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NBPF9 NBPF member 9 [ Homo sapiens (human) ]

Gene ID: 400818, updated on 3-Apr-2024

Summary

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Official Symbol
NBPF9provided by HGNC
Official Full Name
NBPF member 9provided by HGNC
Primary source
HGNC:HGNC:31991
See related
Ensembl:ENSG00000269713 MIM:613999; AllianceGenome:HGNC:31991
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
Also known as
AE01
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, Apr 2013]
Expression
Ubiquitous expression in skin (RPKM 26.6), ovary (RPKM 24.3) and 25 other tissues See more
Orthologs
all
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Genomic context

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See NBPF9 in Genome Data Viewer
Location:
1q21.2
Exon count:
34
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (149052186..149103551, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (145719259..145761198, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (144593688..144832254)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene phosphodiesterase 4D interacting protein Neighboring gene uncharacterized LOC112268272 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:145015143-145015643 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:144994512-144995132 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:144993892-144994511 Neighboring gene NANOG hESC enhancer GRCh37_chr1:144976465-144977040 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:144966957-144967786 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:144961997-144962606 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:144937763-144938539 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:144936334-144936835 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:144932913-144933661 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr1:144931414-144932162 and GRCh37_chr1:144932163-144932912 Neighboring gene RNA, U2 small nuclear 38, pseudogene Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:144891435-144892634 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:144867459-144868658 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:144850469-144850968 Neighboring gene profilin-1-like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1288 Neighboring gene uncharacterized LOC101929790 Neighboring gene uncharacterized LOC102723348 Neighboring gene uncharacterized LOC124904405

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. Lineage-specific gene duplication and loss in human and great ape evolution. Fortna A, et al. PLoS Biol, 2004 Jul. PMID 15252450, Free PMC Article
  4. Why do cellular proteins linked to K63-polyubiquitin chains not associate with proteasomes? Nathan JA, et al. EMBO J, 2013 Feb 20. PMID 23314748, Free PMC Article
  5. 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

See all (9) citations in PubMed

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

Clone Names

  • FLJ37711, FLJ60244, KIAA1245

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 9

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_001037675.4 → NP_001032764.2  neuroblastoma breakpoint family member 9 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks four exons in the 3' coding region, compared to variant 1, and encodes a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AC239804
    Consensus CDS
    CCDS72895.1
    UniProtKB/TrEMBL
    A0A087WWQ1
    Conserved Domains (2) summary
    COG0419
    Location:11 → 401
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    pfam06758
    Location:757 → 822
    DUF1220; Repeat of unknown function (DUF1220)

  2. NM_001277444.2 → NP_001264373.1  neuroblastoma breakpoint family member 9 isoform 1

    See identical proteins and their annotated locations for NP_001264373.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC239804
    Consensus CDS
    CCDS72896.1
    UniProtKB/Swiss-Prot
    A0A075B761, A0A087WVA0, A0A087WY26, P0DPF3, Q3BBV1, Q3BBW0
    UniProtKB/TrEMBL
    A0A494C053
    Conserved Domains (2) summary
    COG0419
    Location:10 → 401
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    pfam06758
    Location:757 → 822
    DUF1220; Repeat of unknown function (DUF1220)

  3. NM_001388366.1 → NP_001375295.1  neuroblastoma breakpoint family member 9 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC239804
    Consensus CDS
    CCDS72896.1
    UniProtKB/Swiss-Prot
    A0A075B761, A0A087WVA0, A0A087WY26, P0DPF3, Q3BBV1, Q3BBW0
    UniProtKB/TrEMBL
    A0A494C053
    Conserved Domains (2) summary
    COG0419
    Location:10 → 401
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    pfam06758
    Location:757 → 822
    DUF1220; Repeat of unknown function (DUF1220)

  4. NM_001388367.1 → NP_001375296.1  neuroblastoma breakpoint family member 9 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC239804
    Consensus CDS
    CCDS72896.1
    UniProtKB/Swiss-Prot
    A0A075B761, A0A087WVA0, A0A087WY26, P0DPF3, Q3BBV1, Q3BBW0
    UniProtKB/TrEMBL
    A0A494C053
    Related
    ENSP00000513968.1, ENST00000698832.1
    Conserved Domains (2) summary
    COG0419
    Location:10 → 401
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    pfam06758
    Location:757 → 822
    DUF1220; Repeat of unknown function (DUF1220)

  5. NM_001388368.1 → NP_001375297.1  neuroblastoma breakpoint family member 9 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC239804
    Consensus CDS
    CCDS72896.1
    UniProtKB/Swiss-Prot
    A0A075B761, A0A087WVA0, A0A087WY26, P0DPF3, Q3BBV1, Q3BBW0
    UniProtKB/TrEMBL
    A0A494C053
    Related
    ENSP00000513601.1, ENST00000698196.1
    Conserved Domains (2) summary
    COG0419
    Location:10 → 401
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    pfam06758
    Location:757 → 822
    DUF1220; Repeat of unknown function (DUF1220)

  6. NM_001388369.1 → NP_001375298.1  neuroblastoma breakpoint family member 9 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC239804
    Consensus CDS
    CCDS72896.1
    UniProtKB/Swiss-Prot
    A0A075B761, A0A087WVA0, A0A087WY26, P0DPF3, Q3BBV1, Q3BBW0
    UniProtKB/TrEMBL
    A0A494C053
    Conserved Domains (2) summary
    COG0419
    Location:10 → 401
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    pfam06758
    Location:757 → 822
    DUF1220; Repeat of unknown function (DUF1220)

  7. NM_001388370.1 → NP_001375299.1  neuroblastoma breakpoint family member 9 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC239804
    Consensus CDS
    CCDS72896.1
    UniProtKB/Swiss-Prot
    A0A075B761, A0A087WVA0, A0A087WY26, P0DPF3, Q3BBV1, Q3BBW0
    UniProtKB/TrEMBL
    A0A494C053
    Related
    ENSP00000482587.1, ENST00000621645.4
    Conserved Domains (2) summary
    COG0419
    Location:10 → 401
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    pfam06758
    Location:757 → 822
    DUF1220; Repeat of unknown function (DUF1220)

  8. NM_001388371.1 → NP_001375300.1  neuroblastoma breakpoint family member 9 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC239804
    UniProtKB/TrEMBL
    A0A087WZE1
    Conserved Domains (2) summary
    COG0419
    Location:11 → 401
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    pfam06758
    Location:720 → 785
    DUF1220; Repeat of unknown function (DUF1220)

  9. NM_001388372.1 → NP_001375301.1  neuroblastoma breakpoint family member 9 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC239804
    Consensus CDS
    CCDS72895.1
    UniProtKB/TrEMBL
    A0A087WWQ1
    Conserved Domains (2) summary
    COG0419
    Location:11 → 401
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    pfam06758
    Location:757 → 822
    DUF1220; Repeat of unknown function (DUF1220)

  10. NM_001388373.1 → NP_001375302.1  neuroblastoma breakpoint family member 9 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC239804
    Consensus CDS
    CCDS72895.1
    UniProtKB/TrEMBL
    A0A087WWQ1
    Conserved Domains (2) summary
    COG0419
    Location:11 → 401
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    pfam06758
    Location:757 → 822
    DUF1220; Repeat of unknown function (DUF1220)

  11. NM_001388374.1 → NP_001375303.1  neuroblastoma breakpoint family member 9 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC239804
    Consensus CDS
    CCDS72895.1
    UniProtKB/TrEMBL
    A0A087WWQ1
    Conserved Domains (2) summary
    COG0419
    Location:11 → 401
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    pfam06758
    Location:757 → 822
    DUF1220; Repeat of unknown function (DUF1220)

  12. NM_001388375.1 → NP_001375304.1  neuroblastoma breakpoint family member 9 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC239804
    Consensus CDS
    CCDS72895.1
    UniProtKB/TrEMBL
    A0A087WWQ1
    Conserved Domains (2) summary
    COG0419
    Location:11 → 401
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    pfam06758
    Location:757 → 822
    DUF1220; Repeat of unknown function (DUF1220)

  13. NM_001388376.1 → NP_001375305.1  neuroblastoma breakpoint family member 9 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC239804
    Consensus CDS
    CCDS72895.1
    UniProtKB/TrEMBL
    A0A087WWQ1
    Conserved Domains (2) summary
    COG0419
    Location:11 → 401
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    pfam06758
    Location:757 → 822
    DUF1220; Repeat of unknown function (DUF1220)

  14. NM_001388377.1 → NP_001375306.1  neuroblastoma breakpoint family member 9 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC239804
    Consensus CDS
    CCDS72895.1
    UniProtKB/TrEMBL
    A0A087WWQ1
    Conserved Domains (2) summary
    COG0419
    Location:11 → 401
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    pfam06758
    Location:757 → 822
    DUF1220; Repeat of unknown function (DUF1220)

  15. NM_001388378.1 → NP_001375307.1  neuroblastoma breakpoint family member 9 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC239804
    Consensus CDS
    CCDS72895.1
    UniProtKB/TrEMBL
    A0A087WWQ1
    Conserved Domains (2) summary
    COG0419
    Location:11 → 401
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    pfam06758
    Location:757 → 822
    DUF1220; Repeat of unknown function (DUF1220)

  16. NM_001388379.1 → NP_001375308.1  neuroblastoma breakpoint family member 9 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC239804
    Consensus CDS
    CCDS72895.1
    UniProtKB/TrEMBL
    A0A087WWQ1
    Conserved Domains (2) summary
    COG0419
    Location:11 → 401
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    pfam06758
    Location:757 → 822
    DUF1220; Repeat of unknown function (DUF1220)

  17. NM_001388381.1 → NP_001375310.1  neuroblastoma breakpoint family member 9 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC239804
    Consensus CDS
    CCDS72895.1
    UniProtKB/TrEMBL
    A0A087WWQ1
    Conserved Domains (2) summary
    COG0419
    Location:11 → 401
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    pfam06758
    Location:757 → 822
    DUF1220; Repeat of unknown function (DUF1220)

  18. NM_001388382.1 → NP_001375311.1  neuroblastoma breakpoint family member 9 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC239804
    Consensus CDS
    CCDS72895.1
    UniProtKB/TrEMBL
    A0A087WWQ1
    Conserved Domains (2) summary
    COG0419
    Location:11 → 401
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    pfam06758
    Location:757 → 822
    DUF1220; Repeat of unknown function (DUF1220)

  19. NM_001388383.1 → NP_001375312.1  neuroblastoma breakpoint family member 9 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC239804
    Consensus CDS
    CCDS72895.1
    UniProtKB/TrEMBL
    A0A087WWQ1
    Related
    ENSP00000483900.1, ENST00000613595.4
    Conserved Domains (2) summary
    COG0419
    Location:11 → 401
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    pfam06758
    Location:757 → 822
    DUF1220; Repeat of unknown function (DUF1220)

  20. NM_001388384.1 → NP_001375313.1  neuroblastoma breakpoint family member 9 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC239804
    Consensus CDS
    CCDS72895.1
    UniProtKB/TrEMBL
    A0A087WWQ1
    Conserved Domains (2) summary
    COG0419
    Location:11 → 401
    SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
    pfam06758
    Location:757 → 822
    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
    149052186..149103551 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047420572.1 → XP_047276528.1  neuroblastoma breakpoint family member 9 isoform X1

    UniProtKB/Swiss-Prot
    A0A075B761, A0A087WVA0, A0A087WY26, P0DPF3, Q3BBV1, Q3BBW0

  2. XM_047420578.1 → XP_047276534.1  neuroblastoma breakpoint family member 9 isoform X2

RNA

  1. XR_007060075.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    145719259..145761198 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P0DPF3.1 GenPept UniProtKB/Swiss-Prot:P0DPF3

Gene LinkOut

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