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RHBDL3 Gene

protein-coding GIFtS: 46
GCID: GC17P030593

Rhomboid, Veinlet-Like 3 (Drosophila)

(Previous names: rhomboid, veinlet-like 4 (Drosophila))
(Previous symbol: RHBDL4)

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disease database

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, ¹⁰fRNAdb, ¹²H-InvDB, ¹³NCBI, ¹⁴NONCODE, and/or ¹⁵RNAdb)
About This Section

Aliases
Rhomboid, Veinlet-Like 3 (Drosophila)¹ ²		EC 3.4.21.105³ ⁸
RHBDL4¹ ² ³		Rhomboid, Veinlet-Like 4 (Drosophila)¹
Ventrhoid Transmembrane Protein² ³		Rhomboid, Veinlet-Like 4²
VRHO² ³		Rhomboid-Related Protein 3²

External Ids:	HGNC: 16502¹	Entrez Gene: 162494²	Ensembl: ENSG00000141314⁷	UniProtKB: P58872³

Export aliases for RHBDL3 gene to outside databases

Previous GC identifers: GC00U991136 GC17P027618 GC17P026782

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

GeneCards Summary for RHBDL3 Gene:

RHBDL3 (rhomboid, veinlet-like 3 (Drosophila)) is a protein-coding gene. GO annotations related to this gene include serine-type endopeptidase activity and calcium ion binding. An important paralog of this gene is RHBDL2.

UniProtKB/Swiss-Prot: RHBL3_HUMAN, P58872

Function: May be involved in regulated intramembrane proteolysis and the subsequent release of functional

polypeptides from their membrane anchors (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)
About This Section

RefSeq DNA sequence at NCBI GenBank:

NC_000017.10 NT_010783.16 NC_018928.2

Regulatory elements:

Regulatory transcription factor binding sites in the RHBDL3 gene promoter:
STAT1 NF-1 p53 NRSF form 1 STAT1beta STAT5A NRSF form 2 STAT1alpha POU2F1 HOXA5
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: RHBDL3 promoter sequence

Search Chromatin IP Primers for RHBDL3

Epigenetics:

DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RHBDL3

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

Entrez Gene cytogenetic band: 17q11.2 Ensembl cytogenetic band: 17q11.2 HGNC cytogenetic band: 17q11.2

RHBDL3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RHBDL3 gene location

GeneLoc information about chromosome 17 GeneLoc Exon Structure

GeneLoc location for GC17P030593: view genomic region (about GC identifiers)

Start:	30,593,195 bp from pter	End:	30,651,680 bp from pter
Size:	58,486 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, antibodies-online, and/or GeneTex,
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.)
About This Section

UniProtKB/Swiss-Prot: RHBL3_HUMAN, P58872 (See protein sequence)

Recommended Name: Rhomboid-related protein 3

Size: 404 amino acids; 45245 Da

Secondary accessions: A6NMH1 Q495Y6

Explore the universe of human proteins at neXtProt for RHBDL3: NX_P58872

Explore proteomics data for RHBDL3 at MOPED

Post-translational modifications:

Modification sites at neXtProt

Modification sites at PhosphoSitePlus

2 DME Specific Peptides for RHBDL3 (P58872)

GRAVWLRF

GVPLEMVHG

See RHBDL3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_612201.1

ENSEMBL proteins:

ENSP00000463941 ENSP00000394849 ENSP00000269051 ENSP00000442092 ENSP00000466508

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

HGNC Gene Families:

EFHAND: EF-hand domain containing

5 InterPro protein domains:

IPR011992 EF-hand-dom_pair

IPR002048 EF_hand_dom

IPR022764 Peptidase_S54_rhomboid_dom

IPR002610 Peptidase_S54_rhomboid

IPR017213 Peptidase_S54_rhomboid_met

Graphical View of Domain Structure for InterPro Entry P58872

ProtoNet protein and cluster: P58872

1 Blocks protein domain: IPB002610 Rhomboid-like protein

UniProtKB/Swiss-Prot: RHBL3_HUMAN, P58872

Similarity: Belongs to the peptidase S54 family

Similarity: Contains 2 EF-hand domains

Find genes that share domains with RHBDL3 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, Sets of similar genes according to GenesLikeMe)
About This Section

Molecular Function:

UniProtKB/Swiss-Prot Summary: RHBL3_HUMAN, P58872

Function: May be involved in regulated intramembrane proteolysis and the subsequent release of functional

polypeptides from their membrane anchors (By similarity)

Catalytic activity: Cleaves type-1 transmembrane domains using a catalytic dyad composed of serine and histidine

that are contributed by different transmembrane domains

Enzyme Number (IUBMB): EC 3.4.21.105¹ ²

Gene Ontology (GO): 2 molecular function terms: About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0004252	serine-type endopeptidase activity	IEA	--
GO:0005509	calcium ion binding	IEA	--

Find genes that share ontologies with RHBDL3 About GenesLikeMe

Phenotypes:
1 MGI phenotypic allele

for Rhbdl3 (no phenotypes)

Find genes that share phenotypes with RHBDL3 About GenesLikeMe

Animal Models:

genOway: Develop your customized and physiologically relevant rodent model for RHBDL3

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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene, Sets of similar genes according to GenesLikeMe)
About This Section

Subcellular locations from UniProtKB/Swiss-Prot

RHBL3_HUMAN, P58872: Membrane; Multi-pass membrane protein (Probable)

Subcellular locations from COMPARTMENTS:

Compartment	Confidence
plasma membrane	3
endoplasmic reticulum	1
nucleus	1
peroxisome	1

About this image

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

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0016021	integral component of membrane	IEA	--

Find genes that share ontologies with RHBDL3 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 GenesLikeMe, 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, Sets of similar genes according to GenesLikeMe)
About This Section

Custom Pathway & Disease-focused RT² Profiler PCR Arrays for RHBDL3
Interactions:

Search GeneGlobe Interaction Network for RHBDL3

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

Selected Interacting proteins for RHBDL3 (P58872³ ENSP00000269051⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 37)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
BMP4	P12644³, ENSP00000245451⁴	I2D: score=1 STRING: ENSP00000245451
CHRD	Q9H2X0³, ENSP00000204604⁴	I2D: score=1 STRING: ENSP00000204604
ETV6	P41212³, ENSP00000266427⁴	I2D: score=1 STRING: ENSP00000266427
NOTCH2	Q04721³, ENSP00000256646⁴	I2D: score=1 STRING: ENSP00000256646
CTNNB1	P35222³	I2D: score=1

About this table

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

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0006508	proteolysis	--	--

Find genes that share ontologies with RHBDL3 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, Sets of similar genes according to GenesLikeMe)
About This Section

Browse Small Molecules at EMD Millipore

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(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 )
About This Section

REFSEQ mRNAs for RHBDL3 gene (5 alternative transcripts):

NM_138328.2 XM_006721733.1 XM_006721734.1 XM_006721735.1 XM_006721736.1

Unigene Cluster for RHBDL3:

Rhomboid, veinlet-like 3 (Drosophila)

Hs.655027 [show with all ESTs]

Unigene Representative Sequence: NM_138328

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

ENST00000578006 ENST00000431505 ENST00000269051(uc002hhe.1 uc010csw.1 uc010csx.1 uc010csy.1)

ENST00000538145 ENST00000536287(uc002hhf.1) ENST00000582967

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Additional mRNA sequence:

AJ313480.1 AK124570.1 AK127490.1 AL133573.1 BC016953.1 BC100975.1 BC100976.1 BC100977.1

BC100978.1 BX647302.1

6 DOTS entries:

DT.40115544 DT.112050 DT.92031890 DT.120900932 DT.75115271 DT.95079942

Selected AceView cDNA sequences (see all 46):

AK124570 BE047684 T16542 AI859187 BC016953 BM717083 AI369789 BX647302

AJ313480 BE904095 AA235710 NM_138328 BM674460 AI197876 BM988137 AK127490

BE220111 BM695873 BE252504 BE221904 BM666952 AI694520 AI828116 BM011465

GeneLoc Exon Structure

4 Alternative Splicing Database (ASD) splice patterns (SP) for RHBDL3 About this scheme

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

ECgene alternative splicing isoforms for RHBDL3

(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 GenesLikeMe, 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)
About This Section

RHBDL3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>^2/3
CGAP TAG: TTGCTCCCCG

About this image

RHBDL3 expression in embryonic tissues and stem cells About this table

Data from LifeMap, the Embryonic Development and Stem Cells Database
selected tissues (see all 3) fully expand


Neural Tube (Nervous System) fully expand to see all 3 entries
Roof Plate Cells Mesencephalic Roof Plate
Mesencephalic Roof Plate

Neural Ectoderm (Nervous System)
Neural ectoderm cells

Eye (Sensory Organs)

RHBDL3 Protein expression data from MOPED¹, PaxDb² and MaxQB³:

About this image

RHBDL3 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.655027

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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 animals.

Orthologs for RHBDL3 gene from Selected species (see all 14) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Rhbdl3^{1 , 5}	rhomboid, veinlet-like 3 (Drosophila)^{1, 5}	90.69(n)¹ 95.69(a)¹		11 (47.73 cM)⁵ 246104¹ NM_139228.3¹ NP_631974.1¹ 80300912⁵
chicken (Gallus gallus)	Aves	RHBDL3¹	rhomboid, veinlet-like 3 (Drosophila)	77.52(n) 85.83(a)		417411 XM_004946181.1 XP_004946238.1
lizard (Anolis carolinensis)	Reptilia	RHBDL3⁶	rhomboid, veinlet-like 3 (Drosophila)	86(a)	1 ↔ 1	GL343198.1(1716909-1796159)
tropical clawed frog (Xenopus tropicalis)	Amphibia	LOC101732375¹	rhomboid-related protein 3-like	73.87(n) 76(a)		101732375 XM_004920714.1 XP_004920771.1
zebrafish (Danio rerio)	Actinopterygii	wufb98c11²	Transcribed sequence with weak similarity to protein more	75.49(n)		AL726021.1
fruit fly (Drosophila melanogaster)	Insecta	stet¹	stem cell tumor	52.87(n) 44.25(a)		38169 NM_176272.2 NP_788450.1

ENSEMBL Gene Tree for RHBDL3 (if available)
TreeFam Gene Tree for RHBDL3 (if available)

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

Paralogs for RHBDL3 gene

RHBDL2² RHBDL1²

2 SIMAP similar genes for RHBDL3 using alignment to 5 protein entries: RHBL3_HUMAN (see all proteins):

RHBDL1 RHBDL2

Find genes that share paralogs with RHBDL3 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)
About This Section

SNP ID	Valid	Clinical significance	Chr 17 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs188533098^1,2		--	30591199(+)	`AATACA/GTGTTC`	1	--	us2k¹		0	--	--	--	--
rs58099756^1,2	C	--	30591266(+)	`ATATG-/TTGATA`	1	--	us2k¹		0	--	--	--	--
rs36096767^1,2	C	--	30591306(+)	`CTCCCA/-TGGGT`	1	--	us2k¹		2		NA CSA	4
rs66494349^1,2	C	--	30591307(+)	`TCCCT-/AGGGTA`	1	--	us2k¹		0	--	--	--	--
rs9915042^1,2	C,F,A,H	--	30591380(+)	`GTGCCC/TTTCTC`	1	--	us2k¹ trp³		11		NA WA CSA EA	374
rs142652511^1,2		--	30591476(+)	`TCATGC/TAAATG`	1	--	us2k¹		0	--	--	--	--
rs57171938^1,2	C,F	--	30591524(+)	`GGGCCC/GCAGCG`	1	--	us2k¹		1		WA	118
rs12451338^1,2	C,F,H	--	30591529(+)	`CCAGCA/GGTCAT`	1	--	us2k¹		14		NA WA CSA EA	378
rs117978214^1,2	C,F	--	30591706(+)	`AAATAG/ATTGAA`	1	--	us2k¹		1		EA	120
rs76989870^1,2	C,F	--	30591764(+)	`ACTCAC/ACTAAT`	1	--	us2k¹		1		EA	120

HapMap Linkage Disequilibrium report for RHBDL3 (30593195 - 30651680 bp)

Structural Variations
Database of Genomic Variants (DGV) 10 variations for RHBDL3: About this table

Variant ID	Type	Subtype	PubMed ID
esv2715834	CNV	Deletion	23290073
esv1001216	CNV	Deletion	20482838
esv2238058	CNV	Deletion	18987734
esv2715835	CNV	Deletion	23290073
esv2672269	CNV	Deletion	23128226
esv2621296	CNV	Insertion	19546169
nsv908068	CNV	Gain	21882294
nsv827949	CNV	Gain	20364138
nsv908069	CNV	Gain	21882294
esv29073	CNV	Gain	19812545

Site Specific Mutation Identification with PCR Assays

SeqTarget long-range PCR primers for resequencing RHBDL3

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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, Sets of similar genes according to GenesLikeMe)
About This Section

(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 RHBDL3 gene integrated from 10 sources:
(articles sorted by number of sources associating them with RHBDL3)

Cloning and expression of Ventrhoid, a novel vertebrate homologue of the Drosophila EGF pathway gene Rhomboid. (PubMed id 11900977)^{1, 2, 3} Jaszai J. and Brand M. (Mech. Dev. 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. (Genome Res. 2004)
Ubiquitin-dependent intramembrane rhomboid protease promotes ERAD of membrane proteins. (PubMed id 22795130)¹ Fleig L....Lemberg M.K. (Mol. Cell 2012)
DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. (PubMed id 16625196)² Zody M.C.... Nusbaum C. (Nature 2006)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)¹ Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

		AND	OR
Aliases
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Query String		PubMed OMIM NCBI Bookshelf
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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: 162494	HGNC: 16502	AceView: RHBDL4	Ensembl:ENSG00000141314	euGenes: HUgn162494
ECgene: RHBDL3	H-InvDB: RHBDL3

(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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Name	Description
PharmGKB entry for RHBDL3	Pharmacogenomics, SNPs, Pathways

Intellectual Property for RHBDL3 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 RHBDL3 gene:
Search GeneIP for patents involving RHBDL3

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, GeneTex, 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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Rhomboid, Veinlet-Like 3 (Drosophila)

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RHBDL3 Gene

Rhomboid, Veinlet-Like 3 (Drosophila)

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