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NBPF20 NBPF member 20 [ Homo sapiens (human) ]

Gene ID: 100288142, updated on 3-Apr-2024

Summary

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Official Symbol
NBPF20provided by HGNC
Official Full Name
NBPF member 20provided by HGNC
Primary source
HGNC:HGNC:32000
See related
Ensembl:ENSG00000162825 MIM:614007; AllianceGenome:HGNC:32000
Gene type
protein coding
RefSeq status
VALIDATED
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 2014]
Expression
Ubiquitous expression in testis (RPKM 6.6), skin (RPKM 5.6) and 25 other tissues See more
Orthologs
all
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Genomic context

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Location:
1q21.1
Exon count:
145
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (145289900..145425603, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (144414641..144542479, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 (PATCHES) NW_003871055.3 (2105313..2241016, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:148241215-148241940 Neighboring gene uncharacterized LOC101060170 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1260 Neighboring gene RNA, variant U1 small nuclear 14 Neighboring gene tRNA-Asn (anticodon GTT) 2-7 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:148356511-148357172 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:148357173-148357832 Neighboring gene profilin 1 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1608 Neighboring gene uncharacterized LOC105371288 Neighboring gene RNA, U1 small nuclear 154, pseudogene Neighboring gene tRNA-Gln (anticodon CTG) 3-1

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. 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
  2. SNIP1 Recruits TET2 to Regulate c-MYC Target Genes and Cellular DNA Damage Response. Chen LL, et al. Cell Rep, 2018 Nov 6. PMID 30404004, Free PMC Article
  3. Proteome-scale mapping of binding sites in the unstructured regions of the human proteome. Benz C, et al. Mol Syst Biol, 2022 Jan. PMID 35044719, Free PMC Article
  4. Integrative oncogene-dependency mapping identifies RIT1 vulnerabilities and synergies in lung cancer. Vichas A, et al. Nat Commun, 2021 Aug 9. PMID 34373451, Free PMC Article
  5. Quantitative mapping of RNA-mediated nuclear estrogen receptor β interactome in human breast cancer cells. Giurato G, et al. Sci Data, 2018 Mar 6. PMID 29509190, 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 20

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.

Genomic

  1. NG_034048.2 RefSeqGene

    Range
    5000..140598
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001278267.1 → NP_001265196.1  neuroblastoma breakpoint family member 20 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC245014
    UniProtKB/Swiss-Prot
    P0DPF2
    UniProtKB/TrEMBL
    H7BY70
    Conserved Domains (1) summary
    pfam06758
    Location:4628 → 4693
    DUF1220; Repeat of unknown function (DUF1220)

  2. NM_001397211.1 → NP_001384140.1  neuroblastoma breakpoint family member 20 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC239860, AC245014
    Consensus CDS
    CCDS91033.1
    UniProtKB/TrEMBL
    A0A8V8TMC1, H7BY70
    Related
    ENSP00000513969.1, ENST00000698833.1

RNA

  1. NR_189122.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC239860, AC245014

  2. NR_189123.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC239860, AC245014

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
    145289900..145425603 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047445970.1 → XP_047301926.1  neuroblastoma breakpoint family member 20 isoform X1

  2. XM_047446015.1 → XP_047301971.1  neuroblastoma breakpoint family member 20 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    144414641..144542479 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P0DPF2.1 GenPept UniProtKB/Swiss-Prot:P0DPF2

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases
Research Materials