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    NBPF4 NBPF member 4 [ Homo sapiens (human) ]

    Gene ID: 148545, updated on 10-Dec-2024

    Summary

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    Official Symbol
    NBPF4provided by HGNC
    Official Full Name
    NBPF member 4provided by HGNC
    Primary source
    HGNC:HGNC:26550
    See related
    Ensembl:ENSG00000196427 MIM:613994; AllianceGenome:HGNC:26550
    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. [provided by RefSeq, Mar 2013]
    Expression
    Biased expression in testis (RPKM 3.9), small intestine (RPKM 0.8) and 2 other tissues See more
    Orthologs
    all
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    Genomic context

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    See NBPF4 in Genome Data Viewer
    Location:
    1p13.3
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (108222464..108272913, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (108256108..108306611, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (108765086..108786698, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2785 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:108649881-108651080 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:108663847-108664348 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:108664349-108664848 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:108668352-108668491 Neighboring gene solute carrier family 25 member 24 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:108702018-108702956 Neighboring gene Sharpr-MPRA regulatory region 7876 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:108804707-108805225 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:108815151-108815652 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:108815653-108816152 Neighboring gene SLC25A24 pseudogene 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:108878070-108878247 Neighboring gene NBPF member 5, pseudogene

    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. NBPF4 mitigates progression in colorectal cancer through the regulation of EZH2-associated ETFA. Chen W, et al. J Cell Mol Med, 2021 Sep. PMID 34405537, 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. Ephrin-As, Eph receptors and integrin α3 interact and colocalise at membrane protrusions of U251MG glioblastoma cells. Makarov A, et al. Cell Biol Int, 2013 Oct. PMID 23686814
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039
    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

    What's a GeneRIF?
    1. NBPF4 mitigates progression in colorectal cancer through the regulation of EZH2-associated ETFA.
      Title: NBPF4 mitigates progression in colorectal cancer through the regulation of EZH2-associated ETFA.
    Submit: New GeneRIF Correction

    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

    Clone Names

    • FLJ32833

    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 4

    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_001143989.3 → NP_001137461.1  neuroblastoma breakpoint family member 4

      See identical proteins and their annotated locations for NP_001137461.1

      Status: REVIEWED

      Source sequence(s)
      AK057395, AK316438, AL359258, DC402863
      Consensus CDS
      CCDS44182.1
      UniProtKB/Swiss-Prot
      Q5T483, Q96M43
      UniProtKB/TrEMBL
      A0AAG2UYQ5, B7ZAX3
      Related
      ENSP00000389237.2, ENST00000415641.8
      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
      108222464..108272913 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047446894.1 → XP_047302850.1  neuroblastoma breakpoint family member 4 isoform X1

      UniProtKB/TrEMBL
      A0AAG2UYQ5, B7ZAX3

    2. XM_047446899.1 → XP_047302855.1  neuroblastoma breakpoint family member 4 isoform X2

      UniProtKB/TrEMBL
      A0AAG2UYQ5, B7ZAX3

    3. XM_047446895.1 → XP_047302851.1  neuroblastoma breakpoint family member 4 isoform X1

      UniProtKB/TrEMBL
      A0AAG2UYQ5, B7ZAX3

    4. XM_047446896.1 → XP_047302852.1  neuroblastoma breakpoint family member 4 isoform X1

      UniProtKB/TrEMBL
      A0AAG2UYQ5, B7ZAX3

    5. XM_047446900.1 → XP_047302856.1  neuroblastoma breakpoint family member 4 isoform X2

      UniProtKB/TrEMBL
      A0AAG2UYQ5, B7ZAX3

    6. XM_047446897.1 → XP_047302853.1  neuroblastoma breakpoint family member 4 isoform X1

      UniProtKB/TrEMBL
      A0AAG2UYQ5, B7ZAX3

    7. XM_047446898.1 → XP_047302854.1  neuroblastoma breakpoint family member 4 isoform X1

      UniProtKB/TrEMBL
      A0AAG2UYQ5, B7ZAX3

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_017852928.1 Reference GRCh38.p14 PATCHES

      Range
      462101..483576
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      108256108..108306611 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054334577.1 → XP_054190552.1  neuroblastoma breakpoint family member 4 isoform X3

      UniProtKB/TrEMBL
      A0AAG2UYQ5, B7ZAX3

    2. XM_054334586.1 → XP_054190561.1  neuroblastoma breakpoint family member 4 isoform X5

      UniProtKB/TrEMBL
      A0AAG2UYQ5, B7ZAX3

    3. XM_054334583.1 → XP_054190558.1  neuroblastoma breakpoint family member 4 isoform X4

      UniProtKB/TrEMBL
      A0AAG2UYQ5, B7ZAX3

    4. XM_054334587.1 → XP_054190562.1  neuroblastoma breakpoint family member 4 isoform X5

      UniProtKB/TrEMBL
      A0AAG2UYQ5, B7ZAX3

    5. XM_054334588.1 → XP_054190563.1  neuroblastoma breakpoint family member 4 isoform X5

      UniProtKB/TrEMBL
      A0AAG2UYQ5, B7ZAX3

    6. XM_054334584.1 → XP_054190559.1  neuroblastoma breakpoint family member 4 isoform X4

      UniProtKB/TrEMBL
      A0AAG2UYQ5, B7ZAX3

    7. XM_054334585.1 → XP_054190560.1  neuroblastoma breakpoint family member 4 isoform X4

      UniProtKB/TrEMBL
      A0AAG2UYQ5, B7ZAX3

    8. XM_054334578.1 → XP_054190553.1  neuroblastoma breakpoint family member 4 isoform X3

      UniProtKB/TrEMBL
      A0AAG2UYQ5, B7ZAX3

    9. XM_054334580.1 → XP_054190555.1  neuroblastoma breakpoint family member 4 isoform X3

      UniProtKB/TrEMBL
      A0AAG2UYQ5, B7ZAX3

    10. XM_054334579.1 → XP_054190554.1  neuroblastoma breakpoint family member 4 isoform X3

      UniProtKB/TrEMBL
      A0AAG2UYQ5, B7ZAX3

    11. XM_054334582.1 → XP_054190557.1  neuroblastoma breakpoint family member 4 isoform X3

      UniProtKB/TrEMBL
      A0AAG2UYQ5, B7ZAX3

    12. XM_054334581.1 → XP_054190556.1  neuroblastoma breakpoint family member 4 isoform X3

      UniProtKB/TrEMBL
      A0AAG2UYQ5, B7ZAX3

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_152488.1: Suppressed sequence

      Description
      NM_152488.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96M43.2 GenPept UniProtKB/Swiss-Prot:Q96M43

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