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NBPF3 NBPF member 3 [ Homo sapiens (human) ]

Gene ID: 84224, updated on 11-Jun-2021

Summary

Official Symbol
NBPF3provided by HGNC
Official Full Name
NBPF member 3provided by HGNC
Primary source
HGNC:HGNC:25076
See related
Ensembl:ENSG00000142794 MIM:612992
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
Also known as
AE2
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. DUF1220 copy number variations in 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, Feb 2013]
Expression
Broad expression in testis (RPKM 10.2), thyroid (RPKM 3.5) and 23 other tissues See more
Orthologs
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Genomic context

See NBPF3 in Genome Data Viewer
Location:
1p36.12
Exon count:
21
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (21436775..21484900)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (21766630..21811393)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene NBPF member 2, pseudogene Neighboring gene heparan sulfate 6-O-sulfotransferase 1 pseudogene 1 Neighboring gene CROCC pseudogene 5 Neighboring gene profilin 1 pseudogene 10 Neighboring gene alkaline phosphatase, biomineralization associated Neighboring gene long intergenic non-protein coding RNA 2596

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Common genetic variants associate with serum phosphorus concentration.
GeneReviews: Not available
Genetic Associations with Plasma B12, B6, and Folate Levels in an Ischemic Stroke Population from the Vitamin Intervention for Stroke Prevention (VISP) Trial.
GeneReviews: Not available
Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma.
GeneReviews: Not available
Genome-wide association study of vitamin B6, vitamin B12, folate, and homocysteine blood concentrations.
GeneReviews: Not available
Genome-wide significant predictors of metabolites in the one-carbon metabolism pathway.
GeneReviews: Not available
Population-based genome-wide association studies reveal six loci influencing plasma levels of liver enzymes.
GeneReviews: Not available

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp434D177

Gene Ontology Provided by GOA

Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
neuroblastoma breakpoint family member 3
Names
protein SHIIIa4

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_001256416.4NP_001243345.1  neuroblastoma breakpoint family member 3 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks one exon and includes an alternate exon in the coding region, compared to variant 1. It encodes isoform 2 which is shorter, compared to isoform 1.
    Source sequence(s)
    AK292580, AK314597, AL136890, AL592309, BC024011
    Consensus CDS
    CCDS57976.1
    UniProtKB/Swiss-Prot
    Q9H094
    Related
    ENSP00000340336.5, ENST00000342104.9
    Conserved Domains (1) summary
    pfam06758
    Location:459521
    DUF1220; Repeat of unknown function (DUF1220)
  2. NM_001256417.4NP_001243346.1  neuroblastoma breakpoint family member 3 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate exon in the coding region, compared to variant 1. The resulting protein (isoform 3) is shorter, compared to isoform 1.
    Source sequence(s)
    AK292580, AK299840, AL136890, AL592309
    Consensus CDS
    CCDS57977.1
    UniProtKB/Swiss-Prot
    Q9H094
    Related
    ENSP00000415711.2, ENST00000454000.6
    Conserved Domains (1) summary
    pfam06758
    Location:401463
    DUF1220; Repeat of unknown function (DUF1220)
  3. NM_001330381.3NP_001317310.1  neuroblastoma breakpoint family member 3 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) contains several alternate internal exons compared to variant 1. The resulting isoform (4) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AL592309
    Consensus CDS
    CCDS81275.1
    UniProtKB/Swiss-Prot
    Q9H094
    Conserved Domains (1) summary
    pfam06758
    Location:411476
    DUF1220; Repeat of unknown function (DUF1220)
  4. NM_001377491.1NP_001364420.1  neuroblastoma breakpoint family member 3 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL592309
  5. NM_001377492.1NP_001364421.1  neuroblastoma breakpoint family member 3 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL592309
  6. NM_001377493.1NP_001364422.1  neuroblastoma breakpoint family member 3 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL592309
  7. NM_001377494.1NP_001364423.1  neuroblastoma breakpoint family member 3 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL592309
  8. NM_001377495.1NP_001364424.1  neuroblastoma breakpoint family member 3 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL592309
  9. NM_001377496.1NP_001364425.1  neuroblastoma breakpoint family member 3 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AL592309
    Conserved Domains (1) summary
    pfam06758
    Location:374439
    DUF1220; Repeat of unknown function (DUF1220)
  10. NM_032264.6NP_115640.1  neuroblastoma breakpoint family member 3 isoform 1

    See identical proteins and their annotated locations for NP_115640.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest protein (isoform 1).
    Source sequence(s)
    AL592309
    Consensus CDS
    CCDS216.1
    UniProtKB/Swiss-Prot
    Q9H094
    Related
    ENSP00000316782.5, ENST00000318249.10
    Conserved Domains (1) summary
    pfam06758
    Location:471533
    DUF1220; Repeat of unknown function (DUF1220)

RNA

  1. NR_046176.4 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains several alternate exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most translational start codon as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK095602, AK292580, AL136890, AL592309
    Related
    ENST00000318220.10

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    21436775..21484900
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011542281.1XP_011540583.1  neuroblastoma breakpoint family member 3 isoform X2

    See identical proteins and their annotated locations for XP_011540583.1

    UniProtKB/Swiss-Prot
    Q9H094
    Conserved Domains (1) summary
    pfam06758
    Location:411476
    DUF1220; Repeat of unknown function (DUF1220)
  2. XM_017002502.1XP_016857991.1  neuroblastoma breakpoint family member 3 isoform X3

    Conserved Domains (1) summary
    pfam06758
    Location:374439
    DUF1220; Repeat of unknown function (DUF1220)
  3. XM_024450190.1XP_024305958.1  neuroblastoma breakpoint family member 3 isoform X2

    Conserved Domains (1) summary
    pfam06758
    Location:411476
    DUF1220; Repeat of unknown function (DUF1220)
  4. XM_006710957.1XP_006711020.1  neuroblastoma breakpoint family member 3 isoform X1

    Conserved Domains (1) summary
    pfam06758
    Location:434496
    DUF1220; Repeat of unknown function (DUF1220)
  5. XM_017002501.1XP_016857990.1  neuroblastoma breakpoint family member 3 isoform X3

    Conserved Domains (1) summary
    pfam06758
    Location:374439
    DUF1220; Repeat of unknown function (DUF1220)
  6. XM_006710959.2XP_006711022.1  neuroblastoma breakpoint family member 3 isoform X2

    See identical proteins and their annotated locations for XP_006711022.1

    UniProtKB/Swiss-Prot
    Q9H094
    Conserved Domains (1) summary
    pfam06758
    Location:411476
    DUF1220; Repeat of unknown function (DUF1220)
  7. XM_017002499.2XP_016857988.1  neuroblastoma breakpoint family member 3 isoform X2

    UniProtKB/Swiss-Prot
    Q9H094
    Related
    ENSP00000484028.1, ENST00000619554.1
    Conserved Domains (1) summary
    pfam06758
    Location:411476
    DUF1220; Repeat of unknown function (DUF1220)
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