Human Gene NBPF7 (uc010oxk.3)
  Description: Homo sapiens neuroblastoma breakpoint family, member 7 (NBPF7), mRNA.
RefSeq Summary (NM_001047980): This gene is a member of the neuroblastoma breakpoint family (NBPF) which consists of dozens of recently duplicated genes primarily located in segmental duplications on human chromosome 1. This gene family has experienced its greatest expansion within the human lineage and has expanded, to a lesser extent, among primates in general. Members of this gene family are characterized by tandemly repeated copies of DUF1220 protein domains. Gene copy number variations in the human chromosomal region 1q21.1, where most DUF1220 domains are located, have been implicated in a number of developmental and neurogenetic diseases such as microcephaly, macrocephaly, autism, schizophrenia, cognitive disability, congenital heart disease, neuroblastoma, and congenital kidney and urinary tract anomalies. Altered expression of some gene family members is associated with several types of cancer. This gene family contains numerous pseudogenes. [provided by RefSeq, Mar 2013]. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments. ##RefSeq-Attributes-START## inferred exon combination :: based on alignments, homology RefSeq Select criteria :: based on longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr1:120,377,388-120,387,503 Size: 10,116 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr1:120,377,388-120,387,158 Size: 9,771 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:120,377,388-120,387,503)mRNA (may differ from genome)Protein (421 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsHGNCHPRD
LynxMalacardsMGIneXtProtOMIMPubMed
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NBPF7_HUMAN
DESCRIPTION: RecName: Full=Putative neuroblastoma breakpoint family member 7;
SUBCELLULAR LOCATION: Cytoplasm (Probable).
MISCELLANEOUS: Encoded by one of the numerous copies of NBPF genes clustered in the p36, p12 and q21 region of the chromosome 1.
SIMILARITY: Belongs to the NBPF family.
SIMILARITY: Contains 2 NBPF domains.
CAUTION: Could be the product of a pseudogene.

-  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): NBPF7
CDC HuGE Published Literature: NBPF7
Positive Disease Associations: Magnesium
Related Studies:
  1. Magnesium
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: NBPF7
Diseases sorted by gene-association score: neuroblastoma (4)

+  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: 1.74 RPKM in Small Intestine - Terminal Ileum
Total median expression: 2.87 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 -99.90345-0.290 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
IPR010630 - NBPF_dom

Pfam Domains:
PF06758 - Repeat of unknown function (DUF1220)

ModBase Predicted Comparative 3D Structure on P0C2Y1
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
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Cellular Component:
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  BC156110 - Synthetic construct Homo sapiens clone IMAGE:100062373, MGC:190488 neuroblastoma breakpoint family, member 7 (NBPF7) mRNA, encodes complete protein.
BC156966 - Synthetic construct Homo sapiens clone IMAGE:100063610, MGC:190825 neuroblastoma breakpoint family, member 7 (NBPF7) mRNA, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: NBPF7_HUMAN, NM_001047980, NP_001041445, P0C2Y1, uc010oxk.2
UCSC ID: uc010oxk.3
RefSeq Accession: NM_001047980
Protein: P0C2Y1 (aka NBPF7_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001047980.2
exon count: 8CDS single in 3' UTR: no RNA size: 1611
ORF size: 1266CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2163.50frame 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.