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NBPF4 NBPF member 4 [ Homo sapiens (human) ]

Gene ID: 148545, updated on 2-Nov-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 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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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