Human Gene NBPF20 (uc021owl.2)
  Description: Homo sapiens neuroblastoma breakpoint family, member 14 (NBPF20), mRNA.
RefSeq Summary (NM_015383): 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, May 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.
Transcript (Including UTRs)
   Position: hg19 chr1:148,250,249-148,322,078 Size: 71,830 Total Exon Count: 23 Strand: -
Coding Region
   Position: hg19 chr1:148,251,875-148,318,716 Size: 66,842 Coding Exon Count: 19 

Page IndexSequence and LinksPrimersMalaCardsGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:148,250,249-148,322,078)mRNA (may differ from genome)Protein (757 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMalacardsMGIOMIM
PubMedUniProtKBBioGrid 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


-  MalaCards Disease Associations
  MalaCards Gene Search: NBPF20
Diseases sorted by gene-association score: neuroblastoma (6)

+  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: 2.52 RPKM in Brain - Cerebellum
Total median expression: 23.40 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 -226.14673-0.336 Picture PostScript Text
3' UTR -538.631626-0.331 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 Q8IX72
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
  AK125792 - Homo sapiens cDNA FLJ43804 fis, clone TESTI4000970.
CR936830 - Homo sapiens mRNA; cDNA DKFZp686H059 (from clone DKFZp686H059).
AK294944 - Homo sapiens cDNA FLJ60520 complete cds, weakly similar to Homo sapiens phosphodiesterase 4D interacting protein, transcript variant 1, mRNA.
AF379632 - Homo sapiens AG4 mRNA, partial cds.
AF419616 - Homo sapiens clone DKFZp564A057 AG02 mRNA, partial cds.
BC027348 - Homo sapiens neuroblastoma breakpoint family, member 9, mRNA (cDNA clone IMAGE:4387990).
AK095459 - Homo sapiens cDNA FLJ38140 fis, clone D9OST2002608.
JD248885 - Sequence 229909 from Patent EP1572962.
JD093596 - Sequence 74620 from Patent EP1572962.
JD345383 - Sequence 326407 from Patent EP1572962.
JD241596 - Sequence 222620 from Patent EP1572962.
JD050936 - Sequence 31960 from Patent EP1572962.
AF379626 - Homo sapiens AC3 mRNA, partial cds.
JD418896 - Sequence 399920 from Patent EP1572962.
JD161978 - Sequence 143002 from Patent EP1572962.
JD052833 - Sequence 33857 from Patent EP1572962.
JD036628 - Sequence 17652 from Patent EP1572962.
AK295639 - Homo sapiens cDNA FLJ61634 complete cds.
JD248850 - Sequence 229874 from Patent EP1572962.
JD436117 - Sequence 417141 from Patent EP1572962.
JD062423 - Sequence 43447 from Patent EP1572962.
AK299612 - Homo sapiens cDNA FLJ56850 complete cds.
JD055884 - Sequence 36908 from Patent EP1572962.
JD055883 - Sequence 36907 from Patent EP1572962.
DQ601814 - Homo sapiens piRNA piR-39880, complete sequence.
JD557792 - Sequence 538816 from Patent EP1572962.
AY894562 - Homo sapiens clone IVg7 NBPF8 isoform 1 mRNA, complete cds, alternatively spliced.
AY894565 - Homo sapiens clone IIIa12 NBPF9 isoform 1 mRNA, complete cds, alternatively spliced.
AY894570 - Homo sapiens clone IIb7 NBPF8 isoform 4 mRNA, complete cds, alternatively spliced.
AY894572 - Homo sapiens clone Ih2 NBPF8 isoform 6 mRNA, complete cds, alternatively spliced.
AY894567 - Homo sapiens clone Ia4 NBPF8 isoform 2 mRNA, complete cds, alternatively spliced.
AY894568 - Homo sapiens clone Ia9 NBPF8 isoform 2 mRNA, complete cds, alternatively spliced.
AF380580 - Homo sapiens AG1 mRNA, partial cds.
BC148331 - Synthetic construct Homo sapiens clone IMAGE:100015301, MGC:182975 neuroblastoma breakpoint family, member 10 (NBPF10) mRNA, encodes complete protein.
AB527190 - Synthetic construct DNA, clone: pF1KA1693, Homo sapiens NBPF9 gene for neuroblastoma breakpoint family, member 9, without stop codon, in Flexi system.
AF379635 - Homo sapiens AG10 pseudogene mRNA, partial sequence.
AF379619 - Homo sapiens AB13 precursor RNA, partial cds.
AF379620 - Homo sapiens AB14 precursor RNA, partial cds.
AF420437 - Homo sapiens AB14 precursor RNA, partial cds.
AF380582 - Homo sapiens AG8 mRNA, partial cds.
JD040586 - Sequence 21610 from Patent EP1572962.
JD372774 - Sequence 353798 from Patent EP1572962.
JD372775 - Sequence 353799 from Patent EP1572962.
JD119189 - Sequence 100213 from Patent EP1572962.
JD021612 - Sequence 2636 from Patent EP1572962.
JD032812 - Sequence 13836 from Patent EP1572962.
DQ578516 - Homo sapiens piRNA piR-46628, complete sequence.
JD148192 - Sequence 129216 from Patent EP1572962.
JD372774 - Sequence 353798 from Patent EP1572962.
JD108450 - Sequence 89474 from Patent EP1572962.
JD119189 - Sequence 100213 from Patent EP1572962.
AF379633 - Homo sapiens AG6 mRNA, partial cds.
AF379636 - Homo sapiens AG11 mRNA, partial cds.
AF161426 - Homo sapiens HSPC308 mRNA, partial cds.
DQ786323 - Homo sapiens clone HLS_IMAGE_843276 mRNA sequence.
BC021111 - Homo sapiens neuroblastoma breakpoint family, member 10, mRNA (cDNA clone IMAGE:5090304).
AK000726 - Homo sapiens cDNA FLJ20719 fis, clone HEP17004.
BC063799 - Homo sapiens neuroblastoma breakpoint family, member 10, mRNA (cDNA clone IMAGE:6526820), partial cds.
AF379632 - Homo sapiens AG4 mRNA, partial cds.
AF379620 - Homo sapiens AB14 precursor RNA, partial cds.
AF379619 - Homo sapiens AB13 precursor RNA, partial cds.
AF420437 - Homo sapiens AB14 precursor RNA, partial cds.
AF380581 - Homo sapiens AG3 mRNA, partial cds.
AF380582 - Homo sapiens AG8 mRNA, partial cds.
DQ786323 - Homo sapiens clone HLS_IMAGE_843276 mRNA sequence.
JD040586 - Sequence 21610 from Patent EP1572962.
JD077036 - Sequence 58060 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: AF419616, NBPF14, NM_015383, NP_056198, Q8IX72, Q8IX72_HUMAN, uc021owl.1
UCSC ID: uc021owl.2
RefSeq Accession: NM_015383
Protein: Q8IX72

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AF419616.1
exon count: 23CDS single in 3' UTR: no RNA size: 4444
ORF size: 2274CDS single in intron: no Alignment % ID: 99.50
txCdsPredict score: 3738.50frame shift in genome: no % Coverage: 99.57
has start codon: yes stop codon in genome: no # of Alignments: 2
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.