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NBPF6 NBPF member 6 [ Homo sapiens (human) ]

Gene ID: 653149, updated on 2-Nov-2024

Summary

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Official Symbol
NBPF6provided by HGNC
Official Full Name
NBPF member 6provided by HGNC
Primary source
HGNC:HGNC:31988
See related
Ensembl:ENSG00000186086 MIM:613996; AllianceGenome:HGNC:31988
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
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]
Expression
Biased expression in testis (RPKM 2.4), small intestine (RPKM 0.7) and 2 other tissues See more
Orthologs
all
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Genomic context

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See NBPF6 in Genome Data Viewer
Location:
1p13.3
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (108421491..108471920)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (108454038..108505300)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (108992965..109014542)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene NBPF member 5, pseudogene Neighboring gene SLC25A24 pseudogene 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:108974404-108974956 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:109030913-109031702 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:109045678-109046211 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1134 Neighboring gene ST13, Hsp70 interacting protein pseudogene 21 Neighboring gene RPL7L1 pseudogene 21

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Evolutionary history and genome organization of DUF1220 protein domains. O'Bleness MS, et al. G3 (Bethesda), 2012 Sep. PMID 22973535, Free PMC Article
  2. A novel gene family NBPF: intricate structure generated by gene duplications during primate evolution. Vandepoele K, et al. Mol Biol Evol, 2005 Nov. PMID 16079250
  3. Mammalian APE1 controls miRNA processing and its interactome is linked to cancer RNA metabolism. Antoniali G, et al. Nat Commun, 2017 Oct 6. PMID 28986522, Free PMC Article
  4. A reference map of the human binary protein interactome. Luck K, et al. Nature, 2020 Apr. PMID 32296183, Free PMC Article
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
neuroblastoma breakpoint family member 6

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001143987.2 → NP_001137459.1  neuroblastoma breakpoint family member 6 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL390038, AL392088
    UniProtKB/TrEMBL
    A0A087WVM6
    Related
    ENSP00000359057.3, ENST00000370040.7
    Conserved Domains (2) summary
    pfam06758
    Location:435 → 500
    DUF1220; Repeat of unknown function (DUF1220)
    cl25723
    Location:5 → 150
    KELK; KELK-motif containing domain of MRCK Ser/Thr protein kinase

  2. NM_001143988.2 → NP_001137460.1  neuroblastoma breakpoint family member 6 isoform 2

    See identical proteins and their annotated locations for NP_001137460.1

    Status: REVIEWED

    Source sequence(s)
    AL390038, AL392088
    Consensus CDS
    CCDS44184.1
    UniProtKB/Swiss-Prot
    A4QN25, Q5VWK0
    UniProtKB/TrEMBL
    A0AAG2UXJ6
    Related
    ENSP00000417277.2, ENST00000495380.7
    Conserved Domains (1) summary
    pfam06758
    Location:410 → 472
    DUF1220; Repeat of unknown function (DUF1220)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    108421491..108471920
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047428683.1 → XP_047284639.1  neuroblastoma breakpoint family member 6 isoform X1

  2. XM_011542012.3 → XP_011540314.1  neuroblastoma breakpoint family member 6 isoform X1

    See identical proteins and their annotated locations for XP_011540314.1

    UniProtKB/TrEMBL
    A0AAG2UXJ6
    Conserved Domains (1) summary
    pfam06758
    Location:428 → 490
    DUF1220; Repeat of unknown function (DUF1220)

  3. XM_047428685.1 → XP_047284641.1  neuroblastoma breakpoint family member 6 isoform X1

  4. XM_047428686.1 → XP_047284642.1  neuroblastoma breakpoint family member 6 isoform X1

  5. XM_017002148.2 → XP_016857637.1  neuroblastoma breakpoint family member 6 isoform X1

    UniProtKB/TrEMBL
    A0AAG2UXJ6
    Conserved Domains (1) summary
    pfam06758
    Location:428 → 490
    DUF1220; Repeat of unknown function (DUF1220)

  6. XM_047428684.1 → XP_047284640.1  neuroblastoma breakpoint family member 6 isoform X1

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_017852928.1 Reference GRCh38.p14 PATCHES

    Range
    234511..256142 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054332116.1 → XP_054188091.1  neuroblastoma breakpoint family member 6 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    108454038..108505300
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054338422.1 → XP_054194397.1  neuroblastoma breakpoint family member 6 isoform X4

  2. XM_054338416.1 → XP_054194391.1  neuroblastoma breakpoint family member 6 isoform X3

  3. XM_054338419.1 → XP_054194394.1  neuroblastoma breakpoint family member 6 isoform X3

  4. XM_054338418.1 → XP_054194393.1  neuroblastoma breakpoint family member 6 isoform X3

  5. XM_054338417.1 → XP_054194392.1  neuroblastoma breakpoint family member 6 isoform X3

  6. XM_054338415.1 → XP_054194390.1  neuroblastoma breakpoint family member 6 isoform X3

  7. XM_054338420.1 → XP_054194395.1  neuroblastoma breakpoint family member 6 isoform X3

  8. XM_054338421.1 → XP_054194396.1  neuroblastoma breakpoint family member 6 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5VWK0.2 GenPept UniProtKB/Swiss-Prot:Q5VWK0

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