Human Gene ODF3 (ENST00000325113.8) Description and Page Index
  Description: Homo sapiens outer dense fiber of sperm tails 3 (ODF3), transcript variant 1, mRNA. (from RefSeq NM_053280)
RefSeq Summary (NM_053280): ODF3 is a component of sperm flagella outer dense fibers, which add stiffness, elastic recoil, and protection against shearing forces during sperm movement.[supplied by OMIM, Apr 2004].
Gencode Transcript: ENST00000325113.8
Gencode Gene: ENSG00000177947.13
Transcript (Including UTRs)
   Position: hg38 chr11:196,738-200,258 Size: 3,521 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg38 chr11:197,305-200,033 Size: 2,729 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsCTDRNA-Seq ExpressionRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:196,738-200,258)mRNA (may differ from genome)Protein (254 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
HGNCHPRDLynxMGIneXtProtOMIM
PubMedStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: ODF3A_HUMAN
DESCRIPTION: RecName: Full=Outer dense fiber protein 3; AltName: Full=Outer dense fiber of sperm tails protein 3; AltName: Full=Sperm tail protein SHIPPO 1; AltName: Full=Transcript induced in spermiogenesis protein 50;
FUNCTION: Outer dense fibers are filamentous structures located on the outside of the axoneme in the midpiece and principal piece of the mammalian sperm tail. May help to maintain the passive elastic structures and elastic recoil of the sperm tail.
SUBCELLULAR LOCATION: Cytoplasm (By similarity). Note=Expressed in the cytoplasmic lobe of spermatids (By similarity).
TISSUE SPECIFICITY: Testis-specific.
MISCELLANEOUS: 'Shippo' is a Japanese word for tail.
SIMILARITY: Belongs to the ODF3 family.
SIMILARITY: Contains 2 STPGR (Sperm-tail PG-rich) repeats.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 9.31 RPKM in Testis
Total median expression: 9.52 RPKM



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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -112.90317-0.356 Picture PostScript Text
3' UTR -66.67225-0.296 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
  InterPro Domains: Graphical view of domain structure
IPR010736 - SHIPPO-rpt

Pfam Domains:
PF07004 - Sperm-tail PG-rich repeat

ModBase Predicted Comparative 3D Structure on Q96PU9
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-  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
Genome BrowserGenome BrowserNo orthologGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsemblEnsembl  
Protein SequenceProtein Sequence Protein Sequence  
AlignmentAlignment Alignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0007275 multicellular organism development
GO:0007283 spermatogenesis
GO:0030154 cell differentiation

Cellular Component:
GO:0001520 outer dense fiber
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  AB067774 - Homo sapiens mRNA for h-SHIPPO 1, complete cds.
AY713299 - Homo sapiens TISP50 (TISP50) mRNA, complete cds.
JD469083 - Sequence 450107 from Patent EP1572962.
AL133658 - Homo sapiens mRNA; cDNA DKFZp434A0527 (from clone DKFZp434A0527).
JD045008 - Sequence 26032 from Patent EP1572962.
BC126222 - Homo sapiens outer dense fiber of sperm tails 3, mRNA (cDNA clone MGC:161500 IMAGE:8991938), complete cds.
BC126248 - Homo sapiens outer dense fiber of sperm tails 3, mRNA (cDNA clone MGC:161526 IMAGE:8991964), complete cds.
BC144022 - Homo sapiens outer dense fiber of sperm tails 3, mRNA (cDNA clone MGC:177559 IMAGE:9052542), complete cds.
HQ258128 - Synthetic construct Homo sapiens clone IMAGE:100072437 outer dense fiber of sperm tails 3 (ODF3) gene, encodes complete protein.
KJ895257 - Synthetic construct Homo sapiens clone ccsbBroadEn_04651 ODF3 gene, encodes complete protein.
FJ436414 - Homo sapiens outer dense fiber 3 (ODF3) mRNA, complete cds, alternatively spliced.
JD416133 - Sequence 397157 from Patent EP1572962.
JD338186 - Sequence 319210 from Patent EP1572962.
JD494386 - Sequence 475410 from Patent EP1572962.
JD287278 - Sequence 268302 from Patent EP1572962.
JD072459 - Sequence 53483 from Patent EP1572962.
JD466416 - Sequence 447440 from Patent EP1572962.
JD425647 - Sequence 406671 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_053280, ODF3A_HUMAN, Q69YX0, Q96PU9, SHIPPO1, TISP50, uc001lob.1, uc001lob.2, uc001lob.3, uc001lob.4
UCSC ID: uc001lob.4
RefSeq Accession: NM_053280
Protein: Q96PU9 (aka ODF3A_HUMAN)
CCDS: CCDS7688.1

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