Human Gene NBPF6 (ENST00000495380.7) from GENCODE V44
  Description: Homo sapiens NBPF member 6 (NBPF6), transcript variant 2, mRNA. (from RefSeq NM_001143988)
RefSeq Summary (NM_001143988): 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. Alternative splicing of this gene results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Mar 2013]. Sequence Note:. ##RefSeq-Attributes-START## RefSeq Select criteria :: based on computational evidence ##RefSeq-Attributes-END##
Gencode Transcript: ENST00000495380.7
Gencode Gene: ENSG00000186086.19
Transcript (Including UTRs)
   Position: hg38 chr1:108,450,343-108,471,920 Size: 21,578 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg38 chr1:108,450,602-108,470,638 Size: 20,037 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsRNA-Seq Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Methods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:108,450,343-108,471,920)mRNA (may differ from genome)Protein (638 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGencodeGeneCardsHGNC
HPRDMalacardsMGIneXtProtOMIMPubMed
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NBPF6_HUMAN
DESCRIPTION: RecName: Full=Neuroblastoma breakpoint family member 6;
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 3 NBPF domains.
SEQUENCE CAUTION: Sequence=CAH70399.1; Type=Erroneous initiation; Sequence=CAI23469.1; Type=Erroneous initiation;

-  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: NBPF6
Diseases sorted by gene-association score: neuroblastoma (8)

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 1.44 RPKM in Testis
Total median expression: 2.40 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 -40.00157-0.255 Picture PostScript Text
3' UTR -389.201282-0.304 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 Q5VWK0
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

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


-  Descriptions from all associated GenBank mRNAs
  BC125161 - Homo sapiens neuroblastoma breakpoint family, member 6, mRNA (cDNA clone IMAGE:40121080), partial cds.
BC125162 - Homo sapiens neuroblastoma breakpoint family, member 4, mRNA (cDNA clone IMAGE:40121081), partial cds.
JD543749 - Sequence 524773 from Patent EP1572962.
JD080011 - Sequence 61035 from Patent EP1572962.
JD555106 - Sequence 536130 from Patent EP1572962.
JD148176 - Sequence 129200 from Patent EP1572962.
JD305166 - Sequence 286190 from Patent EP1572962.
JD264273 - Sequence 245297 from Patent EP1572962.
JD320342 - Sequence 301366 from Patent EP1572962.
JD515043 - Sequence 496067 from Patent EP1572962.
JD561130 - Sequence 542154 from Patent EP1572962.
JD167765 - Sequence 148789 from Patent EP1572962.
JD087456 - Sequence 68480 from Patent EP1572962.
JD340512 - Sequence 321536 from Patent EP1572962.
JD274276 - Sequence 255300 from Patent EP1572962.
JD550466 - Sequence 531490 from Patent EP1572962.
JD174231 - Sequence 155255 from Patent EP1572962.
JD150166 - Sequence 131190 from Patent EP1572962.
JD411455 - Sequence 392479 from Patent EP1572962.
JD360918 - Sequence 341942 from Patent EP1572962.
JD119190 - Sequence 100214 from Patent EP1572962.
JD118262 - Sequence 99286 from Patent EP1572962.
JD469293 - Sequence 450317 from Patent EP1572962.
JD540246 - Sequence 521270 from Patent EP1572962.
JD230357 - Sequence 211381 from Patent EP1572962.
JD182439 - Sequence 163463 from Patent EP1572962.
JD368277 - Sequence 349301 from Patent EP1572962.
JD132178 - Sequence 113202 from Patent EP1572962.
JD364304 - Sequence 345328 from Patent EP1572962.
JD152758 - Sequence 133782 from Patent EP1572962.
JD361220 - Sequence 342244 from Patent EP1572962.
JD409744 - Sequence 390768 from Patent EP1572962.
JD499920 - Sequence 480944 from Patent EP1572962.
JD508347 - Sequence 489371 from Patent EP1572962.
JD089864 - Sequence 70888 from Patent EP1572962.
JD232199 - Sequence 213223 from Patent EP1572962.
JD171072 - Sequence 152096 from Patent EP1572962.
JD091202 - Sequence 72226 from Patent EP1572962.
JD419251 - Sequence 400275 from Patent EP1572962.
JD260685 - Sequence 241709 from Patent EP1572962.
JD079409 - Sequence 60433 from Patent EP1572962.
JD386268 - Sequence 367292 from Patent EP1572962.
JD142019 - Sequence 123043 from Patent EP1572962.
JD090817 - Sequence 71841 from Patent EP1572962.
JD101661 - Sequence 82685 from Patent EP1572962.
JD044499 - Sequence 25523 from Patent EP1572962.
JD047159 - Sequence 28183 from Patent EP1572962.
JD350520 - Sequence 331544 from Patent EP1572962.
JD501658 - Sequence 482682 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000495380.1, ENST00000495380.2, ENST00000495380.3, ENST00000495380.4, ENST00000495380.5, ENST00000495380.6, NBPF6_HUMAN, NM_001143988, Q5VWK0, uc009weq.1, uc009weq.2, uc009weq.3, uc009weq.4, uc009weq.5
UCSC ID: ENST00000495380.7
RefSeq Accession: NM_001143988
Protein: Q5VWK0 (aka NBPF6_HUMAN)

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