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    BNC2 basonuclin zinc finger protein 2 [ Homo sapiens (human) ]

    Gene ID: 54796, updated on 7-Apr-2024

    Summary

    Official Symbol
    BNC2provided by HGNC
    Official Full Name
    basonuclin zinc finger protein 2provided by HGNC
    Primary source
    HGNC:HGNC:30988
    See related
    Ensembl:ENSG00000173068 MIM:608669; AllianceGenome:HGNC:30988
    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
    bn2; BSN2; LUTO
    Summary
    This gene encodes a conserved zinc finger protein. The encoded protein functions in skin color saturation. Mutations in this gene are associated with facial pigmented spots. This gene is also associated with susceptibility to adolescent idiopathic scoliosis. [provided by RefSeq, Jul 2016]
    Expression
    Biased expression in endometrium (RPKM 6.6), ovary (RPKM 5.5) and 13 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Location:
    9p22.3-p22.2
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (16409503..16870670, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (16421369..16882518, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (16409501..16870668, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 171 Neighboring gene uncharacterized LOC107987049 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:16030074-16031273 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:16036253-16036508 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:16060174-16061373 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:16179471-16179971 Neighboring gene NANOG hESC enhancer GRCh37_chr9:16243838-16244339 Neighboring gene long intergenic non-protein coding RNA 3041 Neighboring gene uncharacterized LOC124902124 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:16322644-16323144 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:16329447-16330006 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19788 Neighboring gene uncharacterized LOC124902125 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:16435259-16436458 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28216 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:16485208-16485860 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:16485861-16486512 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:16515916-16516476 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:16515335-16515901 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:16514088-16514670 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:16514766-16515334 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:16626962-16627495 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:16653272-16653772 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:16704398-16705152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:16706560-16707060 Neighboring gene VISTA enhancer hs307 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:16726395-16726896 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:16730147-16730694 Neighboring gene Sharpr-MPRA regulatory region 7975 Neighboring gene NANOG hESC enhancer GRCh37_chr9:16795834-16796335 Neighboring gene Sharpr-MPRA regulatory region 8712 Neighboring gene BNC2 antisense RNA 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:16809986-16810513 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:16810514-16811042 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_107116 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:16867432-16868631 Neighboring gene LSM1 homolog, mRNA degradation associated pseudogene 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:16921666-16922273 Neighboring gene uncharacterized LOC124902126 Neighboring gene uncharacterized LOC105375983 Neighboring gene RNA, 7SL, cytoplasmic 720, pseudogene

    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
    Lower urinary tract obstruction, congenital
    MedGen: C5231427 OMIM: 618612 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide association study identifies a new ovarian cancer susceptibility locus on 9p22.2.
    EBI GWAS Catalog
    A genome-wide search for quantitative trait loci affecting the cortical surface area and thickness of Heschl's gyrus.
    EBI GWAS Catalog
    Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study.
    EBI GWAS Catalog
    Hundreds of variants clustered in genomic loci and biological pathways affect human height.
    EBI GWAS Catalog
    Web-based, participant-driven studies yield novel genetic associations for common traits.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ20043, FLJ34928, DKFZp686A01127

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables rDNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in endochondral bone growth IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mesenchyme development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in roof of mouth development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in tongue development IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    part_of chromatin IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    zinc finger protein basonuclin-2
    Names
    basonuclin 2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_051226.1 RefSeqGene

      Range
      5051..466336
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001317939.2NP_001304868.1  zinc finger protein basonuclin-2 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, contains an alternate penultimate exon and uses an alternate splice site in the 3' terminal exon, compared to variant 1. It encodes isoform 2 which is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AL449983, CR933649
      UniProtKB/TrEMBL
      H0Y6W5
      Related
      ENSP00000408370.1, ENST00000418777.5
      Conserved Domains (1) summary
      sd00017
      Location:401422
      ZF_C2H2; C2H2 Zn finger [structural motif]
    2. NM_001317940.2NP_001304869.1  zinc finger protein basonuclin-2 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has multiple differences, compared to variant 1. These differences result in a distinct 5' UTR and cause translation initiation at an alternate start codon, compared to variant 1. The encoded protein (isoform 3) is shorter and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK299073, AL449983
      UniProtKB/TrEMBL
      B4DR27
      Conserved Domains (1) summary
      sd00017
      Location:942963
      ZF_C2H2; C2H2 Zn finger [structural motif]
    3. NM_017637.6NP_060107.3  zinc finger protein basonuclin-2 isoform 1

      See identical proteins and their annotated locations for NP_060107.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AK131398, AL449983, AY438376, DA494074
      Consensus CDS
      CCDS6482.2
      UniProtKB/Swiss-Prot
      B1APG9, Q6T3A3, Q6ZN30, Q8NAR2, Q9H6J0, Q9NXV0
      UniProtKB/TrEMBL
      B1APH0
      Related
      ENSP00000370047.3, ENST00000380672.9
      Conserved Domains (1) summary
      sd00017
      Location:10371058
      ZF_C2H2; C2H2 Zn finger [structural motif]

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      16409503..16870670 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047423506.1XP_047279462.1  zinc finger protein basonuclin-2 isoform X26

    2. XM_047423501.1XP_047279457.1  zinc finger protein basonuclin-2 isoform X21

      Related
      ENSP00000515060.1, ENST00000700553.1
    3. XM_047423494.1XP_047279450.1  zinc finger protein basonuclin-2 isoform X15

    4. XM_047423514.1XP_047279470.1  zinc finger protein basonuclin-2 isoform X34

    5. XM_047423513.1XP_047279469.1  zinc finger protein basonuclin-2 isoform X33

    6. XM_047423493.1XP_047279449.1  zinc finger protein basonuclin-2 isoform X14

    7. XM_047423512.1XP_047279468.1  zinc finger protein basonuclin-2 isoform X32

      Related
      ENSP00000431516.1, ENST00000484726.5
    8. XM_047423488.1XP_047279444.1  zinc finger protein basonuclin-2 isoform X9

    9. XM_047423487.1XP_047279443.1  zinc finger protein basonuclin-2 isoform X8

    10. XM_047423515.1XP_047279471.1  zinc finger protein basonuclin-2 isoform X35

    11. XM_047423481.1XP_047279437.1  zinc finger protein basonuclin-2 isoform X2

    12. XM_047423486.1XP_047279442.1  zinc finger protein basonuclin-2 isoform X7

    13. XM_047423484.1XP_047279440.1  zinc finger protein basonuclin-2 isoform X5

    14. XM_047423489.1XP_047279445.1  zinc finger protein basonuclin-2 isoform X10

    15. XM_047423510.1XP_047279466.1  zinc finger protein basonuclin-2 isoform X30

    16. XM_047423511.1XP_047279467.1  zinc finger protein basonuclin-2 isoform X31

    17. XM_047423505.1XP_047279461.1  zinc finger protein basonuclin-2 isoform X25

    18. XM_047423517.1XP_047279473.1  zinc finger protein basonuclin-2 isoform X37

    19. XM_047423500.1XP_047279456.1  zinc finger protein basonuclin-2 isoform X20

    20. XM_047423503.1XP_047279459.1  zinc finger protein basonuclin-2 isoform X23

    21. XM_047423516.1XP_047279472.1  zinc finger protein basonuclin-2 isoform X36

    22. XM_047423502.1XP_047279458.1  zinc finger protein basonuclin-2 isoform X22

    23. XM_047423498.1XP_047279454.1  zinc finger protein basonuclin-2 isoform X19

    24. XM_047423508.1XP_047279464.1  zinc finger protein basonuclin-2 isoform X28

    25. XM_047423495.1XP_047279451.1  zinc finger protein basonuclin-2 isoform X16

    26. XM_047423491.1XP_047279447.1  zinc finger protein basonuclin-2 isoform X12

    27. XM_047423492.1XP_047279448.1  zinc finger protein basonuclin-2 isoform X13

      Related
      ENSP00000370042.1, ENST00000380667.6
    28. XM_047423483.1XP_047279439.1  zinc finger protein basonuclin-2 isoform X4

    29. XM_047423480.1XP_047279436.1  zinc finger protein basonuclin-2 isoform X1

    30. XM_047423482.1XP_047279438.1  zinc finger protein basonuclin-2 isoform X3

    31. XM_047423485.1XP_047279441.1  zinc finger protein basonuclin-2 isoform X6

    32. XM_047423490.1XP_047279446.1  zinc finger protein basonuclin-2 isoform X11

    33. XM_047423507.1XP_047279463.1  zinc finger protein basonuclin-2 isoform X27

    34. XM_047423496.1XP_047279452.1  zinc finger protein basonuclin-2 isoform X17

    35. XM_047423504.1XP_047279460.1  zinc finger protein basonuclin-2 isoform X24

    36. XM_047423497.1XP_047279453.1  zinc finger protein basonuclin-2 isoform X18

    37. XM_047423509.1XP_047279465.1  zinc finger protein basonuclin-2 isoform X29

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      16421369..16882518 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)