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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

C21orf2 Gene

protein-coding GIFtS: 49
GCID: GC21M045749

chromosome 21 open reading frame 2

Explore 3 diseases affiliated with
C21orf2 via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, ¹⁰fRNAdb, and/or ¹¹Nature:405,311-319 and CroW21)
About This Section

Aliases
Chromosome 21 Open Reading Frame 2¹ ²		Nuclear Encoded Mitochondrial Protein, CDNA A2-YF511
YF5/A2² ³		Nuclear Encoded Mitochondrial Protein C21orf2²
A2¹		C21orf-HUMF09G8.5³
YF5¹

External Ids:	HGNC: 1260¹	Entrez Gene: 755²	Ensembl: ENSG00000160226⁷	OMIM: 603191⁵	UniProtKB: O43822³

Export aliases for C21orf2 gene to outside databases

Previous GC identifers: GC21M042258 GC21M042341 GC21M044605 GC21M044573 GC21M031119

(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 C21orf2:

Four alternatively spliced transcript variants encoding four different isoforms have been found for this nuclear gene.

All isoforms contain leucine-rich repeats. Three of these isoforms are mitochondrial proteins and one of them lacks

the target peptide, so is not located in mitochondrion. This gene is down-regulated in Down syndrome (DS) brain, which

may represent mitochondrial dysfunction in DS patients. (provided by RefSeq, Sep 2012)

UniProtKB/Swiss-Prot: CU002_HUMAN, O43822

Function: May play roles in cilia formation and/or maintenance (By similarity). Plays a role in the regulation of cell

morphology and cytoskeletal organization

(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, Whole Chromsome Sequence According to Nature (Cited Here with Permission):405,311-319 and CroW21)
About This Section

RefSeq DNA sequence:

NC_000021.8 NC_018932.1 NT_011515.12

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the C21orf2 gene promoter:
Spz1 AML1a Pax-6 STAT5A NF-kappaB GATA-2 YY1 AREB6 NF-kappaB2 NF-kappaB1
Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids

Search SABiosciences Chromatin IP Primers for C21orf2

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat C21orf2

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

Entrez Gene cytogenetic band: 21q22.3 Ensembl cytogenetic band: 21q22.3 HGNC cytogenetic band: 21q22.3
Nature(405: 311-319) cytogenetic band: 21q22.3

C21orf2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C21orf2 gene location

GeneLoc information about chromosome 21 GeneLoc Exon Structure

(about GC identifiers)

GC21M045749:	GeneLoc	Nature:405,311-319
Start:	45,748,827 bp from pter	31,258,219 bp from centromere
End:	45,759,285 bp from pter	31,268,538 bp from centromere
Size:	10,459 bases	10,320 bases
Orientation:	minus strand	minus strand

Whole chromosome sequencing:
cDNA sequence:	Y11392
genomic clones:	Q5B10

(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: CU002_HUMAN, O43822 (See protein sequence)

Recommended Name: Protein C21orf2

Size: 256 amino acids; 28340 Da

Secondary accessions: A8MPS9 O14993 Q99837 Q99838

Alternative splicing: 2 isoforms: O43822-1 O43822-2

Explore the universe of human proteins at neXtProt for C21orf2: NX_O43822

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_O43822

C21orf2 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins (4 alternative transcripts):

NP_001258369.1 NP_001258370.1 NP_001258371.1 NP_004919.1

ENSEMBL proteins:

ENSP00000344566 ENSP00000381047 ENSP00000317302

Human Recombinant Protein Products:

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	Uscn Proteins for C21orf2

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

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005737	cytoplasm	IDA	--
GO:0005886	plasma membrane	IDA	--

C21orf2 for ontologies About GeneDecksing

C21orf2 Antibody Products:

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	Uscn ELISAs and CLIAs for C21orf2

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

C21orf2 for domains About GeneDecksing

3 InterPro domains/families:

IPR003603 U2A'_phosphoprotein32A_C

IPR001611 Leu-rich_rpt

IPR025875 Leu-rich_rpt_4

Graphical View of Domain Structure for InterPro Entry O43822

ProtoNet protein and cluster: O43822

2 Blocks protein families:

IPB001611 Leucine-rich repeat signature

IPB003603 Leucine-rich-associated

UniProtKB/Swiss-Prot: CU002_HUMAN, O43822

Similarity: Contains 3 LRR (leucine-rich) repeats

Similarity: Contains 1 LRRCT domain

Similarity: To C.elegans F09G8.5

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

Function Summary:

UniProtKB/Swiss-Prot: CU002_HUMAN, O43822

Function: May play roles in cilia formation and/or maintenance (By similarity). Plays a role in the regulation of cell

morphology and cytoskeletal organization

Genatlas biochemistry entry for C21orf2:

chromosome 21 open reading frame 2,mitochondrial protein,25kDa,with two alternatively spliced transcripts,widely

expressed,encoded by a nuclear gene in the DFNB8/DFNB10 region

miRNA Products:		OriGene 3'-UTR Clone: C21orf2 Browse MicroRNA Expression Plasmids
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In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C21orf2

Gene Ontology (GO): 1 molecular function term (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0003674	molecular_function	ND	--

C21orf2 for ontologies About GeneDecksing

(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 C21orf2

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

1 Interacting protein for C21orf2 (ENSP00000344566⁴) via UniProtKB, MINT, STRING, and/or I2D

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
UBC	ENSP00000344818⁴	STRING: ENSP00000344818

About this table

Gene Ontology (GO): 4 biological process terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0007010	cytoskeleton organization	IMP	--
GO:0008150	biological_process	ND	--
GO:0008360	regulation of cell shape	IMP	--
GO:0060271	cilium morphogenesis	IEA	--

C21orf2 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 C21orf2
Search CenterWatch for drugs/clinical trials and news about C21orf2 / CU002

(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,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
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 C21orf2 gene (4 alternative transcripts):

NM_001271440.1 NM_001271441.1 NM_001271442.1 NM_004928.2

Unigene Cluster for C21orf2:

Chromosome 21 open reading frame 2

Hs.517331 [show with all ESTs]

Unigene Representative Sequence: AK074162

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

ENST00000339818(uc002zeo.1 uc002zep.2 uc002zer.2 uc002zeq.2)

ENST00000470196 ENST00000496321 ENST00000462742(uc002zes.1) ENST00000397956

ENST00000325223 ENST00000478674

miRNA Products:		OriGene 3'-UTR Clone: C21orf2 Browse OriGene MicroRNA Expression Plasmids
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Inhib. RNA Products:		Browse for Gene Knock-down Tools from EMD Millipore
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Additional cDNA sequence:

AK074162.1 BC031300.1 BC072012.1 U84569.1 U84570.1 Y11392.1 Z93322.1

14 DOTS entries:

DT.75199150 DT.100024554 DT.207415 DT.40307132 DT.95170249 DT.40132285 DT.433168 DT.75131362

DT.121140878 DT.87017391 DT.92425350 DT.121140886 DT.92425351 DT.95170250

24/162 AceView cDNA sequences (see all 162):

Y11392 CA489339 AA496497 BM718028 BX094326 CA427089 BE856252 AA447767

AI081454 Z93322 AI391609 BQ189620 AI282432 CA314162 AI598246 BU733416

NM_004928 BM709571 AI744074 AI301036 AI870362 BM023369 BC072012 AI423069

GeneLoc Exon Structure

5/9 Alternative Splicing Database (ASD) splice patterns (SP) for C21orf2 (see all 9) About this scheme

ExUns:	1	^	2	^	3	^	4	^	5	^	6a	·	6b	·	6c	^	7a	·	7b	·	7c	^	8a	·	8b	^	9	^	10a	·	10b	·	10c	·	10d	^	11	^	12
SP1:									-		-		-												-
SP2:									-		-														-
SP3:									-		-														-
SP4:									-		-
SP5:											-

ECgene alternative splicing isoforms for C21orf2

(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

C21orf2 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: GCCGCAGCCC

About this image
See C21orf2 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for C21orf2

SOURCE GeneReport for Unigene cluster: Hs.517331

SABiosciences Custom PCR Arrays for C21orf2

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In Situ
Assay Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C21orf2

(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 C21orf2 gene from 6/19 species (see all 19) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	1810043G02Rik^{1 , 5}	RIKEN cDNA 1810043G02 gene^{1, 5}	79.52(n)¹ 75.5(a)¹		10 (39.72 cM)⁵ 67884¹ NM_026431.2¹ NP_080707.2¹ 77978524⁵
chicken (Gallus gallus)	Aves	C9H21orf2¹	chromosome 9 open reading frame, human C21orf2	69.09(n) 64.11(a)		424866 NM_001006544.1 NP_001006544.1
lizard (Anolis carolinensis)	Reptilia	C21orf2⁶	--	56(a)	1 ↔ 1	3(33679053-33686129)
zebrafish (Danio rerio)	Actinopterygii	LOC100537391¹	uncharacterized protein C21orf2-like	62.43(n) 55.74(a)		100537391 XM_003199532.1 XP_003199580.1
fruit fly (Drosophila melanogaster)	Insecta	CG15208⁶ CG14995⁶	--	22(a) 21(a)	many → 1 many → 1	X(10794393-10795771) 3L(4094343-4103256)
worm (Caenorhabditis elegans)	Secernentea	F09G8.5⁶	Uncharacterized protein F09G8.5	18(a)	1 ↔ 1	III(8254904-8257548)

ENSEMBL Gene Tree for C21orf2 (if available)
TreeFam Gene Tree for C21orf2 (if available)

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

(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 21 pos	Sequence	#	AA Chg	Type	More	#	Pop	Total sample
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs56825465^1,2	C,	--	31118701(+)	`GCTGCG/ATGGAG`	4	--	ds500¹		2	WA	120
rs73374009^1,2	C,	--	31118880(+)	`CTGGAC/TGTGCT`	4	--	ds500¹		1	WA	2
rs1056725^1,2	C	--	31119200(+)	`AACTGT/CCCACC`	4	--	ut3¹		3	MN NA	188
rs77610661^1,2	F,	--	31119206(+)	`CCACCC/TTCTAT`	4	--	ut3¹		1	WA	118
rs73907165^1,2	C,	--	31119302(+)	`ATGAGT/CGACTG`	4	--	ut3¹		3	WA CSA	121
rs73907166^1,2	C,	--	31119405(+)	`TGGGAG/CAACAG`	4	--	ut3¹		3	WA CSA	121
rs79299307^1,2	F,	--	31119441(+)	`ACCGCT/CCGGCG`	4	--	ut3¹		1	NA	120
rs116171340^1,2	C,F,	--	31119446(+)	`TCGGCG/AGAGGA`	4	--	ut3¹		1	WA	118
rs116737357^1,2	C,F,	--	31119642(+)	`GACTTG/ACGACT`	4	--	ut3¹		1	WA	118
rs73907168^1,2	C,	--	31119685(+)	`CTCCAA/GGGACT`	4	--	ut3¹		4	WA CSA EA	241

HapMap Linkage Disequilibrium report for C21orf2 (45748827 - 45759285 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 1 variation for C21orf2
1 CNV: 7327

SABiosciences Cancer Mutation PCR Assays

QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing C21orf2

DNA2.0 Custom Variant and Variant Library Synthesis for C21orf2

(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

C21orf2 for disorders           About GeneDecksing

OMIM gene information: 603191    OMIM disorders: --

3 diseases for C21orf2:    About MalaCards

friedreich ataxia down syndrome ataxia

1 disease from the University of Copenhagen DISEASES database for C21orf2:

Friedreich ataxia

Export disorders for C21orf2 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 C21orf2 gene, integrated from 9 sources (see all 12):
(articles sorted by number of sources associating them with C21orf2)

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

Characterization of a novel gene, C21orf2, on human chromosome 21q22.3 and its exclusion as the APECED gene by mutation analysis. (PubMed id 9465297)^{1, 2, 3} Scott H.S.... Antonarakis S.E. (1998)
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)
The DNA sequence of human chromosome 21. (PubMed id 10830953)^{1, 2} Hattori M....Yaspo M.L. (2000)
Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)¹ Kim W....Gygi S.P. (2011)
Identification and characterization of a set of conserved and new regulators of cytoskeletal organisation, cell morphology and migration. (PubMed id 21834987)² Bai S.W.... Ridley A.J. (2011)
Large-scale proteomics analysis of the human kinome. (PubMed id 19369195)² Oppermann F.S.... Daub H. (2009)
hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)¹ Lamesch P.... Vidal M. (2007)
Transcriptome analysis of human gastric cancer. (PubMed id 16341674)¹ Oh J.H....Kim N.S. (2005)
Protein levels of genes encoded on chromosome 21 in fetal Down syndrome brain: challenging the gene dosage effect hypothesis (Part III). (PubMed id 12624744)¹ Cheon M.S....Lubec G. (2003)
Reduction of chromatin assembly factor 1 p60 and C21orf2 protein, encoded on chromosome 21, in Down syndrome brain. (PubMed id 15068244)¹ Shim K.S....Lubec G. (2003)

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

		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)
About This Section

Entrez Gene: 755	HGNC: 1260	AceView: C21orf2	Ensembl:ENSG00000160226	euGenes: HUgn755
ECgene: C21orf2	H-InvDB: C21orf2

(According to HUGE)
About This Section

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

Name	Description
PharmGKB entry for C21orf2	Pharmacogenomics, SNPs, Pathways

Intellectual Property for C21orf2 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

About This Section

Patent Information for C21orf2 gene:
Search GeneIP for patents involving C21orf2

GeneCards and IP:
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GeneCards Homepage - Last full update: 19 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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C21orf2 Gene

chromosome 21 open reading frame 2

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C21orf2 Gene

chromosome 21 open reading frame 2

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