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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

SPEF1 Gene

protein-coding GIFtS: 46
GCID: GC20M003758

sperm flagellar 1

(Previous name: chromosome 20 open reading frame 28 )
(Previous symbol: C20orf28)

Explore 1 disease affiliated with
SPEF1 via

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
Sperm Flagellar 1¹ ²		DKFZP434I114¹
C20orf28¹ ² ³ ⁵		Chromosome 20 Open Reading Frame 28¹
SPEF1A¹ ²		Calponin-Homology And Microtubule-Associated Protein²
CLAMP² ⁵		Sperm Flagellar Protein 1²

External Ids:	HGNC: 15874¹	Entrez Gene: 25876²	Ensembl: ENSG00000101222⁷	OMIM: 610674⁵	UniProtKB: Q9Y4P9³

Export aliases for SPEF1 gene to outside databases

Previous GC identifer: GC20M003707

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

Gene Wiki entry for SPEF1

(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_000020.10 NC_018931.1 NT_011387.8

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the SPEF1 gene promoter:
GR STAT3 ZID Nkx2-5 GR-alpha NF-kappaB1
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: SPEF1 promoter sequence

Search SABiosciences Chromatin IP Primers for SPEF1

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SPEF1

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

Entrez Gene cytogenetic band: 20pter-q11.23 Ensembl cytogenetic band: 20p13 HGNC chromosome: 20

SPEF1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SPEF1 gene location

GeneLoc information about chromosome 20 GeneLoc Exon Structure

GeneLoc location for GC20M003758: view genomic region (about GC identifiers)

Start:	3,758,151 bp from pter	End:	3,762,102 bp from pter
Size:	3,952 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: SPEF1_HUMAN, Q9Y4P9 (See protein sequence)

Recommended Name: Sperm flagellar protein 1

Size: 236 amino acids; 26987 Da

Subcellular location: Cytoplasm. Cell projection, cilium, flagellum. Cytoplasm, cytoskeleton, cilium axoneme (By

similarity). Note=Present in the tails of developing and epididymal sperm, internal to the fibrous sheath and around

the outer dense fibers of the sperm flagellum. Also found at the apical tip of cilia (By similarity)

1 PDB 3D structure from and Proteopedia for SPEF1:

2EE7 (3D)

Secondary accessions: A5YM71 D3DVY0 Q5JX78

Alternative splicing: 2 isoforms: Q9Y4P9-1 Q9Y4P9-2 (Gene prediction based on EST data. No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SPEF1: NX_Q9Y4P9

SPEF1 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins: NP_056232.2

ENSEMBL proteins:

ENSP00000369080

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

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005575	cellular_component	ND	--
GO:0005737	cytoplasm	--	--
GO:0005856	cytoskeleton	IEA	--
GO:0035085	cilium axoneme	ISS	--

SPEF1 for ontologies About GeneDecksing

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	Uscn ELISAs and CLIAs for SPEF1

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

SPEF1 for domains About GeneDecksing

2 InterPro domains/families:

IPR001715 CH-domain

IPR010441 DUF1042

Graphical View of Domain Structure for InterPro Entry Q9Y4P9

ProtoNet protein and cluster: Q9Y4P9

2 Blocks protein families:

IPB001715 Calponin-like actin-binding

IPB010441 Protein of unknown function DUF1042

(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

miRNA Products:		Browse 3'-UTR reporter clones for miRNA target validation Browse MicroRNA Expression Plasmids
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SPEF1
		6 QIAGEN miScript miRNA Assays for microRNAs that regulate SPEF1:
		hsa-miR-4314 hsa-miR-875-3p hsa-miR-593 hsa-miR-766 hsa-miR-1299 hsa-miR-3667-3p
		SwitchGear 3'UTR luciferase reporter plasmid: SPEF1 3' UTR sequence

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In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SPEF1

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	--

SPEF1 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 SPEF1

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

3 Interacting proteins for SPEF1 (Q9Y4P9^{2, 3} ENSP00000369080⁴) via UniProtKB, MINT, STRING, and/or I2D

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
ZBED1	O96006²^,³, ENSP00000370616⁴	MINT-66054 I2D: score=5 STRING: ENSP00000370616
PLEKHF2	Q9H8W4²^,³, ENSP00000322373⁴	MINT-66965 I2D: score=5 STRING: ENSP00000322373
ACTG1	P63261³	I2D: score=1

About this table

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

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0008150	biological_process	ND	--

SPEF1 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

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Browse Tocris compounds for SPEF1
Search CenterWatch for drugs/clinical trials and news about SPEF1

(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,
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About This Section

REFSEQ mRNAs for SPEF1 gene:

NM_015417.4

Unigene Cluster for SPEF1:

Sperm flagellar 1

Hs.72620 [show with all ESTs]

Unigene Representative Sequence: BC022476

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

ENST00000471499 ENST00000463490 ENST00000379756(uc002wjj.3)

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		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SPEF1
		6 QIAGEN miScript miRNA Assays for microRNAs that regulate SPEF1:
		hsa-miR-4314 hsa-miR-875-3p hsa-miR-593 hsa-miR-766 hsa-miR-1299 hsa-miR-3667-3p
		SwitchGear 3'UTR luciferase reporter plasmid: SPEF1 3' UTR sequence

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		QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat SPEF1
		QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SPEF1

Additional cDNA sequence:

AK313766.1 AL080154.1 BC022476.1 EF560745.1

2 DOTS entries:

DT.75123052 DT.100748581

24/29 AceView cDNA sequences (see all 29):

CA314157 BM973032 AI243965 CB306557 AI359494 BG152643 AL040853 CB156218

BG702194 BC022476 CB240937 NM_015417 BI821270 AL080154 CA444964 AL040854

BI822734 BF197389 BM981403 AI925267 BI520334 BI520701 BM839513 AA166837

GeneLoc Exon Structure

4 Alternative Splicing Database (ASD) splice patterns (SP) for SPEF1 About this scheme

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

ECgene alternative splicing isoforms for SPEF1

(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

SPEF1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: GGGGAATCTG

About this image

SPEF1 expression in embryonic tissues and stem cells

Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

3 LifeMap In Vivo Development Anatomical Compartments/Cells

Tissue

Anatomical Compartment

Cell

Category (developmental path)

Extraembryonic Mesoderm

Extraembryonic Blood Islands

Primitive Erythrocytes

Blood

Brain

Neural Tube

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

Stem Cell Differentiation: 1 LifeMap Cell

Name

Category

Posterior foregut-like cells (A scalable, suspensi...)

See SPEF1 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for SPEF1

SOURCE GeneReport for Unigene cluster: Hs.72620

SABiosciences Custom PCR Arrays for SPEF1

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In Situ
Assay Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SPEF1

(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 SPEF1 gene from 5/21 species (see all 21) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Spef1^{1 , 5}	sperm flagellar 1^{1, 5}	85.61(n)¹ 88.89(a)¹		2 (63.28 cM)⁵ 70997¹ NM_027641.2¹ NP_081917.1¹ 131170261⁵
chicken (Gallus gallus)	Aves	SPEF1¹	sperm flagellar 1	64.43(n) 57.54(a)		426178 XM_423842.3 XP_423842.3
lizard (Anolis carolinensis)	Reptilia	SPEF1⁶	--	60(a)	1 ↔ 1	GL344063.1(232-21318)
zebrafish (Danio rerio)	Actinopterygii	BC055652.1²	--	71.36(n)		393499 BC055652.1
fruit fly (Drosophila melanogaster)	Insecta	CG12395⁶ CG16719⁶	--	22(a) 18(a)	many → 1 many → 1	X(15955935-15956888) 3L(9678271-9679350)

ENSEMBL Gene Tree for SPEF1 (if available)
TreeFam Gene Tree for SPEF1 (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 20 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs150305364^1,2		--	3757704(+)	`GTAGTA/GTGTTG`	1	--	int¹		0	--	--	--	--
rs138011280^1,2		--	3757750(+)	`GGAAGC/TTGGGA`	1	--	int¹		0	--	--	--	--
rs73895626^1,2	C,F,	--	3758074(+)	`AGGCGG/AGGGTG`	1	--	int¹		4		WA CSA NA	242
rs117635906^1,2		--	3758123(+)	`TCAGAT/AGCAAA`	1	--	int¹		1		EA	120
rs3746642^1,2	C,F,	--	3758184(+)	`AGCCCT/AGAGCC`	1	--	ut3¹ ese³		2		EA	1540
rs910654^1,2	C,F,A,	--	3758426(-)	`ATCCAG/CGCTAG`	1	--	ut3¹ ese³		12		EA NA WA	412
rs181447223^1,2		--	3758567(+)	`GGGGAC/GAGGCT`	1	--	ut3¹		0	--	--	--	--
rs3746643^1,2	C,F,H,	--	3758641(+)	`AGTGGT/CAGGAG`	1	--	ut3¹ ese³		8		EA NS NA	810
rs200753596^1,2		--	3758843(+)	`CCGCGC/TGGCCC`	1	--	ut3¹		0	--	--	--	--
rs199671355^1,2		--	3758880(+)	`TCCGCC/TTGCTG`	2	Q	syn¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for SPEF1 (3758151 - 3762102 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for SPEF1: --

SABiosciences Cancer Mutation PCR Assays

QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SPEF1

DNA2.0 Custom Variant and Variant Library Synthesis for SPEF1

(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

SPEF1 for disorders           About GeneDecksing

OMIM gene information: 610674    OMIM disorders: --

1 disease for SPEF1:    About MalaCards

malaria

Export disorders for SPEF1 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 SPEF1 gene integrated from 9 sources:
(articles sorted by number of sources associating them with SPEF1)

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

Spef1, a conserved novel testis protein found in mouse sperm flagella. (PubMed id 15979255)^{1, 2, 3} Chan S.W.... Kalitsis P. (2005)
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 and comparative analysis of human chromosome 20. (PubMed id 11780052)^{1, 2} Deloukas P....Rogers J. (2001)
Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PubMed id 11230166)^{1, 2} Wiemann S.... Poustka A. (2001)
The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)² Bechtel S.... Schupp I. (2007)
Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)¹ Kimura K.... Sugano S. (2006)
Towards a proteome-scale map of the human protein-protein interaction network. (PubMed id 16189514)¹ Rual J.F....Vidal M. (2005)
CLAMP, a novel microtubule-associated protein with EB-type calponin homology. (PubMed id 16206169)¹ Dougherty G.W....Kachar B. (2005)
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)

(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: 25876	HGNC: 15874	AceView: C20orf28	Ensembl:ENSG00000101222	euGenes: HUgn25876
ECgene: SPEF1	H-InvDB: SPEF1

(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 SPEF1	Pharmacogenomics, SNPs, Pathways

Intellectual Property for SPEF1 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

About This Section

Patent Information for SPEF1 gene:
Search GeneIP for patents involving SPEF1

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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
In Situ Hybridization Assays from
Advanced Cell Diagnostics
About This Section


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	OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for SPEF1		OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for SPEF1
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	OriGene Custom Antibody Services for SPEF1		OriGene Custom Protein Services for SPEF1
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	QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat SPEF1
	QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SPEF1
	QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SPEF1
	QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat SPEF1
	QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SPEF1
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	GenScript Custom Purified and Recombinant Proteins Services for SPEF1		GenScript cDNA clones with any tag delivered in your preferred vector for SPEF1
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	Gene Synthesis: Any Gene in Any Vector		Vector-based siRNA and miRNA, Ready for Transfection
	Gene Mutant Library, Variants up to 10^11		Plasmid Preparation
	Custom Peptide Services

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Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SPEF1

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

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Category			VWF (GIFTS: 73) von Willebrand factor
GIFtS Group

The GeneCards human gene database gene index: 1 3 5 6 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

The GeneCards Human Gene Database

Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

Hot genes Disease genes SPEF1 gene at Home site.

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sperm flagellar 1

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SPEF1 Gene

sperm flagellar 1

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for SPEF1 gene

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for SPEF1 gene

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