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BNC2 basonuclin 2 [ Homo sapiens (human) ]

Gene ID: 54796, updated on 5-Aug-2022

Summary

Official Symbol
BNC2provided by HGNC
Official Full Name
basonuclin 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
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
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Try the new Transcript table

Genomic context

See BNC2 in Genome Data Viewer
Location:
9p22.3-p22.2
Exon count:
17
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (16409503..16870670, complement)
110 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 long intergenic non-protein coding RNA 3041 Neighboring gene uncharacterized LOC124902124 Neighboring gene uncharacterized LOC124902125 Neighboring gene VISTA enhancer hs307 Neighboring gene Sharpr-MPRA regulatory region 7975 Neighboring gene Sharpr-MPRA regulatory region 8712 Neighboring gene BNC2 antisense RNA 1 Neighboring gene LSM1 homolog, mRNA degradation associated pseudogene 1 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

Homology

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
PubMed 
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
located_in 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
PubMed 

General protein information

Preferred Names
zinc finger protein 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
    Q5H9S4
    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
    Q6ZN30, Q9NXV0
    Related
    ENSP00000370047.3, ENST00000380672.9
    Conserved Domains (1) summary
    sd00017
    Location:10371058
    ZF_C2H2; C2H2 Zn finger [structural motif]

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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)