649636(+) GAGGCA/GCCCAG 1 -- int114Minor allele frequency- G:0.19NS NA WA 1712
    rs116708821,2
    C,F,A,H--19649748(+) GGACTG/CTAGTA 1 -- int122Minor allele frequency- C:0.26NS EA NA WA CSA 2351
    rs1863558601,2
    --19649803(+) GTGGAA/TGAGGG 1 -- int10--------

    HapMap Linkage Disequilibrium report for CILP2 (19649057 - 19657468 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for CILP2:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv509723CNV Insertion20534489
    dgv3789n71CNV Loss21882294
    nsv911305CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing CILP2
    DNA2.0 Custom Variant and Variant Library Synthesis for CILP2

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 612419    OMIM disorders: --


    Find genes that share disorders with CILP2           About GenesLikeMe

    Genetic Association Database (GAD): CILP2
    Human Genome Epidemiology (HuGE) Navigator: CILP2 (6 documents)

    Export disorders for CILP2 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)
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    PubMed articles for CILP2 gene, integrated from 10 sources (see all 18):
    (articles sorted by number of sources associating them with CILP2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. One of two chondrocyte-expressed isoforms of cartilage intermediate- layer protein functions as an insulin-like growth factor 1 antagonist. (PubMed id 12746903)1, 2, 9 Johnson K.... Terkeltaub R. (Arthritis Rheum. 2003)
    2. Fine-mapping in African Americans of 8 recently discovered genetic loci for plasma lipids: the Jackson Heart Study. (PubMed id 20570916)1, 4 Keebler M.E....Kathiresan S. (Circ Cardiovasc Genet 2010)
    3. Polymorphisms at newly identified lipid-associated loci are associated with blood lipids and cardiovascular disease in an Asian Malay population. (PubMed id 18987386)1, 4 Tai E.S....Seielstad M. (J. Lipid Res. 2009)
    4. Common variants at 30 loci contribute to polygenic dyslipidemia. (PubMed id 19060906)1, 4 Kathiresan S....Cupples L.A. (Nat. Genet. 2009)
    5. A polygenic basis for four classical Fredrickson hyperlipoproteinemia phenotypes that are characterized by hypertriglyceridemia. (PubMed id 19656773)1, 4 Hegele R.A....Wang J. (Hum. Mol. Genet. 2009)
    6. Newly identified loci that influence lipid concentrations and risk of coronary artery disease. (PubMed id 18193043)1, 4 Willer C.J....Abecasis G.R. (Nat. Genet. 2008)
    7. Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans. (PubMed id 18193044)1, 4 Kathiresan S....Orho-Melander M. (Nat. Genet. 2008)
    8. 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. (Genome Res. 2004)
    9. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    10. Genome-wide association analysis identifies 13 new risk loci for schizophrenia. (PubMed id 23974872)1 Ripke S....Sullivan P.F. (Nat. Genet. 2013)

    (in PubMed, OMIM, and NCBI Bookshelf)
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      Query String
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 148113 HGNC: 24213 AceView: CILP2 Ensembl:ENSG00000160161 euGenes: HUgn148113
    ECgene: CILP2 H-InvDB: CILP2

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for CILP2 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for CILP2 gene:
    Search GeneIP for patents involving CILP2

    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, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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