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C9orf41 Gene

protein-coding GIFtS: 44

GC09M076785

chromosome 9 open reading frame 41
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc , and/or ⁷Ensembl, ⁸miRBase)
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Aliases
FLJ25795 ^¹, ²
OTTHUMP00000021491 ^²

Descriptions
chromosome 9 open reading frame 41 ^²
hypothetical protein LOC138199 ^²

External Ids
HGNC: 23435¹
Entrez Gene: 138199²
UniProtKB: Q8N4J0³
Ensembl: ENSG00000156017⁷

Search outside databases for aliases for C9orf41 gene

Previous GC identifers: GC09M073054 GC09M073053 GC09M074827

(According to Entrez Gene, 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 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
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Genomic View:

UCSC Golden Path with GeneCards custom track

Transcription factor binding sites upstream to the C9orf41 gene

Entrez Gene cytogenetic band: 9q21.13 Ensembl cytogenetic band: 9q21.13 HGNC cytogenetic band: 9q21.31

C9orf41 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 9 GeneLoc Exon Structure

GeneLoc location for GC09M076785: (about GC identifiers)

Start:	76,785,754 bp from pter
End:	76,833,159 bp from pter
Size:	47,406 bases
Orientation:	minus strand

RefSeq DNA sequence:

NC_000009.10 NT_023935.17

(According to ¹UniProtKB, and/or Ensembl, Phosphorylation sites according to ²Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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UniProtKB/Swiss-Prot: CI041_HUMAN, Q8N4J0 (See protein sequence)

Recommended Name: UPF0586 protein C9orf41

Size: 409 amino acids; 47186 Da

Secondary accessions: Q7Z383 Q8N7C5

Post-translational modifications:

View phosphorylation sites using PhosphoSite²

REFSEQ proteins: NP_689633.1

ENSEMBL proteins:

ENSP00000366033 ENSP00000366026 ENSP00000366030

Human Recombinant Proteins

	Browse Drug Discovery Central at Invitrogen for human recombinant proteins
	Browse Purified and Recombinant Proteins at Millipore
	Browse Human Recombinant Proteins at Sigma-Aldrich
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	Browse Abnova for Human Recombinant Proteins

OriGene Purified Recombinant Human Protein: C9orf41

Antibodies for C9orf41:

	Browse Antibodies Central at Invitrogen
	Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
	Sigma-Aldrich Antibodies for C9orf41
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	Search for antibodies at Abcam and the World's Antibody Gateway (free search engine of over 150 antibody companies)
	Browse Abnova for Monoclonal and Polyclonal Antibodies
	Search Novus for antibodies for C9orf41

Assays for C9orf41:

	Browse Invitrogen for biochemical assays
	Browse Kits and Assays available from Millipore
	Browse R&D Systems for biochemical assays
	Browse biochemical assays available from Enzo Life Sciences

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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Graphical View of Domain Structure for InterPro Entry Q8N4J0

ProtoNet protein and cluster: Q8N4J0

1 Blocks protein family: IPB012901 N2227-like

UniProtKB/Swiss-Prot: CI041_HUMAN, Q8N4J0

Similarity: Belongs to the UPF0586 family

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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Inhib. RNA:		Invitrogen RNAi Products for gene knock-down (C9orf41)
		Browse for Gene Knock-down Tools from Millipore
		Browse Abnova for Chimera RNAi Products

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_152420

Applied Biosystems Silencer® siRNAs for C9orf41

Sigma-Aldrich siRNA for C9orf41

Sigma-Aldrich shRNA for C9orf41

Explore Sigma-Aldrich super-pooled esiRNAs

Clones:		Invitrogen Clones for C9orf41
		Browse Clones for the Expression of Recombinant Proteins Available from Millipore

OriGene GFP tagged cDNA clone in CMV expression vector: NM_152420
Myc/DDK tagged cDNA clone in CMV expression vector: NM_152420
untagged cDNA clone in CMV expression vector: NM_152420

Primers:

Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers

OriGene genome-wide validated SYBR primer pairs: NM_152420

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to ¹UniProtKB, ²MINT, and/or ³STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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(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)
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Browse drugs & compounds from Enzo Life Sciences

Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for C9orf41

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
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 Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section

Inhib. RNA:		Invitrogen RNAi Products for gene knock-down (C9orf41)
		Browse for Gene Knock-down Tools from Millipore
		Browse Abnova for Chimera RNAi Products

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_152420

Sigma-Aldrich siRNA for C9orf41

Sigma-Aldrich shRNA for C9orf41

Explore Sigma-Aldrich super-pooled esiRNAs

Applied Biosystems Silencer® siRNAs:

NM_152420

REFSEQ mRNAs for C9orf41 gene:

NM_152420.1

Applied Biosystems TaqMan ® Gene Expression Assays:

NM_152420

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_152420
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_152420
                                 untagged cDNA clone in CMV expression vector: NM_152420

Additional cDNA sequence:

AK098661.1 AK299691.1 BC034033.1 BX538061.1 BX647386.1

2 DOTS entries:

DT.452300 DT.99954579

24/66 AceView cDNA sequences (see all 66 ):

F11142 F08813 BI520526 CK430790 BU615646 AK098661 BQ722426 AI686196

BC034033 AA732427 NM_152420 BX647386 AI478216 BX281771 BU675084 BI560441

AW576495 AA602748 BX538061 BE899104 CB052768 BX481773 BX332562 BM922695

highest scoring ESTs for C9orf41:

AA314096 AW452350 BC034033 BE899104 BF666935 BG719553 BI520526 BI559609 BI560441 BM554478

Unigene Cluster for C9orf41:

Chromosome 9 open reading frame 41

Hs.567688 [show with all ESTs]

Unigene Representative Sequence: BX647386

GeneLoc Exon Structure

4 Alternative Splicing Database (ASD) splice patterns (SP) for C9orf41

ExUns:	1	^	2	^	3a	·	3b	^	4a	·	4b	^	5	^	6	^	7	^	8	^	9	^	10	^	11
SP1:			-		-		-						-
SP2:													-
SP3:
SP4:

About this scheme

ECgene alternative splicing isoforms for C9orf41

3 Ensembl transcripts including schematic representations:

ENST00000376837 ENST00000376830 ENST00000376834

(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 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
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C9orf41 expression in normal and diseased human tissues

Applied Biosystems TaqMan ® Gene Expression Assays for C9orf41

¹ / ² / ³

5 probe-sets matching C9orf41 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
82010_r_at²^{, 3}	U95-D	1	0.75	1.00	1.00	1.00	H50724	0.60	1.00	0.82	1
228324_at²^{, 3}	U133-B	1	1.00	1.00	--	--	BF031819	0.60	1.00	0.82	1
241781_at²^{, 3}	U133-B	1	1.00	1.00	--	--	BF979668	0.60	1.00	0.82	1
228324_at²	U133Plus2	1	1.00	1.00	--	--	--	--	--	--	--
241781_at²	U133Plus2	1	1.00	1.00	--	--	--	--	--	--	--

About this table

Data from

(Publications) and GNF BioGPS
About these images
About these images

CGAP SAGE TAG: AAATTTCCTA

SOURCE GeneReport for Unigene cluster: Hs.567688

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD and/or ⁵MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
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Orthologs for C9orf41 gene from 5/25 species (see all 25 )

Organism	Gene	Locus	Description	Human Similarity	NCBI accessions
dog (Canis familiaris)	LOC476320¹	--	similar to CG11596-PA, isoform A	96(n) 98.04(a)	476320 XM_533523.2 XP_533523.2
chimpanzee (Pan troglodytes)	LOC472958¹	--	similar to Chromosome 9 open reading frame 41	99.92(n) 100(a)	472958 XM_528328.2 XP_528328.2
cow (Bos taurus)	LOC538441¹	--	similar to chromosome 9 open reading frame 41	95.52(n) 97.8(a)	538441 XM_580351.3 XP_580351.3
rat (Rattus norvegicus)	RGD1311863¹	--	similar to RIKEN cDNA 2410127L17	91.08(n) 92(a)	293871 NM_001024974.1 NP_001020145.1
mouse (Mus musculus)	2410127L17Rik¹	--	RIKEN cDNA 2410127L17 gene	90.83(n) 92(a)	67383 NM_026120.4 NP_080396.2

About this table Species with no ortholog for C9orf41

ENSEMBL Gene Tree for C9orf41

(Paralogs according to ¹HomoloGene
and ²Ensembl, Pseudogenes according to ³Pseudogene.org)
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(According to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
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10/191 NCBI SNPs in C9orf41 are shown (see all 191 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay) (see all 85)

AB	SNP ID	Valid	Chr 9 pos	Sequence	Recs	AA Chg	Type	More	Recs	Allele freq	Pop	Total sample	More
AB	Genomic Data				Transcription Data				Allele Frequencies
				--	--	--		--	--				--
	rs7021142^1,2	A,C,F,H	76835125(+)	`TAGTAG/TTAGCT`	1	--	ng3¹		4		EU EA WA	412
	rs10869475^1,2	A,C,F,H	76833374(+)	`CTTAAA/GAGCCG`	1	--	ng3¹		4		EU EA WA	410
	rs1779988^1,2	C,F,H	76788015(+)	`TTTACG/ACATAG`	1	--	ut3¹ ese³		5		MN EU EA WA	602
	rs719507^1,2	A,F,H	76833339(-)	`GTAACC/GGCAGT`	1	--	ng3¹ tfbs³		4		MN EU NA	486
--	rs11790114^1,2	C	76834958(+)	`tgagcC/Tgccac`	1	--	ng3¹		0	--	--	--	--
--	rs773160^1,2	C	76834884(+)	`gttgcC/Gcaggt`	1	--	ng3¹		0	--	--	--	--
	rs12380147^1,2	C,F,H	76803359(+)	`TGAAAA/GTCTCC`	1	D/D	syn¹		5		NA EU EA WA	498
	rs1539732^1,2	A,C,F,H,O	76789192(+)	`TGAAAA/GCTAAG`	1	--	int¹		11		EU EA WA NA	980
	rs2376382^1,2	A,C,F,H,O	76824787(+)	`CTACAC/AAGAAA`	1	--	int¹		10		EU EA WA NA	830
	rs10781258^1,2	A,C,F,H	76808258(+)	`cctaaC/Aacatt`	1	--	int¹		4		EU EA WA	416

About this table

HapMap Linkage Disequilibrium images for C9orf41 (up to first 250kb)

(in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, 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 ¹Novoseek, ²HGNC, ³Entrez Gene, ⁴UniProtKB/Swiss-Prot, ⁵UniProtKB/TrEMBL, ⁶GAD, and/or ⁷PharmGKB)
About This Section

5 PubMed articles for C9orf41 gene:

DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)^{3, 4} Humphray S.J.... Dunham I. (2004)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{3, 4} Gerhard D.S....Malek J. (2004)
Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)^{3, 4} Ota T....Sugano S. (2004)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)^{2, 3} Strausberg R.L....Marra M.A. (2002)
The full-ORF clone resource of the German cDNA Consortium. (PubMed id 17974005)⁴ Bechtel S....Schupp I. (2007)

(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, and/or H-InvDB)
About This Section

Entrez Gene: 138199	HGNC: 23435	AceView: C9orf41	Ensembl:ENSG00000156017	euGenes: HUgn138199
ECgene: C9orf41	H-InvDB: C9orf41

(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

Licensable Technologies for C9orf41
(Available from WIS Yeda, Salk, Tufts)

About This Section

(Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
Enzo Life Sciences, and/or Tocris Bioscience)
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Products for C9orf41:

TaqMan ® Gene Expression Assays

TaqMan ® Genotyping Assays

Free SNP selection tool

Invitrogen iPath Pathways	Invitrogen BLOCK-iT™ RNAi
Invitrogen Antibodies	Invitrogen Assays
Invitrogen Clones	Invitrogen Q-PCR Products
Invitrogen Human Recombinant Kinases	Invitrogen Custom Antibody and Peptide Service
Invitrogen Proteins / Assays / Screening Services	Search Invitrogen catalog for C9orf41-related products

	Millipore Custom Antibody & Bulk Services
	Millipore Preclinical / Clinical Development Services
	Millipore Immunoassay Services
	Millipore Target Screening & Profiling Services

	Predesigned and custom siRNAs for C9orf41		Antibodies for C9orf41
	Explore super-pooled esiRNAs		Browse proteins at Sigma-Aldrich
	Lentivirus-delivered shRNAs for C9orf41		Browse small molecules at Sigma-Aldrich
	"Your Favorite Gene" Pathways		feedback

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	Recombinant & Natural Proteins

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	Tagged/untagged cDNA clones
	Validated SYBR primer pairs
	Purified proteins from HEK293T cells
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	shRNA in GFP-retroviral vector

Search Tocris compounds for C9orf41

Search www.enzolifesicences.com for proteins, assays, substrates, inhibitors & antibodies

Search Novus for antibodies for C9orf41

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C9orf41 Gene

protein-coding GIFtS: 44

Aliases &
Descriptions
for C9orf41

Summaries
for C9orf41

Genomic Location
for C9orf41

Proteins
for C9orf41

Protein Domains/
Families
for C9orf41

Gene Function
for C9orf41

Pathways & Interactions
for C9orf41

Drugs & Compounds
for C9orf41

Transcripts
for C9orf41

Expression
for C9orf41

Orthologs
for C9orf41

Paralogs
for C9orf41

SNPs/Variants
for C9orf41

Disorders & Mutations
for C9orf41

Medical News
for C9orf41

Publications
for C9orf41

Search for C9orf41

Genome Databases showing C9orf41

Other Databases showing C9orf41

Specialized Databases showing C9orf41

Licensable Technologies
for C9orf41

Services
for C9orf41

Gene Index: 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

C9orf41 Gene

protein-coding GIFtS: 44

Aliases & Descriptionsfor C9orf41

Summariesfor C9orf41

Genomic Locationfor C9orf41

Proteinsfor C9orf41

Protein Domains/Familiesfor C9orf41

Gene Functionfor C9orf41

Pathways & Interactionsfor C9orf41

Drugs & Compoundsfor C9orf41

Transcriptsfor C9orf41

Expression for C9orf41

Orthologsfor C9orf41

Paralogsfor C9orf41

SNPs/Variantsfor C9orf41

Disorders & Mutationsfor C9orf41

Medical Newsfor C9orf41

Publicationsfor C9orf41

Search for C9orf41

Genome Databases showing C9orf41

Other Databases showing C9orf41

Specialized Databases showing C9orf41

Licensable Technologiesfor C9orf41

Servicesfor C9orf41

Gene Index: 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

Aliases &
Descriptions
for C9orf41

Summaries
for C9orf41

Genomic Location
for C9orf41

Proteins
for C9orf41

Protein Domains/
Families
for C9orf41

Gene Function
for C9orf41

Pathways & Interactions
for C9orf41

Drugs & Compounds
for C9orf41

Transcripts
for C9orf41

Expression
for C9orf41

Orthologs
for C9orf41

Paralogs
for C9orf41

SNPs/Variants
for C9orf41

Disorders & Mutations
for C9orf41

Medical News
for C9orf41

Publications
for C9orf41

Licensable Technologies
for C9orf41

Services
for C9orf41