Human Gene NPNT (uc011cff.2)
  Description: Homo sapiens nephronectin (NPNT), transcript variant 4, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr4:106,816,597-106,892,828 Size: 76,232 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr4:106,816,810-106,890,147 Size: 73,338 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:106,816,597-106,892,828)mRNA (may differ from genome)Protein (536 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMalacardsMGIOMIM
PubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: E9PF04_HUMAN
DESCRIPTION: SubName: Full=Nephronectin;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): NPNT
CDC HuGE Published Literature: NPNT
Positive Disease Associations: Blood Pressure Determination , Heart Rate , pulmonary function
Related Studies:
  1. Blood Pressure Determination
    , , . [PubMed 0]
  2. Heart Rate
    , , . [PubMed 0]
  3. pulmonary function
    Hancock ,et al. 2009, Meta-analyses of genome-wide assocation studies identify multiple loci associated with pulmonary function, Nature genetics 2010 42- 1 : 45-52. [PubMed 20010835]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: NPNT
Diseases sorted by gene-association score: fraser syndrome 1 (5)

-  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: 108.58 RPKM in Thyroid
Total median expression: 550.11 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -118.30213-0.555 Picture PostScript Text
3' UTR -731.772681-0.273 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
IPR008985 - ConA-like_lec_gl_sf
IPR000742 - EG-like_dom
IPR001881 - EGF-like_Ca-bd
IPR013032 - EGF-like_CS
IPR000152 - EGF-type_Asp/Asn_hydroxyl_site
IPR018097 - EGF_Ca-bd_CS
IPR000998 - MAM_dom

Pfam Domains:
PF00629 - MAM domain, meprin/A5/mu
PF02363 - Cysteine rich repeat
PF07645 - Calcium-binding EGF domain
PF12662 - Complement Clr-like EGF-like
PF12947 - EGF domain

SCOP Domains:
57196 - EGF/Laminin
57184 - Growth factor receptor domain

ModBase Predicted Comparative 3D Structure on E9PF04
FrontTopSide
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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  LF206343 - JP 2014500723-A/13846: Polycomb-Associated Non-Coding RNAs.
AK295772 - Homo sapiens cDNA FLJ60269 complete cds, highly similar to Homo sapiens nephronectin (NPNT), mRNA.
AK302477 - Homo sapiens cDNA FLJ58816 complete cds, highly similar to Homo sapiens nephronectin (NPNT), mRNA.
AK304279 - Homo sapiens cDNA FLJ59819 complete cds, highly similar to Homo sapiens nephronectin (NPNT), mRNA.
AY358336 - Homo sapiens clone DNA41379 DFLL295 (UNQ295) mRNA, complete cds.
AK304721 - Homo sapiens cDNA FLJ61085 complete cds, highly similar to Homo sapiens nephronectin (NPNT), mRNA.
AK290029 - Homo sapiens cDNA FLJ77480 complete cds, highly similar to Homo sapiens nephronectin (NPNT), mRNA.
AL832465 - Homo sapiens mRNA; cDNA DKFZp313L231 (from clone DKFZp313L231).
BC131587 - Homo sapiens nephronectin, mRNA (cDNA clone IMAGE:40113283).
BC166654 - Synthetic construct Homo sapiens clone IMAGE:100066380, MGC:195517 nephronectin (NPNT) mRNA, encodes complete protein.
MA441920 - JP 2018138019-A/13846: Polycomb-Associated Non-Coding RNAs.
LF211937 - JP 2014500723-A/19440: Polycomb-Associated Non-Coding RNAs.
JD458791 - Sequence 439815 from Patent EP1572962.
JD398275 - Sequence 379299 from Patent EP1572962.
LF212971 - JP 2014500723-A/20474: Polycomb-Associated Non-Coding RNAs.
MA447514 - JP 2018138019-A/19440: Polycomb-Associated Non-Coding RNAs.
MA448548 - JP 2018138019-A/20474: Polycomb-Associated Non-Coding RNAs.
LF353356 - JP 2014500723-A/160859: Polycomb-Associated Non-Coding RNAs.
JD168678 - Sequence 149702 from Patent EP1572962.
JD364823 - Sequence 345847 from Patent EP1572962.
JD042969 - Sequence 23993 from Patent EP1572962.
LF353350 - JP 2014500723-A/160853: Polycomb-Associated Non-Coding RNAs.
LF353349 - JP 2014500723-A/160852: Polycomb-Associated Non-Coding RNAs.
JD308002 - Sequence 289026 from Patent EP1572962.
JD315047 - Sequence 296071 from Patent EP1572962.
JD086910 - Sequence 67934 from Patent EP1572962.
JD164743 - Sequence 145767 from Patent EP1572962.
JD231594 - Sequence 212618 from Patent EP1572962.
JD333888 - Sequence 314912 from Patent EP1572962.
JD357261 - Sequence 338285 from Patent EP1572962.
AK172856 - Homo sapiens cDNA FLJ24017 fis, clone LNG13731.
JD345851 - Sequence 326875 from Patent EP1572962.
JD133689 - Sequence 114713 from Patent EP1572962.
JD509066 - Sequence 490090 from Patent EP1572962.
JD111799 - Sequence 92823 from Patent EP1572962.
JD206622 - Sequence 187646 from Patent EP1572962.
LF353348 - JP 2014500723-A/160851: Polycomb-Associated Non-Coding RNAs.
JD090714 - Sequence 71738 from Patent EP1572962.
JD039477 - Sequence 20501 from Patent EP1572962.
JD332521 - Sequence 313545 from Patent EP1572962.
JD091855 - Sequence 72879 from Patent EP1572962.
JD484319 - Sequence 465343 from Patent EP1572962.
JD087654 - Sequence 68678 from Patent EP1572962.
JD175331 - Sequence 156355 from Patent EP1572962.
JD497460 - Sequence 478484 from Patent EP1572962.
JD315660 - Sequence 296684 from Patent EP1572962.
JD410968 - Sequence 391992 from Patent EP1572962.
JD272351 - Sequence 253375 from Patent EP1572962.
JD244624 - Sequence 225648 from Patent EP1572962.
JD470007 - Sequence 451031 from Patent EP1572962.
JD495234 - Sequence 476258 from Patent EP1572962.
JD560039 - Sequence 541063 from Patent EP1572962.
JD074985 - Sequence 56009 from Patent EP1572962.
LF353347 - JP 2014500723-A/160850: Polycomb-Associated Non-Coding RNAs.
LF353346 - JP 2014500723-A/160849: Polycomb-Associated Non-Coding RNAs.
MA588933 - JP 2018138019-A/160859: Polycomb-Associated Non-Coding RNAs.
MA588927 - JP 2018138019-A/160853: Polycomb-Associated Non-Coding RNAs.
MA588926 - JP 2018138019-A/160852: Polycomb-Associated Non-Coding RNAs.
MA588925 - JP 2018138019-A/160851: Polycomb-Associated Non-Coding RNAs.
MA588924 - JP 2018138019-A/160850: Polycomb-Associated Non-Coding RNAs.
MA588923 - JP 2018138019-A/160849: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: E9PF04, E9PF04_HUMAN, NM_001184692, NP_001171621
UCSC ID: uc011cff.2
RefSeq Accession: NM_001184692
Protein: E9PF04 CCDS: CCDS54787.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001184692.1
exon count: 11CDS single in 3' UTR: no RNA size: 4505
ORF size: 1611CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3416.00frame shift in genome: no % Coverage: 100.00
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.