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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

CLIP3 Gene

protein-coding GIFtS: 48
GCID: GC19M036505

CAP-GLY domain containing linker protein 3

Search for CLIP3
in

MalaCards

our new
Human Malady Compendium

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

Aliases
CAP-GLY Domain Containing Linker Protein 3¹ ²		Cytoplasmic Linker Protein 170-Related 59 KDa Protein² ³
CLIPR-59¹ ² ³		CLIP-170-Related 59 KDa Protein² ³
CLIPR59² ³ ⁵		CAP-Gly Domain-Containing Linker Protein 3²
RSNL1¹ ²		Restin-Like 1²

External Ids:	HGNC: 24314¹	Entrez Gene: 25999²	Ensembl: ENSG00000105270⁷	OMIM: 607382⁵	UniProtKB: Q96DZ5³

Export aliases for CLIP3 gene to outside databases

Previous GC identifers: GC19M041198 GC19M033011

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

Entrez Gene summary for CLIP3:

This gene encodes a member of the cytoplasmic linker protein 170 family. Members of this protein family contain a

cytoskeleton-associated protein glycine-rich domain and mediate the interaction of microtubules with cellular

organelles. The encoded protein plays a role in T cell apoptosis by facilitating the association of tubulin and the

lipid raft ganglioside GD3. The encoded protein also functions as a scaffold protein mediating membrane localization

of phosphorylated protein kinase B. Alternatively spliced transcript variants have been observed for this gene.

(provided by RefSeq, Dec 2010)

UniProtKB/Swiss-Prot: CLIP3_HUMAN, Q96DZ5

Function: Functions as a cytoplasmic linker protein. Involved in TGN-endosome dynamics

(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_000019.9 NC_018930.1 NT_011109.16

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the CLIP3 gene promoter:
MAZR MyoD Lmo2 FOXO3 E47 FOXO3b HOXA5 FOXO1a FOXO3a FOXO1
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: CLIP3 promoter sequence

Search SABiosciences Chromatin IP Primers for CLIP3

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CLIP3

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

Entrez Gene cytogenetic band: 19q13.12 Ensembl cytogenetic band: 19q13.12 HGNC cytogenetic band: 19q13

CLIP3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CLIP3 gene location

GeneLoc information about chromosome 19 GeneLoc Exon Structure

GeneLoc location for GC19M036505: view genomic region (about GC identifiers)

Start:	36,505,562 bp from pter	End:	36,524,245 bp from pter
Size:	18,684 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: CLIP3_HUMAN, Q96DZ5 (See protein sequence)

Recommended Name: CAP-Gly domain-containing linker protein 3

Size: 547 amino acids; 59560 Da

Subunit: Homodimer

Subcellular location: Cytoplasm. Golgi apparatus, Golgi stack. Note=Localized to Golgi stacks as well as on

tubulovesicular elements juxtaposed to Golgi cisternae

Miscellaneous: The N-terminal half is dispensable for proper Golgi targeting, whereas the GoLD region is required

1 PDB 3D structure from and Proteopedia for CLIP3:

2CP0 (3D)

Secondary accessions: A8K0E4 Q8WWL1 Q96C99 Q9UFT7

Explore the universe of human proteins at neXtProt for CLIP3: NX_Q96DZ5

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_Q96DZ5

CLIP3 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins (2 alternative transcripts):

NP_001186499.1 NP_056341.1

ENSEMBL proteins:

ENSP00000353732 ENSP00000466832 ENSP00000466026 ENSP00000468689

Human Recombinant Protein Products for CLIP3:

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	Uscn Proteins for CLIP3

Gene Ontology (GO): 5/8 cellular component terms (GO ID links to tree view) (see all 8): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005792	microsome	--	--
GO:0005795	Golgi stack	IEA	--
GO:0005802	trans-Golgi network	ISS	--
GO:0005886	plasma membrane	IMP	15262990
GO:0031901	early endosome membrane	IDA	11854307

CLIP3 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

CLIP3 for domains About GeneDecksing

3 InterPro domains/families:

IPR000938 CAP-Gly_domain

IPR002110 Ankyrin_rpt

IPR020683 Ankyrin_rpt-contain_dom

Graphical View of Domain Structure for InterPro Entry Q96DZ5

ProtoNet protein and cluster: Q96DZ5

2 Blocks protein families:

IPB000938 CAP-Gly domain

IPB002110 Ankyrin repeat signature

UniProtKB/Swiss-Prot: CLIP3_HUMAN, Q96DZ5

Domain: Microtubule association is inhibited by the ANK repeats and the Golgi localization region (GoLD)

Similarity: Contains 3 ANK repeats

Similarity: Contains 2 CAP-Gly domains

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, Sirion Biotech, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, Sirion Biotech, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Molecular Function:

UniProtKB/Swiss-Prot Summary: CLIP3_HUMAN, Q96DZ5

Function: Functions as a cytoplasmic linker protein. Involved in TGN-endosome dynamics

Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005515	protein binding	--	--
GO:0008017	microtubule binding	IMP	--
GO:0035594	ganglioside binding	IDA	--

CLIP3 for ontologies About GeneDecksing

Animal Models:

inGenious Targeting Laboratory - Customizable classic, inducible, and humanized mouse model solutions for CLIP3

miRNA Products:		OriGene 3'-UTR Clone: CLIP3 Browse MicroRNA Expression Plasmids
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		hsa-miR-3938 hsa-miR-3607-3p hsa-miR-300 hsa-miR-1914* hsa-miR-485-3p hsa-miR-486-3p hsa-miR-624 hsa-miR-4314

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In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLIP3

(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 Central^TM Interacting Genes and Proteins Networks for CLIP3

STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

5/6 Interacting proteins for CLIP3 (Q96DZ5³ ENSP00000353732⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 6)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
PRKCG	P05129³	I2D: score=2
AKT1	P31749³	I2D: score=1
AKT2	P31751³	I2D: score=1
WNK1	Q9H4A3³	I2D: score=1
HDAC2	ENSP00000381331⁴	STRING: ENSP00000381331

About this table

Gene Ontology (GO): 5/10 biological process terms (GO ID links to tree view) (see all 10): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0001934	positive regulation of protein phosphorylation	ISS	--
GO:0010828	positive regulation of glucose transport	ISS	--
GO:0018230	peptidyl-L-cysteine S-palmitoylation	IMP	15262990
GO:0031115	negative regulation of microtubule polymerization	IMP	15262990
GO:0043065	positive regulation of apoptotic process	IMP	--

CLIP3 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 CLIP3
Search CenterWatch for drugs/clinical trials and news about CLIP3

(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,
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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 CLIP3 gene (2 alternative transcripts):

NM_001199570.1 NM_015526.2

Unigene Cluster for CLIP3:

CAP-GLY domain containing linker protein 3

Hs.466539 [show with all ESTs]

Unigene Representative Sequence: NM_001199570

6 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000360535(uc010eeq.2 uc002ocz.2) ENST00000593074 ENST00000585466

ENST00000590559 ENST00000592017 ENST00000586457

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		hsa-miR-3938 hsa-miR-3607-3p hsa-miR-300 hsa-miR-1914* hsa-miR-485-3p hsa-miR-486-3p hsa-miR-624 hsa-miR-4314

		SwitchGear 3'UTR luciferase reporter plasmid: CLIP3 3' UTR sequence

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Additional cDNA sequence:

AJ427922.1 AK056445.1 AK090732.1 AK092354.1 AK094738.1 AK289509.1 AK294748.1 AL110254.1

AL117468.1 BC013116.1 BC014486.1 BC128090.1

18 DOTS entries:

DT.100814048 DT.100814049 DT.100769524 DT.92041890 DT.450253 DT.95312646 DT.100814050 DT.95312599

DT.121465224 DT.121465243 DT.121465280 DT.92418511 DT.102833405 DT.121465241 DT.121465290 DT.121465301

DT.95209940 DT.99963088

24/257 AceView cDNA sequences (see all 257):

BE766503 AA972275 CB155136 AI146378 T32142 BE765941 BQ670139 BQ069461

AL117468 AI648538 BC013116 BM705757 CF243058 AJ427922 CB044599 BQ006380

AA909063 BQ006250 CN483846 BU734958 BP347330 AK092354 AI288440 AK094738

GeneLoc Exon Structure

3 Alternative Splicing Database (ASD) splice patterns (SP) for CLIP3 About this scheme

ExUns:	1a	·	1b	^	2a	·	2b	^	3	^	4	^	5	^	6	^	7	^	8a	·	8b	·	8c	^	9	^	10a	·	10b	^	11	^	12	^	13	^	14	^	15a	·	15b
SP1:
SP2:							-		-		-		-		-		-		-
SP3:									-		-		-		-		-		-		-

ECgene alternative splicing isoforms for CLIP3

(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

CLIP3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: ACTCCTGTCC

About this image

CLIP3 expression in embryonic tissues and stem cells
Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

Stem Cell Differentiation: 1 LifeMap Cell

Name

Category

Mesendoderm-like cells (Generation of mesend...)

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

See CLIP3 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for CLIP3

SOURCE GeneReport for Unigene cluster: Hs.466539

SABiosciences Custom PCR Arrays for CLIP3

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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 CLIP3 gene from 2/13 species (see all 13) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
lizard (Anolis carolinensis)	Reptilia	CLIP3⁶	--	56(a)	1 ↔ 1	GL344980.1(5208-14728)
zebrafish (Danio rerio)	Actinopterygii	LOC562450¹	similar to LOC495693 protein	71.62(n) 78.95(a)		562450 XM_685830.5 XP_690922.4

ENSEMBL Gene Tree for CLIP3 (if available)
TreeFam Gene Tree for CLIP3 (if available)

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

Paralogs for CLIP3 gene

CLIP2² CEP350² TBCB² CLIP4² CLIP1² DCTN1² ENSG00000264324²

2 SIMAP similar genes for CLIP3 using alignment to 3 protein entries: CLIP3_HUMAN (see all proteins):

CLIP4 FLJ21069

CLIP3 for paralogs About GeneDecksing

(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

SNP ID	Valid	Clinical significance	Chr 19 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs200176352^1,2	C	--	36505152(+)	`ATTACA/GGACGC`	4	--	ds500¹ us2k¹		1		EU	1297
rs146993120^1,2		--	36505395(+)	`GGGACC/GGGGGC`	4	--	ds500¹ us2k¹		0	--	--	--	--
rs187990595^1,2		--	36505581(+)	`CTTTAC/TTGAAG`	4	--	ut3¹ us2k¹		0	--	--	--	--
rs181338818^1,2		--	36505668(+)	`AGGTCC/TGCCCT`	4	--	ut3¹ us2k¹		0	--	--	--	--
rs1043822^1,2	C,A	--	36505683(-)	`AGGCCC/G/TAGGGG`	6	--	us2k¹ ut3¹		7		EA MN NA CSA WA	2009
rs11545920^1,2	C,H	--	36505761(-)	`TCAATC/TTACGT`	4	--	ut3¹ us2k¹		2		NS NA	180
rs186414893^1,2		--	36505823(+)	`TATTAA/GAGATG`	4	--	ut3¹ us2k¹		0	--	--	--	--
rs145012329^1,2		--	36505829(+)	`AGATGA/GAGGCT`	4	--	ut3¹ us2k¹		0	--	--	--	--
rs73034048^1,2	C	--	36505841(+)	`TAGGAT/CTTGGG`	4	--	ut3¹ us2k¹		1		NA	120
rs191098050^1,2		--	36506086(+)	`ATTTGG/TGATTC`	4	--	us2k¹ ut3¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for CLIP3 (36505562 - 36524245 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 1 variation for CLIP3
1 CNV: 5098

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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

CLIP3 for disorders About MalaCards

CLIP3 for disorders About GeneDecksing

OMIM gene information: 607382 OMIM disorders: --

Export disorders for CLIP3 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 CLIP3 gene, integrated from 9 sources (see all 13):
(articles sorted by number of sources associating them with CLIP3)

Utopia: connect your pdf to the dynamic
world of online information

CLIPR-59, a new trans-Golgi/TGN cytoplasmic linker protein belonging to the CLIP-170 family. (PubMed id 11854307)^{1, 2, 3} Perez F....Goud B. (2002)
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. (2004)
Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)^{1, 2} Ota T.... Sugano S. (2004)
ClipR-59 interacts with Akt and regulates Akt cellular compartmentalization. (PubMed id 19139280)^{1, 9} Ding J. and Du K. (2009)
CLIPR-59 is a lipid raft-associated protein containing a cytoskeleton-associated protein glycine-rich domain (CAP-Gly) that perturbs microtubule dynamics. (PubMed id 15262990)^{1, 9} Lallemand-Breitenbach V....Perez F. (2004)
Methods for quantification of in vivo changes in prote in ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)¹ Udeshi N.D....Carr S.A. (2012)
Functional dissection of lysine deacetylases reveals t hat HDAC1 and p300 regulate AMPK. (PubMed id 22318606)¹ Lin Y.Y....Boeke J.D. (2012)
CLIPR-59 regulates TNF-a-induced apoptosis by controll ing ubiquitination of RIP1. (PubMed id 22297296)¹ Fujikura D....Miyazaki T. (2012)
Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)¹ Danielsen J.M....Nielsen M.L. (2011)
Role of GD3-CLIPR-59 association in lymphoblastoid T cell apoptosis triggered by CD95/Fas. (PubMed id 20052288)¹ Sorice M....Malorni W. (2010)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
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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: 25999	HGNC: 24314	AceView: CLIPR-59	Ensembl:ENSG00000105270	euGenes: HUgn25999
ECgene: CLIP3	H-InvDB: CLIP3

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
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Name	Description
PharmGKB entry for CLIP3	Pharmacogenomics, SNPs, Pathways

Intellectual Property for CLIP3 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

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Patent Information for CLIP3 gene:
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CLIP3 Gene

CAP-GLY domain containing linker protein 3

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CLIP3 Gene

CAP-GLY domain containing linker protein 3

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