ODF3 Gene
protein-coding GIFtS: 43
GCID: GC11P000196
|
|
outer dense fiber of sperm tails 3
| |
Aliases
for ODF3 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| Outer Dense Fiber Of Sperm Tails 31 2 | | Transcript Induced In Spermiogenesis Protein 502 3 | | SHIPPO11 2 3 5 | | TISP502 3 | | CT1351 2 | | Cancer/Testis Antigen 1352 | | HSHIPPO1 | | Outer Dense Fiber Protein 32 | | Outer Dense Fiber Of Sperm Tails Protein 32 3 | | Sperm Tail Protein SHIPPO12 | | Sperm Tail Protein SHIPPO 12 3 | | |
Export aliases for ODF3 gene to outside databasesPrevious GC identifers: GC11M000109 GC11M000998 GC11P000186 GC11P000016 |
Summaries
for ODF3 gene(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 ODF3:
ODF3 is a component of sperm flagella outer dense fibers, which add stiffness, elastic recoil, and protection againstshearing forces during sperm movement.(supplied by OMIM, Apr 2004)
UniProtKB/Swiss-Prot: ODF3A_HUMAN, Q96PU9Function: Outer dense fibers are filamentous structures located on the outside of the axoneme in the midpiece andprincipal piece of the mammalian sperm tail. May help to maintain the passive elastic structures and elastic recoil ofthe sperm tail
|
Genomic Views
for ODF3 gene
(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_000011.9 NC_018922.1 NT_009237.18
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the ODF3 gene promoter:
Elk-1 NF-1 NF-1/L p53 Nkx2-5 Tal-1beta E47 Roaz Pax-4a MRF-2
Other transcription factors
Search SABiosciences Chromatin IP Primers for ODF3
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ODF3 |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 11p15.5 Ensembl cytogenetic band: 11p15.5 HGNC cytogenetic band: 11p15.5ODF3 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome 11 GeneLoc Exon Structure GeneLoc location for GC11P000196: view genomic region
(about GC identifiers)
Start:
|
196,738 bp from pter |
End:
|
200,261 bp from pter |
Size:
|
3,524 bases |
Orientation:
|
plus strand |
|
Proteins
for ODF3 gene
(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: ODF3A_HUMAN, Q96PU9 (See
protein sequence)Recommended Name: Outer dense fiber protein 3 Size: 254 amino acids; 27710 Da
Subcellular location: Cytoplasm (By similarity). Note=Expressed in the cytoplasmic lobe of spermatids (By similarity)
Miscellaneous: 'Shippo' is a Japanese word for tail
Secondary accessions: Q69YX0Alternative splicing: 2 isoforms: Q96PU9-1 Q96PU9-2 (No experimental confirmation available)Explore the universe of human proteins at neXtProt for ODF3: NX_Q96PU9
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q96PU9
ODF3 Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins: NP_444510.2
ENSEMBL proteins: ENSP00000325868 ENSP00000436588 ENSP00000339623
Human Recombinant Protein Products:
Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view): About this table
ODF3 for ontologies About GeneDecksing
ODF3 Antibody Products:
Assay Products for ODF3: |
Protein
Domains /
Families
for ODF3 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
ODF3 for domains About GeneDecksing
1 InterPro domain/family:Graphical View of Domain Structure for InterPro Entry Q96PU9ProtoNet protein and cluster: Q96PU9 UniProtKB/Swiss-Prot: ODF3A_HUMAN, Q96PU9Similarity: Belongs to the ODF3 familySimilarity: Contains 2 STPGR (Sperm-tail PG-rich) repeats |
Function
for ODF3 gene
(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: ODF3A_HUMAN, Q96PU9Function: Outer dense fibers are filamentous structures located on the outside of the axoneme in the midpiece andprincipal piece of the mammalian sperm tail. May help to maintain the passive elastic structures and elastic recoil ofthe sperm tail
Clone
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OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for ODF3
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
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In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ODF3 |
|
Pathways & Interactions
for ODF3 gene
(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 CentralTM Interacting Genes and Proteins Networks for ODF3
Gene Ontology (GO): 3 biological process terms (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0007275 | multicellular organismal development |
IEA | -- | | GO:0007283 | spermatogenesis |
IEA | -- | | GO:0030154 | cell differentiation |
IEA | -- |
ODF3 for ontologies About GeneDecksing
|
Drugs & Compounds
for ODF3 gene(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 Tocris compounds for ODF3
Search CenterWatch for drugs/clinical trials and news about ODF3 / ODF3A
|
Transcripts
for ODF3 gene(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 ODF3 gene: NM_053280.3 Unigene Cluster for ODF3: Outer dense fiber of sperm tails 3 Hs.350949 [show with all ESTs]Unigene Representative Sequence: AL1336584 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000325113(uc001lob.3 uc010qvk.2) ENST00000531679(uc001loc.3)
ENST00000525282 ENST00000342593
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for ODF3 (see all 3)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for ODF3
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript: all cDNA clones in your preferred vector: ODF3 (NM_053280) | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for ODF3 | | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat ODF3 |
Additional cDNA sequence: AB067774.1 AL133658.1 AY713299.1 BC126222.1 BC126248.1 BC144022.1 FJ436414.1 1 DOTS entry: DT.40127582 6 AceView cDNA sequences: NM_053280 BX093806 AL133658 AB067774 AI126587 AA977621
GeneLoc Exon Structure
|
Expression
for ODF3 gene
(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
| ODF3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: GCTGCCCGTG
About this image
See ODF3 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for ODF3
SOURCE GeneReport for Unigene cluster: Hs.350949
UniProtKB/Swiss-Prot: ODF3A_HUMAN, Q96PU9Tissue specificity: Testis-specific
SABiosciences Custom PCR Arrays for ODF3
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for ODF3
Browse OriGene validated miRNA SYBR primer pairs
| | | SABiosciences RT2 qPCR Primer Assay in human, mouse, rat ODF3 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat ODF3 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat ODF3 | In Situ
Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ODF3 |
Orthologs
for ODF3 gene
(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 ODF3 gene from 4/20 species (see all 20) About this table
| Organism |
Taxonomic
classification |
Gene |
Description |
Human
Similarity |
Orthology
Type |
Details |
lizard
(Anolis carolinensis) |
Reptilia |
ODF36 |
-- |
51(a) |
1 ↔ 1 |
1(77247622-77254130) |
African clawed frog
(Xenopus laevis) |
Amphibia |
MGC526792 |
hypothetical protein MGC52679 |
73.51(n) |
|
BC041210.1 |
zebrafish
(Danio rerio) |
Actinopterygii |
odf3b1 |
outer dense fiber of sperm tails 3B |
56.57(n)
52.59(a) |
|
335524 NM_199958.1 NP_956252.1 |
fruit fly
(Drosophila melanogaster) |
Insecta |
CG80866CG102526 |
-- |
4(a)30(a) |
possible orthologpossible ortholog |
2L(8244160-8257502) 3R(19520936-19522000) |
ENSEMBL Gene Tree for ODF3 (if available)
TreeFam Gene Tree for ODF3 (if available) |
Paralogs
for ODF3 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for ODF3 gene
- ODF3B2 ODF3L22 ODF3L12
3 SIMAP similar genes for ODF3 using alignment to 4 protein entries: ODF3A_HUMAN (see all proteins):ODF3B ODF3L1 ODF3L2
ODF3 for paralogs About GeneDecksing
|
Genomic Variants
for ODF3 gene(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
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr 11 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for ODF3 (196738 - 200261 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 1 variation for ODF3
1 CNV: 71209 | SABiosciences Cancer Mutation PCR Assays |
|
Disorders
/ Diseases
for ODF3 gene
(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
|
ODF3 for disorders About GeneDecksing
OMIM gene information: 608356
OMIM disorders: --
3  diseases for ODF3: About MalaCardsuterine fibroid salpingitis acne
Export disorders for ODF3 gene to outside databases
|
Publications
for ODF3 gene (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 ODF3 gene integrated from 9 sources:
(articles sorted by number of sources associating them with ODF3) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- Molecular cloning and characterization of a complementary DNA encoding sperm tail protein SHIPPO 1. (PubMed id 11870087)1, 2, 3, 9 Egydio de Carvalho C....Nishimune Y. (2002)
- Expression of splice variants of cancer-testis genes ODF3 and ODF4 in the testis of a prostate cancer patient. (PubMed id 23096689)1 Ghafouri-Fard S. and Modarressi M.H. (2012)
- A genome-wide association study identifies three loci associated with susceptibility to uterine fibroids. (PubMed id 21460842)1 Cha P.C....Nakamura Y. (2011)
- The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (2007)
- 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)
|
External Searches for ODF3 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing ODF3 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing ODF3 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing ODF3 gene(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 ODF3 | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for ODF3 gene:
Search GeneIP for patents involving ODF3
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for ODF3 gene(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
|
 | |
 | |
 |
| | |  | Browse OriGene Antibodies | | OriGene shRNA RFP for ODF3 | | | OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for ODF3 | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for ODF3 | | | OriGene Protein Over-expression Lysate for ODF3 | | Browse OriGene Fluorogenic Cell Assay Kits | | | OriGene siRNA for ODF3 | | Browse 3'-UTR reporter clones for miRNA target validation | | | OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for ODF3 | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for ODF3 | | | Browse OriGene GFP tagged cDNA clones in CMV expression vector | | Browse OriGene MicroRNA Expression Plasmids | | | Browse OriGene basic RS shRNAs | | Browse OriGene validated miRNA SYBR primer pairs | | | OriGene Purified Protein for ODF3 | | OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
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| | | QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat ODF3 | | | Search QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing ODF3 | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ODF3 | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat ODF3 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat ODF3 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat ODF3 |
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| |  |  |  |  | | | | |
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 |
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 | | | ODF3 Proteins, Antibodies, CLIAs, and ELISAs |
| | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ODF3 |
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| | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat ODF3 |
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