Human Gene ODF2 (uc004bvc.3) Description and Page Index
  Description: Homo sapiens outer dense fiber of sperm tails 2 (ODF2), transcript variant 1, mRNA.
RefSeq Summary (NM_153435): 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. This gene encodes one of the major outer dense fiber proteins. Alternative splicing results in multiple transcript variants. The longer transcripts, also known as 'Cenexins', encode proteins with a C-terminal extension that are differentially targeted to somatic centrioles and thought to be crucial for the formation of microtubule organizing centers. [provided by RefSeq, Oct 2010].
Transcript (Including UTRs)
   Position: hg19 chr9:131,218,285-131,263,571 Size: 45,287 Total Exon Count: 21 Strand: +
Coding Region
   Position: hg19 chr9:131,218,371-131,262,534 Size: 44,164 Coding Exon Count: 21 

Page IndexSequence and LinksGenetic AssociationsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsPathways
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:131,218,285-131,263,571)mRNA (may differ from genome)Protein (893 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMGIOMIMPubMed
ReactomeStanford SOURCETreefamUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ODF2
CDC HuGE Published Literature: ODF2

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 175.84 RPKM in Testis
Total median expression: 604.91 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -36.8086-0.428 Picture PostScript Text
3' UTR -291.951037-0.282 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  ModBase Predicted Comparative 3D Structure on Q5BJF6-3
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  AK301842 - Homo sapiens cDNA FLJ56168 complete cds, highly similar to Homo sapiens outer dense fiber of sperm tails 2 (ODF2), transcript variant 2, mRNA.
AK093367 - Homo sapiens cDNA FLJ36048 fis, clone TESTI2017954, highly similar to Homo sapiens outer dense fiber of sperm tails 2 (ODF2), transcript variant 2, mRNA.
AK301754 - Homo sapiens cDNA FLJ56166 complete cds, highly similar to Homo sapiens outer dense fiber of sperm tails 2 (ODF2), transcript variant 2, mRNA.
AY366499 - Homo sapiens outer dense fiber of sperm tails 2 (ODF2) mRNA, complete cds; alternatively spliced.
AK302684 - Homo sapiens cDNA FLJ55346 complete cds, highly similar to Homo sapiens outer dense fiber of sperm tails 2 (ODF2), transcript variant 1, mRNA.
HM005674 - Homo sapiens clone HTL-T-51e testis tissue sperm-binding protein Li 51e mRNA, complete cds.
AK300793 - Homo sapiens cDNA FLJ59435 complete cds, highly similar to Homo sapiens outer dense fiber of sperm tails 2 (ODF2), transcript variant 2, mRNA.
AK295662 - Homo sapiens cDNA FLJ59899 complete cds, moderately similar to Homo sapiens outer dense fiber of sperm tails 2 (ODF2), transcript variant 1, mRNA.
AK309917 - Homo sapiens cDNA, FLJ99958.
AK299303 - Homo sapiens cDNA FLJ55042 complete cds, highly similar to Homo sapiens outer dense fiber of sperm tails 2 (ODF2), transcript variant 1, mRNA.
BC010629 - Homo sapiens outer dense fiber of sperm tails 2, mRNA (cDNA clone MGC:9034 IMAGE:3874501), complete cds.
AK301855 - Homo sapiens cDNA FLJ56030 complete cds, highly similar to Homo sapiens outer dense fiber of sperm tails 2 (ODF2), transcript variant 2, mRNA.
AK308278 - Homo sapiens cDNA, FLJ98226.
BC091500 - Homo sapiens outer dense fiber of sperm tails 2, mRNA (cDNA clone MGC:111096 IMAGE:30378678), complete cds.
AF012549 - Homo sapiens outer dense fiber protein 2 (odf2) mRNA, complete cds.
AY319414 - Homo sapiens outer dense fiber of sperm tails 2 isoform 3 (ODF2) mRNA, complete cds.
EU832188 - Synthetic construct Homo sapiens clone HAIB:100067217; DKFZo004A0826 outer dense fiber of sperm tails 2 protein (ODF2) gene, encodes complete protein.
AF053970 - Homo sapiens outer dense fiber protein 2/2 mRNA, complete cds.
EU832198 - Synthetic construct Homo sapiens clone HAIB:100067227; DKFZo004B0626 outer dense fiber of sperm tails 2 protein (ODF2) gene, encodes complete protein.
EU832104 - Synthetic construct Homo sapiens clone HAIB:100067133; DKFZo008B0625 outer dense fiber of sperm tails 2 protein (ODF2) gene, encodes complete protein.
DQ444713 - Homo sapiens cenexin 1 variant 1 mRNA, complete cds, alternatively spliced.
DQ444714 - Homo sapiens cenexin 1 mRNA, complete cds.
CU679765 - Synthetic construct Homo sapiens gateway clone IMAGE:100020068 5' read ODF2 mRNA.
KJ901614 - Synthetic construct Homo sapiens clone ccsbBroadEn_11008 ODF2 gene, encodes complete protein.
LF205619 - JP 2014500723-A/13122: Polycomb-Associated Non-Coding RNAs.
DQ578249 - Homo sapiens piRNA piR-46361, complete sequence.
LF346582 - JP 2014500723-A/154085: Polycomb-Associated Non-Coding RNAs.
LF346583 - JP 2014500723-A/154086: Polycomb-Associated Non-Coding RNAs.
LF346585 - JP 2014500723-A/154088: Polycomb-Associated Non-Coding RNAs.
LF346586 - JP 2014500723-A/154089: Polycomb-Associated Non-Coding RNAs.
AK126816 - Homo sapiens cDNA FLJ44866 fis, clone BRALZ2014054.
BC012785 - Homo sapiens outer dense fiber of sperm tails 2, mRNA (cDNA clone IMAGE:3951577), partial cds.
JD140446 - Sequence 121470 from Patent EP1572962.
JD251822 - Sequence 232846 from Patent EP1572962.
JD068219 - Sequence 49243 from Patent EP1572962.
JD068024 - Sequence 49048 from Patent EP1572962.
JD357036 - Sequence 338060 from Patent EP1572962.
JD298534 - Sequence 279558 from Patent EP1572962.
JD049865 - Sequence 30889 from Patent EP1572962.
JD279444 - Sequence 260468 from Patent EP1572962.
JD488799 - Sequence 469823 from Patent EP1572962.
JD362884 - Sequence 343908 from Patent EP1572962.
JD348882 - Sequence 329906 from Patent EP1572962.
JD439810 - Sequence 420834 from Patent EP1572962.
MA582159 - JP 2018138019-A/154085: Polycomb-Associated Non-Coding RNAs.
MA582160 - JP 2018138019-A/154086: Polycomb-Associated Non-Coding RNAs.
MA582162 - JP 2018138019-A/154088: Polycomb-Associated Non-Coding RNAs.
MA582163 - JP 2018138019-A/154089: Polycomb-Associated Non-Coding RNAs.
MA441196 - JP 2018138019-A/13122: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q5BJF6 (Reactome details) participates in the following event(s):

R-HSA-380272 Plk1-mediated phosphorylation of Nlp
R-HSA-380283 Recruitment of additional gamma tubulin/ gamma TuRC to the centrosome
R-HSA-380294 Loss of C-Nap-1 from centrosomes
R-HSA-380311 Recruitment of Plk1 to centrosomes
R-HSA-380455 Recruitment of CDK11p58 to the centrosomes
R-HSA-380303 Dissociation of Phospho-Nlp from the centrosome
R-HSA-5626220 C2CD3 binds the mother centriole
R-HSA-380508 Translocation of NuMA to the centrosomes
R-HSA-2574845 AJUBA binds centrosome-associated AURKA
R-HSA-8853405 TPX2 binds AURKA at centrosomes
R-HSA-3000319 BORA binds PLK1 and AURKA
R-HSA-2574840 AJUBA facilitates AURKA autophosphorylation
R-HSA-3000310 AURKA phosphorylates PLK1
R-HSA-5626223 C2CD3 and OFD1 recruit 5 distal appendage proteins to the centriole
R-HSA-5626681 Recruitment of transition zone proteins
R-HSA-5626227 CP110 and CEP97 dissociate from the centriole
R-HSA-380316 Association of NuMA with microtubules
R-HSA-8853419 TPX2 promotes AURKA autophosphorylation
R-HSA-5626228 The distal appendage proteins recruit TTBK2
R-HSA-5638009 CEP164 recruits RAB3IP-carrying Golgi-derived vesicles to the basal body
R-HSA-5626699 MARK4 binds ODF2 in the centriole
R-HSA-5617816 RAB3IP stimulates nucleotide exchange on RAB8A
R-HSA-380259 Loss of Nlp from mitotic centrosomes
R-HSA-380270 Recruitment of mitotic centrosome proteins and complexes
R-HSA-380284 Loss of proteins required for interphase microtubule organization from the centrosome
R-HSA-5620912 Anchoring of the basal body to the plasma membrane
R-HSA-380320 Recruitment of NuMA to mitotic centrosomes
R-HSA-2565942 Regulation of PLK1 Activity at G2/M Transition
R-HSA-8854518 AURKA Activation by TPX2
R-HSA-380287 Centrosome maturation
R-HSA-5617833 Cilium Assembly
R-HSA-68877 Mitotic Prometaphase
R-HSA-69275 G2/M Transition
R-HSA-1852241 Organelle biogenesis and maintenance
R-HSA-68886 M Phase
R-HSA-453274 Mitotic G2-G2/M phases
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-1640170 Cell Cycle

-  Other Names for This Gene
  Alternate Gene Symbols: NM_153435, NP_702913, Q5BJF6-3
UCSC ID: uc004bvc.3
RefSeq Accession: NM_153435
Protein: Q5BJF6-3

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_153435.1
exon count: 21CDS single in 3' UTR: no RNA size: 3805
ORF size: 2682CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5521.00frame shift in genome: no % Coverage: 99.97
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.