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

CLCC1 Gene

protein-coding   GIFtS: 50
GCID: GC01M109472

chloride channel CLIC-like 1

 Explore 1 disease affiliated with
CLCC1 via our new
 Human Malady Compendium 
Biological research products
for CLCC1
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Chloride Channel CLIC-Like 11 2     Mid-1-Related Chloride Channel 12
MCLC1 2 3     Mid1-Related Chloride Channel2
Mid-1-Related Chloride Channel Protein 12 3     KIAA07613
Chloride Channel CLIC-Like Protein 12     

External Ids:    HGNC: 296751   Entrez Gene: 231552   Ensembl: ENSG000001219407   UniProtKB: Q96S663   

Export aliases for CLCC1 gene to outside databases

Previous GC identifers: GC01M109185 GC01M108820 GC01M107364


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

UniProtKB/Swiss-Prot: CLCC1_HUMAN, Q96S66
Function: Seems to act as a chloride ion channel (By similarity)

Gene Wiki entry for CLCC1


(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000001.10  NC_018912.1  NT_032977.9  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CLCC1 gene promoter:
         Nkx3-1   GR   ER-alpha   Nkx3-1 v4   GR-beta   Nkx3-1 v1   Nkx3-1 v2   Nkx3-1 v3   GR-alpha   Hlf   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCLCC1 promoter sequence
   Search SABiosciences Chromatin IP Primers for CLCC1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CLCC1


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

Entrez Gene cytogenetic band: 1p13.3   Ensembl cytogenetic band:  1p13.3   HGNC cytogenetic band: 1p13.3

CLCC1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CLCC1 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M109472:  view genomic region     (about GC identifiers)

Start:
109,472,130 bp from pter      End:
109,506,111 bp from pter
Size:
33,982 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: CLCC1_HUMAN, Q96S66 (See protein sequence)
Recommended Name: Chloride channel CLIC-like protein 1 precursor  
Size: 551 amino acids; 62023 Da
Subcellular location: Membrane; Multi-pass membrane protein (Potential). Endoplasmic reticulum. Golgi apparatus.
Nucleus (By similarity)
Secondary accessions: O94861 Q8WYP8 Q8WYP9 Q9BU25
Alternative splicing: 4 isoforms:  Q96S66-1   Q96S66-2   Q96S66-3   Q96S66-4   

Explore the universe of human proteins at neXtProt for CLCC1: NX_Q96S66

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q96S66

  • CLCC1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001041675.1  NP_055942.1  

    ENSEMBL proteins: 
     ENSP00000349456   ENSP00000358993   ENSP00000358987   ENSP00000337243   ENSP00000306552  
     ENSP00000358988   ENSP00000411591   ENSP00000358986   ENSP00000358985  

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    Uscn Proteins for CLCC1

    Gene Ontology (GO): 5/7 cellular component terms (GO ID links to tree view) (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--
    GO:0005737cytoplasm ----
    GO:0005783endoplasmic reticulum IDA--
    GO:0005792microsome ----
    GO:0005794Golgi apparatus IEA--


    CLCC1 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    CLCC1 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR009231 Chloride_chnl_CLIC-like

    Graphical View of Domain Structure for InterPro Entry Q96S66

    ProtoNet protein and cluster: Q96S66

    UniProtKB/Swiss-Prot: CLCC1_HUMAN, Q96S66
    Similarity: Belongs to the chloride channel MCLC family


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: CLCC1_HUMAN, Q96S66
    Function: Seems to act as a chloride ion channel (By similarity)

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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005254chloride channel activity ----


    CLCC1 for ontologies           About GeneDecksing



    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for CLCC1

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    2 Interacting proteins for CLCC1 (Q96S663 ENSP000003494564) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CLN3Q132863I2D: score=1 
    UBCENSP000003448184STRING: ENSP00000344818
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006821chloride transport ----


    CLCC1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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 CLCC1

    1 HMDB Compound for CLCC1    About this table
    CompoundSynonyms CAS #PubMed Ids
    ChlorineCl2 (see all 13)16887-00-6--
    Search CenterWatch for drugs/clinical trials and news about CLCC1 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    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, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for CLCC1 gene (2 alternative transcripts): 
    NM_001048210.1  NM_015127.3  

    Unigene Cluster for CLCC1:

    Chloride channel CLIC-like 1
    Hs.658489  [show with all ESTs]
    Unigene Representative Sequence: NM_001048210
    11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000356970(uc021ora.1) ENST00000473062 ENST00000369976(uc001dwh.1)
    ENST00000482889 ENST00000369970(uc009wes.1 uc009wet.1) ENST00000348264
    ENST00000302500 ENST00000369971(uc001dwf.1) ENST00000415331(uc001dwg.1)
    ENST00000369969 ENST00000369968

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    8/36 QIAGEN miScript miRNA Assays for microRNAs that regulate CLCC1 (see all 36):
    hsa-miR-3607-3p hsa-miR-199a-3p hsa-miR-578 hsa-miR-30d hsa-miR-570 hsa-miR-374c hsa-miR-30a hsa-miR-29a*
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    Additional cDNA sequence: 

    AB018304.2 AB052915.1 AB052916.1 AB052917.1 AB052918.1 AK090563.1 BC002939.2 

    12 DOTS entries:

    DT.92446330  DT.415885  DT.102830358  DT.40126708  DT.121337663  DT.92446325  DT.100781101  DT.40223109 
    DT.307186  DT.86847607  DT.100781105  DT.100791168 

    24/140 AceView cDNA sequences (see all 140):

    AB052917 BQ685798 BQ440467 CA390024 BQ081843 AL119069 BQ029527 BU185550 
    BE274308 BU187644 AB052918 AB018304 CR622878 AW768439 AA933615 BQ718929 
    AB052915 AL553562 BM548948 AB052916 BQ008193 CR606058 BF983620 AW575585 

    GeneLoc Exon Structure

    5/9 Alternative Splicing Database (ASD) splice patterns (SP) for CLCC1 (see all 9)    About this scheme

    ExUns: 1a · 1b · 1c · 1d · 1e · 1f · 1g ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14
    SP1:                          -     -     -     -                                                                                                   
    SP2:                                      -     -     -                                                                                             
    SP3:                                                                                                                                                
    SP4:                                      -                                                                                                         
    SP5:                                                                                                                                                


    ECgene alternative splicing isoforms for CLCC1

    (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

    CLCC1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: AGCCATTGTG

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See CLCC1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CLCC1

    SOURCE GeneReport for Unigene cluster: Hs.658489
        SABiosciences Custom PCR Arrays for CLCC1
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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)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for CLCC1 gene from 5/11 species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Clcc11 , 5 chloride channel CLIC-like 11, 5 80.09(n)1
    74.95(a)1
      3 (47.49 cM)5
    2297251  NM_001177770.11  NP_001171241.11 
     1086539135 
    chicken
    (Gallus gallus)
    Aves CLCC11 chloride channel CLIC-like 1 60.56(n)
    51.99(a)
      424343  XM_422186.3  XP_422186.2 
    lizard
    (Anolis carolinensis)
    Reptilia CLCC16
    --
    57(a)
    1 ↔ 1
    GL343211.1(2084162-2095540)
    African clawed frog
    (Xenopus laevis)
    Amphibia LOC3979472 hypothetical protein LOC397947 76.5(n)    X92871.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC1003324601 chloride channel CLIC-like protein 1-like 53.56(n)
    43.6(a)
      100332460  XM_002667211.1  XP_002667257.1 


    ENSEMBL Gene Tree for CLCC1 (if available)
    TreeFam Gene Tree for CLCC1 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    10/678 NCBI SNPs in CLCC1 are shown (see all 678    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs8398541,2
    C,F,A,H,--109471634(-) CCAGAA/CTGAAT 3 -- ds5001 int121Minor allele frequency- C:0.46NS EA NA WA CSA 2340
    rs1502242831,2
    C,--109471646(+) CTATT-/TCTTAAC 3 -- ds5001 int10--------
    rs2007290701,2
    C--109471647(+) TATTTC/TTTAAC 3 -- ds5001 int10--------
    rs726992401,2
    C,F,--109471729(+) TTGCCG/ACCCAT 3 -- ds5001 int12Minor allele frequency- A:0.04NA EA 240
    rs1872822061,2
    --109471755(+) ACTGCC/TCAACT 3 -- int1 ds50010--------
    rs1930752351,2
    --109471787(+) GCCATA/GTAGAT 3 -- int1 ds50010--------
    rs1161742341,2
    F,--109471849(+) AAGCCG/AGCACT 3 -- ds5001 int11Minor allele frequency- A:0.06WA 118
    rs125653721,2
    C,F,H,--109471920(+) GGTTTC/GTACAT 3 -- int1 ds500118Minor allele frequency- N:0.00NS EA NA CSA WA 1418
    rs1835397811,2
    --109472022(+) TCCTTG/TTGACC 3 -- ds5001 int10--------
    rs1462911811,2
    --109472292(+) ACAGTA/GTGTCT 3 -- int1 ut310--------

    HapMap Linkage Disequilibrium report for CLCC1 (109472130 - 109506111 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 6 variations for CLCC1
         6 CNVs: 84460 84461 37882 64563 4241 84459

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    (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.)
    About This Section

    CLCC1 for disorders           About GeneDecksing

    1 disease for CLCC1:    About MalaCards
    nephrocalcinosis

    Human Genome Epidemiology (HuGE) Navigator: CLCC1 (1 document)

    Export disorders for CLCC1 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 CLCC1 gene, integrated from 9 sources (see all 20):
    (articles sorted by number of sources associating them with CLCC1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification of a novel chloride channel expressed in the endoplasmic reticulum, golgi apparatus, and nucleus. (PubMed id 11279057)1, 2, 3, 9 Nagasawa M....Kojima I. (2001)
    2. Prediction of the coding sequences of unidentified human genes. XI. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 9872452)1, 2, 3 Nagase T.... Ohara O. (1998)
    3. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    4. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
    5. System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. (PubMed id 21406692)2 Rigbolt K.T....Blagoev B. (2011)
    6. Ubiquitin ligase substrate identification through qua ntitative proteomics at both the protein and peptide levels. (PubMed id 21987572)1 Lee K.A....Doedens J.R. (2011)
    7. Global identification of modular cullin-RING ligase su bstrates. (PubMed id 21963094)1 Emanuele M.J....Elledge S.J. (2011)
    8. Identification of type 2 diabetes-associated combinat ion of SNPs using support vector machine. (PubMed id 20416077)1 Ban H.J....Park K.J. (2010)
    9. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (2010)
    10. Dynamics of cullin-RING ubiquitin ligase network revea led by systematic quantitative proteomics. (PubMed id 21145461)1 Bennett E.J....Harper J.W. (2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 23155 HGNC: 29675 AceView: MCLC Ensembl:ENSG00000121940 euGenes: HUgn23155
    ECgene: CLCC1 H-InvDB: CLCC1

    (According to HUGE)
    About This Section
    HUGE: KIAA0761

    (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 CLCC1 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 CLCC1 gene:
    Search GeneIP for patents involving CLCC1

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



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