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    NBPF9 NBPF member 9 [ Homo sapiens (human) ]

    Gene ID: 400818, updated on 21-Dec-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_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (149052186..149103551, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (145719259..145761198, complement)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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)

    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
    NBPF family member NBPF9; 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  NBPF family member NBPF9 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
      A0AAG2UVQ9
      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  NBPF family member NBPF9 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
      A0AAG2UXD5
      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  NBPF family member NBPF9 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC239804
      Consensus CDS
      CCDS72896.1
      UniProtKB/Swiss-Prot
      A0A075B761, A0A087WVA0, A0A087WY26, P0DPF3, Q3BBV1, Q3BBW0
      UniProtKB/TrEMBL
      A0AAG2UXD5
      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  NBPF family member NBPF9 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC239804
      Consensus CDS
      CCDS72896.1
      UniProtKB/Swiss-Prot
      A0A075B761, A0A087WVA0, A0A087WY26, P0DPF3, Q3BBV1, Q3BBW0
      UniProtKB/TrEMBL
      A0AAG2UXD5
      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  NBPF family member NBPF9 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC239804
      Consensus CDS
      CCDS72896.1
      UniProtKB/Swiss-Prot
      A0A075B761, A0A087WVA0, A0A087WY26, P0DPF3, Q3BBV1, Q3BBW0
      UniProtKB/TrEMBL
      A0AAG2UXD5
      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  NBPF family member NBPF9 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC239804
      Consensus CDS
      CCDS72896.1
      UniProtKB/Swiss-Prot
      A0A075B761, A0A087WVA0, A0A087WY26, P0DPF3, Q3BBV1, Q3BBW0
      UniProtKB/TrEMBL
      A0AAG2UXD5
      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  NBPF family member NBPF9 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC239804
      Consensus CDS
      CCDS72896.1
      UniProtKB/Swiss-Prot
      A0A075B761, A0A087WVA0, A0A087WY26, P0DPF3, Q3BBV1, Q3BBW0
      UniProtKB/TrEMBL
      A0AAG2UXD5
      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  NBPF family member NBPF9 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  NBPF family member NBPF9 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC239804
      Consensus CDS
      CCDS72895.1
      UniProtKB/TrEMBL
      A0AAG2UVQ9
      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  NBPF family member NBPF9 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC239804
      Consensus CDS
      CCDS72895.1
      UniProtKB/TrEMBL
      A0AAG2UVQ9
      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  NBPF family member NBPF9 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC239804
      Consensus CDS
      CCDS72895.1
      UniProtKB/TrEMBL
      A0AAG2UVQ9
      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  NBPF family member NBPF9 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC239804
      Consensus CDS
      CCDS72895.1
      UniProtKB/TrEMBL
      A0AAG2UVQ9
      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  NBPF family member NBPF9 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC239804
      Consensus CDS
      CCDS72895.1
      UniProtKB/TrEMBL
      A0AAG2UVQ9
      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  NBPF family member NBPF9 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC239804
      Consensus CDS
      CCDS72895.1
      UniProtKB/TrEMBL
      A0AAG2UVQ9
      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  NBPF family member NBPF9 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC239804
      Consensus CDS
      CCDS72895.1
      UniProtKB/TrEMBL
      A0AAG2UVQ9
      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  NBPF family member NBPF9 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC239804
      Consensus CDS
      CCDS72895.1
      UniProtKB/TrEMBL
      A0AAG2UVQ9
      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  NBPF family member NBPF9 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC239804
      Consensus CDS
      CCDS72895.1
      UniProtKB/TrEMBL
      A0AAG2UVQ9
      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  NBPF family member NBPF9 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC239804
      Consensus CDS
      CCDS72895.1
      UniProtKB/TrEMBL
      A0AAG2UVQ9
      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  NBPF family member NBPF9 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC239804
      Consensus CDS
      CCDS72895.1
      UniProtKB/TrEMBL
      A0AAG2UVQ9
      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  NBPF family member NBPF9 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC239804
      Consensus CDS
      CCDS72895.1
      UniProtKB/TrEMBL
      A0AAG2UVQ9
      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_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
      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
      UniProtKB/TrEMBL
      A0AAG2UXD5

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

      UniProtKB/TrEMBL
      A0A494C053

    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

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

    Chemical Information
    Molecular Biology Databases
    Research Materials