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    NBPF6 NBPF member 6 [ Homo sapiens (human) ]

    Gene ID: 653149, updated on 3-Apr-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_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (108421491..108471920)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (108454038..108505300)
    105.20220307 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
    • 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)

    Genotypes

    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
      B7ZAX3
      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_2023_10

    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
      B7ZAX3
      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
      B7ZAX3
      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

    Gene LinkOut

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