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ODF1 Gene

protein-coding GIFtS: 51

GC08P103633

outer dense fiber of sperm tails 1
(Previous name: outer dense fibre of sperm tails 1 )
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)
About This Section

Aliases
HSPB10 ^¹, ²
MGC129928 ^²
MGC129929 ^²
ODF ^²
ODF2 ^²
ODF27 ^¹, ²
ODFP ^², ³
ODFPG ^¹, ²
ODFPGA ^²
ODFPGB ^²
RT7 ^¹, ²
SODF ^²

Descriptions
outer dense fiber of sperm tails 1 ^²
outer dense fiber of sperm tails, 27-kD ^²
outer dense fibre of sperm tails 1 ^¹

External Ids
HGNC: 8113¹
Entrez Gene: 4956²
UniProtKB: Q14990³
Ensembl: ENSG00000155087⁷

Search outside databases for aliases for ODF1 gene

Previous GC identifers: GC08P102569 GC08P103632 GC08P103232 GC08P103520

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

EntrezGene summary for ODF1:

The outer dense fibers are cytoskeletal structures that surround the axoneme in the middle piece

and principal piece of the sperm tail. The fibers function in maintaining the elastic structure

and recoil of the sperm tail as well as in protecting the tail from shear forces during epididymal

transport and ejaculation. Defects in the outer dense fibers lead to abnormal sperm morphology and

infertility. The human outer dense fibers contains at least 10 major proteins and this gene

encodes the main protein. [provided by RefSeq]

UniProtKB/Swiss-Prot: ODFP1_HUMAN, Q14990

Function: Component of the outer dense fibers (ODF) of spermatozoa. ODF are filamentous structures

located on the outside of the axoneme in the midpiece and principal piece of the mammalian sperm

tail and may help to maintain the passive elastic structures and elastic recoil of the sperm tail

Gene Wiki entry for ODF1

(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)
About This Section

Genomic View:

UCSC Golden Path with GeneCards custom track

Transcription factor binding sites upstream to the ODF1 gene

Entrez Gene cytogenetic band: 8q22.3 Ensembl cytogenetic band: 8q22.3 HGNC cytogenetic band: 8q22

ODF1 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 8 GeneLoc Exon Structure

GeneLoc location for GC08P103633: (about GC identifiers)

Start:	103,633,036 bp from pter
End:	103,642,422 bp from pter
Size:	9,387 bases
Orientation:	plus strand

RefSeq DNA sequence:

NC_000008.9 NT_008046.15

(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: ODFP1_HUMAN, Q14990 (See protein sequence)

Recommended Name: Outer dense fiber protein 1

Size: 250 amino acids; 28366 Da

Subunit: Interacts with SPAG4 and KLC3 (By similarity)

Secondary accessions: Q3SX72

Post-translational modifications:

View phosphorylation sites using PhosphoSite²

REFSEQ proteins: NP_077721.2

ENSEMBL proteins:

ENSP00000285402

Human Recombinant Proteins

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OriGene Purified Recombinant Human Protein: ODF1

1 Gene Ontology (GO) cellular component term (links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0001520	outer dense fiber	NAS	--

About this table

Antibodies for ODF1:

	Browse Antibodies Central at Invitrogen
	Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
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	Browse R&D Systems for Antibodies
	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 ODF1

Assays for ODF1:

	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)
About This Section

ProtoNet protein and cluster: Q14990

1 Blocks protein family: IPB002068 Heat shock protein Hsp20

UniProtKB/Swiss-Prot: ODFP1_HUMAN, Q14990

Domain: The C-terminal contains many C-X-P repeats

(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 (ODF1)
		Browse for Gene Knock-down Tools from Millipore
		Browse Abnova for Chimera RNAi Products

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_024410

Applied Biosystems Silencer® siRNAs for ODF1

Sigma-Aldrich siRNA for ODF1

Sigma-Aldrich shRNA for ODF1

Explore Sigma-Aldrich super-pooled esiRNAs

Clones:		Browse Clone Ranger at Invitrogen for clones
		Browse Clones for the Expression of Recombinant Proteins Available from Millipore

OriGene GFP tagged cDNA clone in CMV expression vector: NM_024410
Myc/DDK tagged cDNA clone in CMV expression vector: NM_024410
untagged cDNA clone in CMV expression vector: NM_024410

Primers:

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

OriGene genome-wide validated SYBR primer pairs: NM_024410

UniProtKB/Swiss-Prot: ODFP1_HUMAN, Q14990

Function: Component of the outer dense fibers (ODF) of spermatozoa. ODF are filamentous structures

located on the outside of the axoneme in the midpiece and principal piece of the mammalian sperm

tail and may help to maintain the passive elastic structures and elastic recoil of the sperm tail

Genatlas biochemistry entry for ODF1:

outer dense fiber protein 1,component of the filamentous structures of the sperm tail

1 Gene Ontology (GO) molecular function term (links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005198	structural molecule activity	NAS	--

About this table

(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.)
About This Section

Gene Network Central^TM Interacting Genes and Proteins Network for ODF1

5/15 Interacting proteins for ODF1 (ENSP00000285402³) via UniProtKB, MINT, and/or STRING (see all 15 )

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
SPAG4	ENSP00000363391³	STRING (score=.993)
TRIP6	ENSP00000200457³	STRING (score=.969)
ODF2	ENSP00000361882³	STRING (score=.896)
SPAG5	ENSP00000323300³	STRING (score=.881)
MSH6	ENSP00000234420³	STRING (score=.879)

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3 Gene Ontology (GO) biological process terms (links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0007275	multicellular organismal development	IEA	--
GO:0007283	spermatogenesis	NAS	--
GO:0030154	cell differentiation	IEA	--

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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)
About This Section

Browse drugs & compounds from Enzo Life Sciences

Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for ODF1
1 Novoseek chemical compound relationship for ODF1 gene

Compound	Score	Articles	PubMed IDs for Articles with Shared Sentences (# sentences)
leucine	42.87	5	10373309 (2), 16211599 (1)

About this table

(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 (ODF1)
		Browse for Gene Knock-down Tools from Millipore
		Browse Abnova for Chimera RNAi Products

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_024410

Sigma-Aldrich siRNA for ODF1

Sigma-Aldrich shRNA for ODF1

Explore Sigma-Aldrich super-pooled esiRNAs

Applied Biosystems Silencer® siRNAs:

NM_024410

REFSEQ mRNAs for ODF1 gene:

NM_024410.3

Applied Biosystems TaqMan ® Gene Expression Assays:

NM_024410

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_024410
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_024410
                                 untagged cDNA clone in CMV expression vector: NM_024410

Additional cDNA sequence:

AK315276.1 BC104456.1 BC104457.1

1 DOTS entry:

DT.438515

14 AceView cDNA sequences:

T29842 NM_024410 AW951615 BX093384 AW949852 BU561235 BG214987 AA383076

AW665671 AW268564 AW663738 AI285947 AA383166 BP369982

highest scoring ESTs for ODF1:

AI285947 AW663738 AW665671 AW949852 AW951615 BG214987 BX093384 AA383076 AW268564 NM_024410

Unigene Cluster for ODF1:

Outer dense fiber of sperm tails 1

Hs.159274 [show with all ESTs]

Unigene Representative Sequence: NM_024410

GeneLoc Exon Structure

1 Ensembl transcript including schematic representation:

ENST00000285402

(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 )
About This Section

ODF1 expression in normal and diseased human tissues

Applied Biosystems TaqMan ® Gene Expression Assays for ODF1

¹ / ² / ³

3 probe-sets matching ODF1 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
36375_at²^{, 3}	U95-A	1	1.00	1.00	1.00	1.00	X74614	0.20	1.00	0.72	1
214485_at²^{, 3}	U133-A	1	1.00	1.00	--	--	NM_024410	0.60	1.00	0.82	1
214485_at²	U133Plus2	1	1.00	1.00	--	--	--	--	--	--	--

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Data from

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

CGAP SAGE TAG: GCCCCTGTTG

SOURCE GeneReport for Unigene cluster: Hs.159274
Expression variation in blood from EXPOLDB for ODF1
UniProtKB/Swiss-Prot: ODFP1_HUMAN, Q14990
Tissue specificity: Testis

(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)
About This Section

Orthologs for ODF1 gene from 5 species

Organism	Gene	Locus	Description	Human Similarity	NCBI accessions
dog (Canis familiaris)	ODF1¹	--	outer dense fiber of sperm tails 1	87.42(n) 95.98(a)	475057 XM_532292.2 XP_532292.1
chimpanzee (Pan troglodytes)	ODF1¹	--	outer dense fiber of sperm tails 1	97.87(n) 98(a)	464323 XM_519893.2 XP_519893.1
cow (Bos taurus)	ODF1¹	--	outer dense fiber of sperm tails 1	88.27(n) 96(a)	281366 NM_174131.3 NP_776556.2
rat (Rattus norvegicus)	Odf1¹	--	outer dense fiber of sperm tails 1	85.66(n) 97.67(a)	24610 NM_024126.4 NP_077040.1
mouse (Mus musculus)	Odf1^{1, 5}	15 (9.90 cM)⁵	outer dense fiber of sperm tails 1^{1, 5}	85.11(n)¹ 95.74(a)¹	18285¹ NM_008757.2¹ NP_032783.1¹ BC145758⁵ BX632868⁵ (see all 8)

About this table Species with no ortholog for ODF1

ENSEMBL Gene Tree for ODF1

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

(According to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
About This Section

10/112 NCBI SNPs in ODF1 are shown (see all 112 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay) (see all 97)

AB	SNP ID	Valid	Chr 8 pos	Sequence	Recs	AA Chg	Type	More	Recs	Pop	Total sample	More
AB	Genomic Data				Transcription Data				Allele Frequencies
				--	--	--		--	--			--
	rs892506^1,2	A,C,F,H,O	103631772(+)	`AAGTCG/ACTGTG`	1	--	ng5¹		20	NA EA EU WA	1538
	rs892504^1,2	A,C,F,H,O	103631479(+)	`CAGAAC/AGTCCT`	1	--	ng5¹		7	EU EA WA NA	560
	rs2289033^1,2	A,C,F,H,O	103642505(-)	`CTATTC/GCCATC`	1	--	ng3¹		17	EA NA EU WA	2490
	rs892505^1,2	A,C,F,H	103631715(+)	`TTAAGG/ATGAGT`	1	--	ng5¹		4	EU EA WA	418
	rs3808357^1,2	A,C,F,H	103633083(-)	`CACTCC/AGGGAA`	1	--	ut5¹ ese³		12	EA EU WA NA	2262
	rs2511735^1,2	A,C,F,H	103631057(+)	`ttcacC/Taaatc`	1	--	ng5¹		4	EU EA WA	418
	rs919952^1,2	A,C,F,H	103632560(+)	`GCTGAC/TTTGAG`	1	--	ng5¹		8	EU EA WA	838
	rs892507^1,2	A,C,F,H	103632357(+)	`CATCCG/AGAGGC`	1	--	ng5¹		6	NA EA WA	526
	rs3808359^1,2	A,C,F,H	103632488(-)	`GTCATG/AGCTGT`	1	--	ng5¹		5	EA EU WA	1920
	rs2511736^1,2	A,C,F,H	103632351(+)	`ACAAGG/ACATCC`	1	--	ng5¹		4	EU EA WA	412

About this table

HapMap Linkage Disequilibrium images for ODF1 (up to first 250kb)

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

OMIM: 182878

1 Novoseek disease relationship for ODF1 gene

Disease	Score	Articles	PubMed IDs for Articles with Shared Sentences (# sentences)
infertility male	52.40	1	9621304 (1)

About this table

(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

10/24 PubMed articles for ODF1 gene (see all 24 ):

Sequence, expression, and chromosomal assignment of a human sperm outer dense fiber gene. (PubMed id 8305202)^{1, 2, 3, 4} Gastmann O....Hoyer-Fender S. (1993)
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)
A homozygous deletion of 27 basepairs in the coding region of the human outer dense fiber protein gene does not result in a pathologic phenotype. (PubMed id 8111388)^{3, 4} Hofferbert S....Engel W. (1993)
Spag4, a novel sperm protein, binds outer dense-fiber protein Odf1 and localizes to microtubules of manchette and axoneme. (PubMed id 10373309)^{1, 3} Shao X....van der Hoorn F.A. (1999)
Outer dense fibre proteins from human sperm tail: molecular cloning and expression analyses of two cDNA transcripts encoding proteins of approximately 70 kDa. (PubMed id 10381817)^{1, 3} Petersen C.... Hoyer-Fender S. (1999)
Isolation and partial characterization of the outer dense fiber proteins from human spermatozoa. (PubMed id 1418683)^{1, 3} Henkel R....Miska W. (1992)
Keratins: unraveling the coordinated construction of scaffolds in spermatogenic cells. (PubMed id 11774369)^{1, 3} Kierszenbaum A.L. (2002)
Association of kinesin light chain with outer dense fibers in a microtubule-independent fashion. (PubMed id 12594206)³ Bhullar B....van der Hoorn F.A. (2003)
Novel RING finger protein OIP1 binds to conserved amino acid repeats in sperm tail protein ODF1. (PubMed id 12533418)³ Zarsky H.A....van der Hoorn F.A. (2003)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)³ Strausberg R.L....Marra M.A. (2002)

(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: 4956	HGNC: 8113	AceView: ODF1	Ensembl:ENSG00000155087	euGenes: HUgn4956
ECgene: ODF1	H-InvDB: ODF1

(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 ODF1
(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)
About This Section

Products for ODF1:

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 ODF1-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 ODF1		Browse antibodies at Sigma-Aldrich
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	Lentivirus-delivered shRNAs for ODF1		Browse small molecules at Sigma-Aldrich
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ODF1 Gene

protein-coding GIFtS: 51

Aliases &
Descriptions
for ODF1

Summaries
for ODF1

Genomic Location
for ODF1

Proteins
for ODF1

Protein Domains/
Families
for ODF1

Gene Function
for ODF1

Pathways & Interactions
for ODF1

Drugs & Compounds
for ODF1

Transcripts
for ODF1

Expression
for ODF1

Orthologs
for ODF1

Paralogs
for ODF1

SNPs/Variants
for ODF1

Disorders & Mutations
for ODF1

Medical News
for ODF1

Publications
for ODF1

Search for ODF1

Genome Databases showing ODF1

Other Databases showing ODF1

Specialized Databases showing ODF1

Licensable Technologies
for ODF1

Services
for ODF1

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

ODF1 Gene

protein-coding GIFtS: 51

Aliases & Descriptionsfor ODF1

Summariesfor ODF1

Genomic Locationfor ODF1

Proteinsfor ODF1

Protein Domains/Familiesfor ODF1

Gene Functionfor ODF1

Pathways & Interactionsfor ODF1

Drugs & Compoundsfor ODF1

Transcriptsfor ODF1

Expression for ODF1

Orthologsfor ODF1

Paralogsfor ODF1

SNPs/Variantsfor ODF1

Disorders & Mutationsfor ODF1

Medical Newsfor ODF1

Publicationsfor ODF1

Search for ODF1

Genome Databases showing ODF1

Other Databases showing ODF1

Specialized Databases showing ODF1

Licensable Technologiesfor ODF1

Servicesfor ODF1

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 ODF1

Summaries
for ODF1

Genomic Location
for ODF1

Proteins
for ODF1

Protein Domains/
Families
for ODF1

Gene Function
for ODF1

Pathways & Interactions
for ODF1

Drugs & Compounds
for ODF1

Transcripts
for ODF1

Expression
for ODF1

Orthologs
for ODF1

Paralogs
for ODF1

SNPs/Variants
for ODF1

Disorders & Mutations
for ODF1

Medical News
for ODF1

Publications
for ODF1

Licensable Technologies
for ODF1

Services
for ODF1