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CRIP3 Gene

protein-coding   GIFtS: 40
GCID: GC06M043267

Cysteine-Rich Protein 3

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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
Cysteine-Rich Protein 31 2     TLP-A2
Chromosome 6 LIM Domain Only Protein2 3     bA480N24.22
CRP-32 3     Thymus LIM Protein TLP-A2
h6LIMo2 3     CRP33
TLP2     

External Ids:    HGNC: 177511   Entrez Gene: 4012622   Ensembl: ENSG000001462157   UniProtKB: Q6Q6R53   

Export aliases for CRIP3 gene to outside databases

Previous GC identifers: GC00U914157 GC06U900618 GC06M043382 GC06M042991


(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 CRIP3 Gene:
CRIP3 (cysteine-rich protein 3) is a protein-coding gene. An important paralog of this gene is CSRP2.


(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_000006.11  NT_007592.16  NC_018917.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the CRIP3 gene promoter:
         E2F-4   E2F-3a   NF-1/L   E2F-5   NF-1   Nkx2-5   XBP-1   E2F-2   E2F   E2F-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCRIP3 promoter sequence
   Search Chromatin IP Primers for CRIP3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CRIP3


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

Entrez Gene cytogenetic band: 6p21.1   Ensembl cytogenetic band:  6p21.1   HGNC cytogenetic band: 6p21

CRIP3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CRIP3 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M043267:  view genomic region     (about GC identifiers)

Start:
43,267,448 bp from pter      End:
43,276,535 bp from pter
Size:
9,088 bases      Orientation:
minus 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: CRIP3_HUMAN, Q6Q6R5 (See protein sequence)
Recommended Name: Cysteine-rich protein 3  
Size: 217 amino acids; 24088 Da
Secondary accessions: A2A436 Q5T043 Q6Q6R4 Q6Q6R6 Q6Q6R7
Alternative splicing: 4 isoforms:  Q6Q6R5-1   Q6Q6R5-2   Q6Q6R5-3   Q6Q6R5-4   

Explore the universe of human proteins at neXtProt for CRIP3: NX_Q6Q6R5

Explore proteomics data for CRIP3 at MOPED


See CRIP3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_996805.2  
ENSEMBL proteins: 
 ENSP00000414553   ENSP00000361650   ENSP00000397775   ENSP00000274990  

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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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1 InterPro protein domain:
 IPR001781 Znf_LIM

Graphical View of Domain Structure for InterPro Entry Q6Q6R5

ProtoNet protein and cluster: Q6Q6R5

1 Blocks protein domain: IPB001781 Zn-binding protein

UniProtKB/Swiss-Prot: CRIP3_HUMAN, Q6Q6R5
Similarity: Contains 2 LIM zinc-binding domains


Find genes that share domains with CRIP3           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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     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0008270zinc ion binding IEA--
     
Find genes that share ontologies with CRIP3           About GenesLikeMe


Phenotypes:
     1 GenomeRNAi human phenotype for CRIP3:
 Increased S DNA content 

     2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Crip3):
 hematopoietic system  immune system 

Find genes that share phenotypes with CRIP3           About GenesLikeMe

Animal Models:
   genOway: Develop your customized and physiologically relevant rodent model for CRIP3

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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
CRIP3_HUMAN, Q6Q6R5: Cytoplasm (By similarity)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
nucleus3
cytosol2
cytoskeleton1

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

GO IDQualified GO termEvidencePubMed IDs
GO:0005737cytoplasm IEA--

Find genes that share ontologies with CRIP3           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 CRIP3
Interactions:

    Search GeneGlobe Interaction Network for CRIP3

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

1 Interacting protein for CRIP3 (ENSP000003616504) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
PRKG2ENSP000002643994STRING: ENSP00000264399
About this table

Gene Ontology (GO): 1 biological process term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0042098T cell proliferation IEA--

Find genes that share ontologies with CRIP3           About GenesLikeMe



(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
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  Browse compounds at ApexBio 

Browse Tocris compounds for CRIP3



(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 CRIP3 gene: 
NM_206922.2  

Unigene Cluster for CRIP3:

Cysteine-rich protein 3
Hs.653165  [show with all ESTs]
Unigene Representative Sequence: AK124657
7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000416431 ENST00000372569(uc003ouu.1) ENST00000451294 ENST00000477866
ENST00000274990(uc010jyn.2) ENST00000487744 ENST00000485819
miRNA
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hsa-miR-1911
SwitchGear 3'UTR luciferase reporter plasmidCRIP3 3' UTR sequence
Inhib. RNA
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Additional mRNA sequence: 

AK124657.1 AY555741.1 AY555742.1 AY555743.1 AY555744.1 BC068247.1 

8 DOTS entries:

DT.100019750  DT.100666858  DT.97801718  DT.121405507  DT.443865  DT.91739223  DT.102837846  DT.95153325 

Selected AceView cDNA sequences (see all 202):

T05190 AW444504 BP356370 AI285090 AA482194 BU730224 AI656764 AA380339 
BQ002909 BM727284 BM841286 BM704270 BX107982 BI917114 CA429114 BM313434 
AA808266 AA865024 BG119408 BE551519 AA315878 BU521261 AI989980 BC030687 

GeneLoc Exon Structure

4 Alternative Splicing Database (ASD) splice patterns (SP) for CRIP3    About this scheme

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


ECgene alternative splicing isoforms for CRIP3

(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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CRIP3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
CRIP3 Expression
About this image


CRIP3 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 
 Heart (Cardiovascular System)
         Cardiac progenitor cells
CRIP3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

CRIP3 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.653165

UniProtKB/Swiss-Prot: CRIP3_HUMAN, Q6Q6R5
Tissue specificity: Expressed in most tissues, but not in skeletal muscle

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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 animals.

Orthologs for CRIP3 gene from Selected species (see all 10)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Crip31 , 5 cysteine-rich protein 31, 5 88.07(n)1
88.24(a)1
  17 (22.90 cM)5
1145701  NM_181664.21  NP_858050.11 
 464289265 
tropical clawed frog
(Xenopus tropicalis)
Amphibia crip31 cysteine-rich protein 3 69.02(n)
72.73(a)
  548528  NM_001015811.1  NP_001015811.1 
zebrafish
(Danio rerio)
Actinopterygii LOC5565151 cysteine-rich protein 3-like 66.67(n)
71.07(a)
  556515  XM_679338.5  XP_684430.1 
worm
(Caenorhabditis elegans)
Secernentea valv-16
exc-96
Protein EXC-9 (exc-9) mRNA, complete cds
52(a)
48(a)
many ↔ many
many ↔ many
IV(7444634-7445365) WBGene00015216
IV(7939812-7940850) WBGene00017644


ENSEMBL Gene Tree for CRIP3 (if available)
TreeFam Gene Tree for CRIP3 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for CRIP3 gene
CSRP22  CSRP12  CRIP22  ENSG000002573412  CRIP12  CSRP32  
6 SIMAP similar genes for CRIP3 using alignment to 3 protein entries:     CRIP3_HUMAN (see all proteins):
CRIP1    CRIP2    DKFZp686P2249    CSRP1    CSRP2    CSRP3

Find genes that share paralogs with CRIP3           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 CRIP3 (see all 99)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 6 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs680343411,2
C--43189153(-) ACTAC-/T/TT  
        
TTTTT
1 -- us2k12NA 4
rs2001695871,2
C--43273783(+) CCCAGC/TGTCTG 1 -- int10--------
rs1398407521,2
C--43273793(+) GGGAT-/GGGGCT 1 -- int10--------
rs1458356321,2
C,F--43273959(+) CACCTC/GAGCAT 2 Q E mis11Minor allele frequency- G:0.00NA 4548
rs28416441,2
C,H--43274044(-) GAGAAG/AGTGAT 2 /K syn1 ese35Minor allele frequency- A:0.00NS EA NA 422
rs1416656891,2
C--43274058(+) TGGTGA/GTGGAA 1 -- int10--------
rs751905111,2
C,F--43274077(+) TAATGC/TTTCCA 1 -- int11Minor allele frequency- T:0.02WA 118
rs1861039181,2
C--43274268(+) GGGGAA/CGAGGC 1 -- int10--------
rs2009181841,2
--43274285(+) TATGTC/GTGAGG 1 -- int10--------
rs791583631,2
F--43274560(+) TGATAT/CAGGAG 1 -- int11Minor allele frequency- C:0.07WA 118

HapMap Linkage Disequilibrium report for CRIP3 (43267448 - 43276535 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for CRIP3:    About this table    
Variant IDTypeSubtypePubMed ID
dgv6840n71CNV Loss21882294

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing CRIP3
DNA2.0 Custom Variant and Variant Library Synthesis for CRIP3

(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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  --

(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 CRIP3 gene integrated from 10 sources:
(articles sorted by number of sources associating them with CRIP3)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The human and mouse orthologous LIM-only proteins respectively encoded in chromosome 6 and 17 show a different expression pattern. (PubMed id 15380775)1, 2, 3 Casrouge A.... Kanellopoulos J. (Microbes Infect. 2004)
  2. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)1, 2 Mungall A.J.... Beck S. (Nature 2003)
  3. Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation. (PubMed id 15146197)1 Brandenberger R.... Stanton L.W. (Nat. Biotechnol. 2004)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 401262 HGNC: 17751 AceView: ZNF318andTLP Ensembl:ENSG00000146215 euGenes: HUgn401262
ECgene: CRIP3 H-InvDB: CRIP3

(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 CRIP3 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 CRIP3 gene:
Search GeneIP for patents involving CRIP3

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
Advanced Cell Diagnostics, Animal models from genOway)
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 Custom PCR Arrays for CRIP3 Search Chromatin IP Primers for CRIP3
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 GenScript Custom Purified and Recombinant Proteins Services for CRIP3 GenScript cDNA clones with any tag delivered in your preferred vector for CRIP3
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 Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies

 Novus Tissue Slides
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 Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CRIP3
 Browse compounds at ApexBio
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  Search antibodies-online for antibodies for CRIP3
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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