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C5orf42 Gene

protein-coding GIFtS: 36

GC05M037144

chromosome 5 open reading frame 42
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database

		Products

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

Aliases & Descriptions
chromosome 5 open reading frame 42¹ ²		Transmembrane protein ENSP00000382582²
FLJ13231¹ ²		OTTHUMP00000218308²
DKFZp686K02105²		hypothetical protein LOC65250²
OTTHUMP00000218309²		FLJ21126²
OTTHUMP00000218310²

External Ids:	HGNC: 25801¹	Entrez Gene: 65250²	Ensembl: ENSG00000197603⁷	UniProtKB: Q9H799³

Export aliases for C5orf42 gene to outside databases

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

(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 60), Regulatory elements and Epigenetics data according to Qiagen and/or SABiosciences)
About This Section

Regulatory elements:

Search SABiosciences Regulatory transcription factor binding sites for C5orf42
Other transcription factors

Search SABiosciences Chromatin IP Primers for C5orf42

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays

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

Entrez Gene cytogenetic band: 5p13.2 Ensembl cytogenetic band: 5p13.2 HGNC cytogenetic band: 5p13.2

C5orf42 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C5orf42 gene location

GeneLoc gene densities for chromosome 5 GeneLoc Exon Structure

GeneLoc location for GC05M037144: view genomic region (about GC identifiers)

Start:	37,059,009 bp from pter
End:	37,247,894 bp from pter
Size:	188,886 bases
Orientation:	minus strand

RefSeq DNA sequence:

NC_000005.9 NT_006576.16

(According to ¹UniProtKB, neXtProt, and/or Ensembl, Phosphorylation sites according to ²Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Millipore, Sigma-Aldrich, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, and/or ProSpec,
Biochemical Assays by Millipore, Sigma-Aldrich, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Dec 2010 and Entrez Gene, Antibodies by Millipore, Sigma-Aldrich, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, and/or Epitomics)
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UniProtKB/Swiss-Prot: CE042_HUMAN, Q9H799 (See protein sequence)

Recommended Name: Uncharacterized protein C5orf42

Size: 2095 amino acids; 236489 Da

Sequence caution: Sequence=AAH28410.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A

sequence; Sequence=BAB14999.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAB14999.1;

Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=BAB15539.1;

Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAC04822.1; Type=Erroneous initiation;

Note=Translation N-terminally extended;

Secondary accessions: Q4G174 Q8N8L4 Q9H5T1 Q9H8T9

Alternative splicing: 4 isoforms: Q9H799-1 Q9H799-2 Q9H799-3 Q9H799-4

Explore the universe of human proteins at neXtProt for C5orf42: NX_Q9H799

Post-translational modifications:

View phosphorylation sites using PhosphoSite²

REFSEQ proteins: NP_075561.3

ENSEMBL proteins:

ENSP00000424223 ENSP00000373391 ENSP00000389014 ENSP00000382582 ENSP00000421690 ENSP00000426337

ENSP00000274258

Human Recombinant Proteins

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2 Gene Ontology (GO) cellular component terms (GO ID links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0016020	membrane	IEA	--
GO:0016021	integral to membrane	IEA	--

About this table

C5orf42 for ontologies About GeneDecksing

Antibodies for C5orf42:

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Assays for C5orf42:

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	GenScript Custom Assay Services for C5orf42
	Browse Enzo Life Sciences for kits & assays
	Browse ELISAs and CLIAs at Uscn

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

ProtoNet protein and cluster: Q9H799

(According to UniProtKB, IUBMB,and/or Genatlas, Animal models from MGI Dec 24 2010,
shRNA from OriGene, Sigma-Aldrich, RNAi from Millipore, siRNAs from Sigma-Aldrich, OriGene, Qiagen, Super-pooled esiRNAs from Sigma-Aldrich, microRNA from Sigma-Aldrich, Qiagen, SABiosciences, Clones from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, Cell Lines from GenScript, Ontologies according to Gene Ontology Consortium 01 Dec 2010 via Entrez Gene.)
About This Section

Inhib. RNA:		Browse for Gene Knock-down Tools from Millipore
		Browse Nano Scale siRNA at Sigma-Aldrich Sigma-Aldrich esiRNA and siRNA for C5orf42 Sigma-Aldrich shRNA for C5orf42
		OriGene 29mer shRNA kits in GFP-retroviral vector (see all 3): C5orf42 OriGene shRNA RFP (see all 3): C5orf42 OriGene basic RS shRNA (see all 3): C5orf42 OriGene siRNA: C5orf42
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing of C5orf42

miRNA:		Sigma-Aldrich microRNA Mimics for C5orf42 Browse microRNA target validation systems at Sigma-Aldrich
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of C5orf42
		5 SABiosciences Assays for microRNAs that regulate C5orf42:
		hsa-miR-483-3p hsa-miR-23b hsa-miR-539 hsa-miR-23a hsa-miR-488

Gene
Editing:

Browse CompoZr Knockout ZFN at Sigma-Aldrich

Clones:		Browse Clones for the Expression of Recombinant Proteins Available from Millipore
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		OriGene GFP tagged cDNA clones in CMV expression vector: C5orf42 OriGene Myc/DDK tagged cDNA clones in CMV expression vector: C5orf42 OriGene untagged cDNA clones in CMV expression vector (see all 3): C5orf42 OriGene 3'-UTR clone: C5orf42 Browse MicroRNA Expression Plasmids
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Cell
Lines:

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(Pathways according to Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB, Sets of similar genes according to GeneDecks, PCR Arrays from SABiosciences, Proteins Network according to SABiosciences, Sigma-Aldrich, Interactions according to ¹UniProtKB, ²MINT, and/or ³STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Dec 2010 via Entrez Gene).
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SABiosciences Custom Pathway-Focused PCR Arrays for C5orf42

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for C5orf42

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Browse Small Molecules at Sigma-Aldrich

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for C5orf42

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 228 Homo sapiens; Dec 8 2010) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Millipore,
siRNAs from Sigma-Aldrich, OriGene, Qiagen, Super-pooled esiRNAs from Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene, microRNA from Sigma-Aldrich, Qiagen, SABiosciences,
Tagged/untagged cDNA clones from OriGene, Sigma-Aldrich, GenScript, Primers from OriGene and/or SABiosciences)
About This Section

Inhib. RNA:		Browse for Gene Knock-down Tools from Millipore
		Browse Nano Scale siRNA at Sigma-Aldrich Sigma-Aldrich esiRNA and siRNA for C5orf42 Sigma-Aldrich shRNA for C5orf42
		OriGene 29mer shRNA kits in GFP-retroviral vector (see all 3): C5orf42 OriGene shRNA RFP (see all 3): C5orf42 OriGene basic RS shRNA (see all 3): C5orf42 OriGene siRNA: C5orf42
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing of C5orf42

miRNA:		Sigma-Aldrich microRNA Mimics for C5orf42 Browse microRNA target validation systems at Sigma-Aldrich
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of C5orf42
		5 SABiosciences Assays for microRNAs that regulate C5orf42:
		hsa-miR-483-3p hsa-miR-23b hsa-miR-539 hsa-miR-23a hsa-miR-488

Clones:		Browse FLAG tag genes at Sigma-Aldrich
		OriGene GFP tagged cDNA clones in CMV expression vector: C5orf42 OriGene Myc/DDK tagged cDNA clones in CMV expression vector: C5orf42 OriGene untagged cDNA clones in CMV expression vector (see all 3): C5orf42 OriGene 3'-UTR Clone: C5orf42 Browse OriGene MicroRNA Expression Plasmids
		GenScript Custom cDNA clone Services for C5orf42

Primers:		OriGene genome-wide validated SYBR primer pairs: C5orf42 Browse OriGene validated miRNA SYBR primer pairs
		SABiosciences RT² qPCR Primer Assay for C5orf42: PPH58117A

REFSEQ mRNAs for C5orf42 gene:

NM_023073.3

Additional cDNA sequence:

AK023293.1 AK024779.1 AK026735.1 AK055192.1 AK096581.1 AL832176.1 AL833065.2 BC028410.1

BC074774.2 BC144069.1 BC144070.1 BC144072.1 BC150594.1 BX647602.1 BX649121.1

17 DOTS entries:

DT.208169 DT.40206154 DT.97837723 DT.95340958 DT.91993381 DT.97826088 DT.100024825 DT.120836438

DT.95257112 DT.100776375 DT.120808928 DT.120808929 DT.120836410 DT.437718 DT.97771136 DT.120836431

DT.99985631

24/77 AceView cDNA sequences (see all 77):

BF942228 BQ678036 AK024779 AK055192 AI591353 AK023293 BC028410 BF942061

BQ010099 BU189724 AI865979 AI436046 AA883329 AA156427 BU685554 AL833065

AI568062 BU161191 CA415468 BX119100 BF942008 BE550141 AU133557 AA452174

Unigene Cluster for C5orf42:

Chromosome 5 open reading frame 42

Hs.586199 [show with all ESTs]

Unigene Representative Sequence: NM_023073

GeneLoc Exon Structure

5/9 Alternative Splicing Database (ASD) splice patterns (SP) for C5orf42 (see all 9)

ExUns:	1	^	2	^	3	^	4a	·	4b	^	5	^	6	^	7a	·	7b	^	8	^	9	^	10a	·	10b	^	11	^	12	^	13	^	14a	·	14b	^	15a	·	15b	·	15c	^	16	^	17a	·	17b	·	17c	^	18	^
SP1:															-
SP2:																																					-
SP3:
SP4:															-
SP5:																																					-						-

ExUns:	19a	·	19b	^	20	^	21	^	22	^	23	^	24a	·	24b	^	25	^	26	^	27
SP1:
SP2:
SP3:									-				-
SP4:
SP5:

About this scheme

ECgene alternative splicing isoforms for C5orf42
18/19 Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 19):

ENST00000514429 ENST00000388739 ENST00000508405 ENST00000425232(uc003jkp.1)

ENST00000399674 ENST00000511781 ENST00000511210 ENST00000504716 ENST00000511824

ENST00000505121 ENST00000512288 ENST00000508244(uc003jko.1 uc003jks.2 uc011coz.1 uc011cpa.1 uc003jkr.1 uc011cpb.1)

ENST00000510830 ENST00000515380 ENST00000509957 ENST00000509849 ENST00000505431

ENST00000507718

(Experimental results according to ¹GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to ²GeneAnnot , ³GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 228 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Primers from OriGene and/or SABiosciences )
About This Section

C5orf42 expression in normal and diseased human tissues

¹ / ²

5 probe-sets matching C5orf42 gene

Affymetrix probe-set	Array	# genes	Sensitivity	Specificity	Correlation	Length	Gb_Accession	Consensus	Uniqueness	Score	Rank
Affymetrix probe-set	Array	GeneAnnot data			GeneNote data		GeneTide data
83619_at²	U95-E	1	1.00	1.00	0.97	0.77	--	--	--	--	--
45431_at²	U95-B	1	1.00	1.00	0.78	1.26	--	--	--	--	--
219381_at²	U133-A	1	0.82	1.00	--	--	--	--	--	--	--
1562387_at²	U133Plus2	1	1.00	1.00	--	--	--	--	--	--	--
219381_at²	U133Plus2	1	0.82	1.00	--	--	--	--	--	--	--

About this table

C5orf42 for expression About GeneDecksing

Data from Genenote (Publications) and GNF BioGPS
About these images

C5orf42 gene electronic northern expression

About these images

CGAP SAGE TAG: --

SOURCE GeneReport for Unigene cluster: Hs.586199

Primers:		OriGene genome-wide validated SYBR primer pairs: C5orf42 Browse OriGene validated miRNA SYBR primer pairs
		SABiosciences RT² qPCR Primer Assay for C5orf42: PPH58117A

SABiosciences Custom PCR Arrays for C5orf42

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD and/or ⁵MGI Dec 24 2010, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section

Orthologs for C5orf42 gene from 5/7 species (see all 7)

Organism	Gene	Locus	Description	Human Similarity	NCBI accessions
dog (Canis familiaris)	LOC479361¹	--	hypothetical LOC479361	81.52(n) 73.33(a)	479361 XM_536501.2 XP_536501.2
chimpanzee (Pan troglodytes)	LOC461916¹	--	hypothetical LOC461916	99.28(n) 98.66(a)	461916 XM_001144342.1 XP_001144342.1
cow (Bos taurus)	LOC533903¹	--	hypothetical LOC533903	83.41(n) 74.9(a)	533903 XM_613463.3 XP_613463.3
rat (Rattus norvegicus)	RGD1310081¹	--	similar to hypothetical protein FLJ13231	75.02(n) 63.99(a)	310137 XM_001081956.1 XP_001081956.1
mouse (Mus musculus)	2410089E03Rik⁵	15 (3.82 cM)	RIKEN cDNA 2410089E03 gene	--	CN536226

About this table Species with no ortholog for C5orf42

ENSEMBL Gene Tree for C5orf42 (if available)

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

(SNPs according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Resequencing Primers from Qiagen)
About This Section

SNP ID	Valid	Chr 5 pos	Sequence	Recs	AA Chg	Type	More	Recs	Allele freq	Pop	Total sample	More
Genomic Data				Transcription Related Data				Allele Frequencies
			--	--	--		--	--
rs301861^1,2	C,A,	37135936(-)	`tttttC/Tttttg`	1	--	int¹ trp³		0	--	--	--	--
rs301862^1,2	C,F,	37135285(-)	`aaaatA/Cagaaa`	1	--	int¹		6		NS EA NA WA	540
rs301863^1,2	C,H,	37133558(-)	`actacG/Aaaaca`	1	--	int¹		6		NA EA WA	168
rs301864^1,2	C,A	37132686(+)	`cttgtA/Catccg`	1	--	int¹		0	--	--	--	--
rs301865^1,2	C,H	37132503(+)	`gtgcaG/Ttggcg`	1	--	int¹		6		NA WA	12
rs301866^1,2	C,A,H	37131854(+)	`gtctcA/Gaactc`	1	--	int¹		0	--	--	--	--
rs301867^1,2	C,F,A,H,	37130856(-)	`TTTTAG/TGGGGA`	1	--	int¹		15		EA NA NS WA	810
rs301868^1,2		37130230(+)	`tcctaA/Cgtgaa`	1	--	int¹		0	--	--	--	--
rs301869^1,2	C,F,A,H,	37140597(+)	`ATAGTT/ACTACC`	1	--	int¹		17		EA NA NS WA	1192
rs301870^1,2	C,F,O,A,H,	37139291(+)	`CAATTT/GCTTAA`	1	--	int¹		7		NA NS EA	560

About this table

HapMap Linkage Disequilibrium images for C5orf42 (up to first 250kb)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for C5orf42: --

QIAGEN SeqTarget long-range PCR primers for resequencing C5orf42

(in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, LSDB, HGMD, GAD, HuGE Navigator, and/or TGDB.)
About This Section

(Possibly Related Articles in Doctor's Guide)
About This Section

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶UniProtKB/TrEMBL, and/or ⁷Novoseek)
About This Section

6 PubMed articles for C5orf42 gene integrated from 7 sources:
(articles sorted by number of sources associating them with C5orf42)

The DNA sequence and comparative analysis of human chromosome 5. (PubMed id 15372022)^{1, 2} Schmutz J.... Rubin E.M. (2004)
Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)^{1, 2} Ota T.... Sugano S. (2004)
A human MAP kinase interactome. (PubMed id 20936779)¹ Bandyopadhyay S....Ideker T. (2010)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)² Gerhard D.S....Malek J. (2004)
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. (2002)
Shotgun sequencing of the human transcriptome with ORF expressed sequence tags. (PubMed id 10737800)¹ Dias Neto E....Simpson A.J.G. (2000)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
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: 65250	HGNC: 25801	AceView: FLJ13231	Ensembl:ENSG00000197603	euGenes: HUgn65250
ECgene: C5orf42	H-InvDB: C5orf42

(According to HUGE)
About This Section

(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Intellectual Property for C5orf42 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from XenneX, Inc.)

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Patent Information for C5orf42 gene:
Search GeneIP for patents involving C5orf42

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

(Antibodies, recombinant proteins, and assays by Millipore, Sigma-Aldrich, R&D Systems, Qiagen, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Epitomics, ProSpec, Uscn,
Clones available from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, PCR Arrays from SABiosciences, Drugs and/or compounds by Sigma-Aldrich, Tocris Bioscience, and/or Enzo Life Sciences)
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	QIAGEN Custom miScript Target Protector blocks miRNA-binding site of C5orf42
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C5orf42 Gene

protein-coding GIFtS: 36

Aliases &
Descriptions
for C5orf42 gene

Summaries
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for C5orf42 gene

Proteins
for C5orf42 gene

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Pathways & Interactions
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Drugs & Compounds
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Expression
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Orthologs
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C5orf42 Gene

protein-coding GIFtS: 36

Aliases & Descriptionsfor C5orf42 gene

Summariesfor C5orf42 gene

Genomic Viewsfor C5orf42 gene

Proteinsfor C5orf42 gene

Protein Domains/Familiesfor C5orf42 gene

Gene Functionfor C5orf42 gene

Pathways & Interactionsfor C5orf42 gene

Drugs & Compoundsfor C5orf42 gene

Transcriptsfor C5orf42 gene

Expression for C5orf42 gene

Orthologsfor C5orf42 gene

Paralogsfor C5orf42 gene

Genomic Variantsfor C5orf42 gene

Disorders & Mutationsfor C5orf42 gene

Medical Newsfor C5orf42 gene

Publicationsfor C5orf42 gene

External Searches for C5orf42 gene

Genome Databases showing C5orf42 gene

Other Databases showing C5orf42 gene

Specialized Databases showing C5orf42 gene

Intellectual Propertyfor C5orf42 gene

Productsfor C5orf42 gene

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Aliases &
Descriptions
for C5orf42 gene

Summaries
for C5orf42 gene

Genomic Views
for C5orf42 gene

Proteins
for C5orf42 gene

Protein Domains/
Families
for C5orf42 gene

Gene Function
for C5orf42 gene

Pathways & Interactions
for C5orf42 gene

Drugs & Compounds
for C5orf42 gene

Transcripts
for C5orf42 gene

Expression
for C5orf42 gene

Orthologs
for C5orf42 gene

Paralogs
for C5orf42 gene

Genomic Variants
for C5orf42 gene

Disorders & Mutations
for C5orf42 gene

Medical News
for C5orf42 gene

Publications
for C5orf42 gene

Intellectual Property
for C5orf42 gene

Products
for C5orf42 gene