Human Gene NEO1 (uc002avn.4)
  Description: Homo sapiens neogenin 1 (NEO1), transcript variant 3, mRNA.
RefSeq Summary (NM_002499): This gene encodes a cell surface protein that is a member of the immunoglobulin superfamily. The encoded protein consists of four N-terminal immunoglobulin-like domains, six fibronectin type III domains, a transmembrane domain and a C-terminal internal domain that shares homology with the tumor suppressor candidate gene DCC. This protein may be involved in cell growth and differentiation and in cell-cell adhesion. Defects in this gene are associated with cell proliferation in certain cancers. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2010].
Transcript (Including UTRs)
   Position: hg19 chr15:73,344,825-73,597,547 Size: 252,723 Total Exon Count: 28 Strand: +
Coding Region
   Position: hg19 chr15:73,345,017-73,595,037 Size: 250,021 Coding Exon Count: 28 

Page IndexSequence and LinksPrimersGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:73,344,825-73,597,547)mRNA (may differ from genome)Protein (1454 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCLynxMGIOMIMPubMed
TreefamUniProtKBWikipediaBioGrid CRISPR DB

-  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): NEO1
CDC HuGE Published Literature: NEO1
Positive Disease Associations: Body Fat Distribution
Related Studies:
  1. Body Fat Distribution
    , , . [PubMed 0]

-  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: 20.89 RPKM in Colon - Transverse
Total median expression: 463.97 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 -107.10192-0.558 Picture PostScript Text
3' UTR -832.532510-0.332 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
IPR003961 - Fibronectin_type3
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR013098 - Ig_I-set
IPR003599 - Ig_sub
IPR003598 - Ig_sub2
IPR010560 - Neogenin_C

Pfam Domains:
PF00041 - Fibronectin type III domain
PF00047 - Immunoglobulin domain
PF06583 - Neogenin C-terminus
PF07679 - Immunoglobulin I-set domain
PF13895 - Immunoglobulin domain
PF13927 - Immunoglobulin domain

SCOP Domains:
48726 - Immunoglobulin
49265 - Fibronectin type III

ModBase Predicted Comparative 3D Structure on B7ZKN0
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 orthologGenome BrowserNo orthologGenome BrowserNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGD FlyBase  
 Protein Sequence Protein Sequence  
 Alignment Alignment  

-  Descriptions from all associated GenBank mRNAs
  LF208525 - JP 2014500723-A/16028: Polycomb-Associated Non-Coding RNAs.
LF213955 - JP 2014500723-A/21458: Polycomb-Associated Non-Coding RNAs.
U61262 - Human neogenin mRNA, complete cds.
U72391 - Human neogenin mRNA, complete cds.
BC117161 - Homo sapiens neogenin homolog 1 (chicken), mRNA (cDNA clone MGC:150770 IMAGE:40125712), complete cds.
BC143270 - Homo sapiens neogenin homolog 1 (chicken), mRNA (cDNA clone MGC:176789 IMAGE:9051772), complete cds.
BC143271 - Homo sapiens neogenin homolog 1 (chicken), mRNA (cDNA clone MGC:176790 IMAGE:9051773), complete cds.
BC143279 - Homo sapiens cDNA clone IMAGE:9051781, containing frame-shift errors.
AB528479 - Synthetic construct DNA, clone: pF1KE1062, Homo sapiens NEO1 gene for neogenin homolog 1, without stop codon, in Flexi system.
MA449532 - JP 2018138019-A/21458: Polycomb-Associated Non-Coding RNAs.
MA444102 - JP 2018138019-A/16028: Polycomb-Associated Non-Coding RNAs.
AB209412 - Homo sapiens mRNA for neogenin homolog 1 variant protein.
JD462599 - Sequence 443623 from Patent EP1572962.
JD125552 - Sequence 106576 from Patent EP1572962.
JD395375 - Sequence 376399 from Patent EP1572962.
JD258905 - Sequence 239929 from Patent EP1572962.
JD408692 - Sequence 389716 from Patent EP1572962.
DQ581077 - Homo sapiens piRNA piR-49189, complete sequence.
LF377316 - JP 2014500723-A/184819: Polycomb-Associated Non-Coding RNAs.
LF377311 - JP 2014500723-A/184814: Polycomb-Associated Non-Coding RNAs.
LF377304 - JP 2014500723-A/184807: Polycomb-Associated Non-Coding RNAs.
MA612893 - JP 2018138019-A/184819: Polycomb-Associated Non-Coding RNAs.
MA612888 - JP 2018138019-A/184814: Polycomb-Associated Non-Coding RNAs.
MA612881 - JP 2018138019-A/184807: Polycomb-Associated Non-Coding RNAs.
LF377298 - JP 2014500723-A/184801: Polycomb-Associated Non-Coding RNAs.
LF377297 - JP 2014500723-A/184800: Polycomb-Associated Non-Coding RNAs.
LF377295 - JP 2014500723-A/184798: Polycomb-Associated Non-Coding RNAs.
LF377292 - JP 2014500723-A/184795: Polycomb-Associated Non-Coding RNAs.
LF377291 - JP 2014500723-A/184794: Polycomb-Associated Non-Coding RNAs.
LF377290 - JP 2014500723-A/184793: Polycomb-Associated Non-Coding RNAs.
LF377288 - JP 2014500723-A/184791: Polycomb-Associated Non-Coding RNAs.
LF377282 - JP 2014500723-A/184785: Polycomb-Associated Non-Coding RNAs.
LF377281 - JP 2014500723-A/184784: Polycomb-Associated Non-Coding RNAs.
LF377280 - JP 2014500723-A/184783: Polycomb-Associated Non-Coding RNAs.
LF377279 - JP 2014500723-A/184782: Polycomb-Associated Non-Coding RNAs.
LF377278 - JP 2014500723-A/184781: Polycomb-Associated Non-Coding RNAs.
LF377275 - JP 2014500723-A/184778: Polycomb-Associated Non-Coding RNAs.
JD440268 - Sequence 421292 from Patent EP1572962.
JD190209 - Sequence 171233 from Patent EP1572962.
LF377268 - JP 2014500723-A/184771: Polycomb-Associated Non-Coding RNAs.
JD253692 - Sequence 234716 from Patent EP1572962.
JD163821 - Sequence 144845 from Patent EP1572962.
LF377267 - JP 2014500723-A/184770: Polycomb-Associated Non-Coding RNAs.
JD440693 - Sequence 421717 from Patent EP1572962.
LF377266 - JP 2014500723-A/184769: Polycomb-Associated Non-Coding RNAs.
JD250753 - Sequence 231777 from Patent EP1572962.
AL355708 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 44260.
AL390182 - Homo sapiens mRNA; cDNA DKFZp547A066 (from clone DKFZp547A066).
AL359597 - Homo sapiens mRNA; cDNA DKFZp547B146 (from clone DKFZp547B146).
LF377265 - JP 2014500723-A/184768: Polycomb-Associated Non-Coding RNAs.
DQ578639 - Homo sapiens piRNA piR-46751, complete sequence.
MA612875 - JP 2018138019-A/184801: Polycomb-Associated Non-Coding RNAs.
MA612874 - JP 2018138019-A/184800: Polycomb-Associated Non-Coding RNAs.
MA612872 - JP 2018138019-A/184798: Polycomb-Associated Non-Coding RNAs.
MA612869 - JP 2018138019-A/184795: Polycomb-Associated Non-Coding RNAs.
MA612868 - JP 2018138019-A/184794: Polycomb-Associated Non-Coding RNAs.
MA612867 - JP 2018138019-A/184793: Polycomb-Associated Non-Coding RNAs.
MA612865 - JP 2018138019-A/184791: Polycomb-Associated Non-Coding RNAs.
MA612859 - JP 2018138019-A/184785: Polycomb-Associated Non-Coding RNAs.
MA612858 - JP 2018138019-A/184784: Polycomb-Associated Non-Coding RNAs.
MA612857 - JP 2018138019-A/184783: Polycomb-Associated Non-Coding RNAs.
MA612856 - JP 2018138019-A/184782: Polycomb-Associated Non-Coding RNAs.
MA612855 - JP 2018138019-A/184781: Polycomb-Associated Non-Coding RNAs.
MA612852 - JP 2018138019-A/184778: Polycomb-Associated Non-Coding RNAs.
MA612845 - JP 2018138019-A/184771: Polycomb-Associated Non-Coding RNAs.
MA612844 - JP 2018138019-A/184770: Polycomb-Associated Non-Coding RNAs.
MA612843 - JP 2018138019-A/184769: Polycomb-Associated Non-Coding RNAs.
MA612842 - JP 2018138019-A/184768: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04514 - Cell adhesion molecules (CAMs)

-  Other Names for This Gene
  Alternate Gene Symbols: AB528479, B7ZKN0, B7ZKN0_HUMAN, NM_002499, NP_001166095
UCSC ID: uc002avn.4
RefSeq Accession: NM_002499
Protein: B7ZKN0 CCDS: CCDS10247.1, CCDS58378.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AB528479.1
exon count: 28CDS single in 3' UTR: no RNA size: 4379
ORF size: 4365CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 8930.00frame shift in genome: no % Coverage: 99.61
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.