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H2BFM Gene

protein-coding   GIFtS: 41
GCID: GC0XP103268

H2B Histone Family, Member M

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
H2B Histone Family, Member M1 2
Histone H2B.S2 3
H2B/s2 3
Histone H2B Type F-M2

External Ids:    HGNC: 278671   Entrez Gene: 2864362   Ensembl: ENSG000001018127   UniProtKB: P0C1H63   

Export aliases for H2BFM gene to outside databases

Previous GC identifers: GC0XP103098 GC0XP103177 GC0XP092950


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for H2BFM Gene:
H2BFM (H2B histone family, member M) is a protein-coding gene. Diseases associated with H2BFM include systemic lupus erythematosus, and lupus erythematosus. GO annotations related to this gene include protein heterodimerization activity. An important paralog of this gene is HIST1H2BA.

UniProtKB/Swiss-Prot: H2BFM_HUMAN, P0C1H6
Function: Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA
accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role
in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is
regulated via a complex set of post-translational modifications of histones, also called histone code, and
nucleosome remodeling




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000023.11  NT_011651.18  NC_018934.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the H2BFM gene promoter:
         MEF-2A   MEF-2   AP-4   aMEF-2   GATA-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for H2BFM

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat H2BFM


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: Xq22.2   Ensembl cytogenetic band:  Xq22.2   HGNC cytogenetic band: Xq22.2

H2BFM Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
H2BFM gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XP103268:  view genomic region     (about GC identifiers)

Start:
103,268,269 bp from pter      End:
103,297,021 bp from pter
Size:
28,753 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: H2BFM_HUMAN, P0C1H6 (See protein sequence)
Recommended Name: Histone H2B type F-M  
Size: 257 amino acids; 28267 Da
Subunit: The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one
H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA
Miscellaneous: In contrast to other H2B histones, it does not contain the conserved residue in C-terminus that is
the target of monoubiquitination
Secondary accessions: A6NP82

Explore the universe of human proteins at neXtProt for H2BFM: NX_P0C1H6

Explore proteomics data for H2BFM at MOPED


See H2BFM Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001157888.1  
ENSEMBL proteins: 
 ENSP00000347119   ENSP00000402466   ENSP00000243297  

H2BFM Human Recombinant Protein Products:

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
RIH: Histones / Replication-independent

3 InterPro protein domains:
 IPR009072 Histone-fold
 IPR000558 Histone_H2B
 IPR007125 Histone_core_D

Graphical View of Domain Structure for InterPro Entry P0C1H6

ProtoNet protein and cluster: P0C1H6

UniProtKB/Swiss-Prot: H2BFM_HUMAN, P0C1H6
Similarity: Belongs to the histone H2B family


H2BFM for domains           About GeneDecksing


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: H2BFM_HUMAN, P0C1H6
Function: Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA
accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role
in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is
regulated via a complex set of post-translational modifications of histones, also called histone code, and
nucleosome remodeling

     Gene Ontology (GO): 3 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003677DNA binding IEA--
GO:0043565sequence-specific DNA binding ----
GO:0046982protein heterodimerization activity IEA--
     
H2BFM for ontologies           About GeneDecksing


Animal Models:
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
H2BFM_HUMAN, P0C1H6: Nucleus. Chromosome
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
nucleus5
mitochondrion3
cytosol1

Gene Ontology (GO): 4 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0000786nucleosome IEA--
GO:0005622intracellular ----
GO:0005634nucleus IDA--
GO:0005730NOT nucleolus IDA--

H2BFM for ontologies           About GeneDecksing


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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SuperPaths for H2BFM About                                                                                                See pathways by source

SuperPathContained pathways About
1RNA Polymerase I Promoter Opening
Systemic lupus erythematosus0.40
Alcoholism0.34
2Viral carcinogenesis
Viral carcinogenesis

Pathways by source                                                                                                                                                                 See SuperPaths
Show all pathways



3 Kegg Pathways  (Kegg details for H2BFM):
    Alcoholism
Viral carcinogenesis
Systemic lupus erythematosus


H2BFM for pathways           About GeneDecksing

    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for H2BFM
Interactions:

    Search GeneGlobe Interaction Network for H2BFM

STRING Interaction Network Preview (showing 5 interactants - click image to see 17)

Selected Interacting proteins for H2BFM (ENSP000002432974) via UniProtKB, MINT, STRING, and/or I2D (see all 17)
InteractantInteraction Details
GeneCardExternal ID(s)
MGMTENSP000003021114STRING: ENSP00000302111
BTAF1ENSP000002659904STRING: ENSP00000265990
IPO9ENSP000003547424STRING: ENSP00000354742
POLR3AENSP000003614464STRING: ENSP00000361446
DDB1ENSP000003017644STRING: ENSP00000301764
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Gene Ontology (GO): 1 biological process term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006334nucleosome assembly IEA--

H2BFM for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
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Browse Tocris compounds for H2BFM



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for H2BFM gene: 
NM_001164416.1  

Unigene Cluster for H2BFM:

H2B histone family, member M
Hs.376474  [show with all ESTs]
Unigene Representative Sequence: NM_001164416
3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000355016(uc004els.2) ENST00000417637 ENST00000243297
miRNA
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Primer
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Pre-validated RT2 qPCR Primer Assay in human, mouse / rat H2BFM
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Additional mRNA sequence: AK093522.1 

1 DOTS entry:

DT.99998582 

4 AceView cDNA sequences:

AI018051 AK093522 AX748182 AI827900 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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H2BFM expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: AAACAAAAGC
H2BFM Expression
About this image

H2BFM Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

H2BFM Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.376474
    Custom PCR Arrays for H2BFM
Primer
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for H2BFM

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of animals and fungi.

Orthologs for H2BFM gene from Selected species (see all 10)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia H2bfm1 , 5 RIKEN cDNA 1700014N06 gene5
H2B histone family, member M1
59.69(n)1
52.33(a)1
  X (59.10 cM)5
693891  NM_027067.21  NP_081343.11 
 1369273255 
chicken
(Gallus gallus)
Aves --
Histone H2B
40(a)
1 → many
2(142049-143378)
zebrafish
(Danio rerio)
Actinopterygii zgc:1717596
zgc:171759
34(a)
many ↔ many
7(76814613-76821072) ENSDARG00000074491
fruit fly
(Drosophila melanogaster)
Insecta His2B:CG339106
His2B:CG33910
43(a)
many ↔ many
2L(21418259-21418843)
worm
(Caenorhabditis elegans)
Secernentea his-396
his-346
(see all 17)
Protein HIS-29 (his-29) mRNA, complete cds
(see all 17)
45(a)
43(a)
(see all 17)
many ↔ many
many ↔ many
(see all 17)
V(8536314-8536716) WBGene00001913
IV(8335972-8336340) WBGene00001908
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HTB26
HTB16
Histone H2B, core histone protein required for chr...
Histone H2B, core histone protein required for chr...
34(a)
34(a)
many ↔ many
many ↔ many
II(236492-236887) YBL002W
IV(914317-914712) YDR224C


ENSEMBL Gene Tree for H2BFM (if available)
TreeFam Gene Tree for H2BFM (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for H2BFM gene
HIST1H2BA2  H2BFWT2  
Selected SIMAP similar genes for H2BFM using alignment to 3 protein entries:     H2BFM_HUMAN (see all proteins) (see all similar genes):
ABCF2    HIST2H2BF    HIST1H2BL    HIST1H2BA    HIST1H2BB    HIST1H2BC
HIST1H2BD    HIST1H2BE    HIST1H2BF    HIST1H2BG    HIST1H2BI    HIST1H2BJ
HIST1H2BK    HIST1H2BM    HIST1H2BN    HIST2H2BE    HIST3H2BB    HIST1H2BH

H2BFM for paralogs           About GeneDecksing


1 Pseudogenes.org Pseudogene for H2BFM
PGOHUM00000241933


(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for H2BFM (see all 71)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr X posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1824236001,2
--103292722(+) TAGTTG/TTTTTA 1 -- us2k10--------
rs1891428161,2
--103292884(+) TCCCCA/TAAAGC 1 -- us2k10--------
rs1399249651,2
--103292980(+) GTCGTG/TTTGAC 1 -- us2k10--------
rs1496840611,2
--103292990(+) CCAATC/GAGAGA 1 -- us2k10--------
rs1908333871,2
--103293234(+) CCAGAA/GGTAGG 1 -- us2k10--------
rs1830281521,2
--103293322(+) AATAAA/CAAGTG 1 -- us2k10--------
rs1873603421,2
--103293354(+) TTCTCC/TTCAAT 1 -- us2k10--------
rs1918970071,2
--103293678(+) TTCTGC/GACTGT 1 -- us2k10--------
rs1455267781,2
C--103294112(+) GTTTCC/TCACAC 1 -- us2k10--------
rs1849292321,2
--103294291(+) AGACTC/TTGTGT 1 -- us2k10--------

HapMap Linkage Disequilibrium report for H2BFM (103268269 - 103297021 bp)

Structural Variations
     Database of Genomic Variants (DGV) 10 variations for H2BFM:    About this table    
Variant IDTypeSubtypePubMed ID
nsv508787CNV Insertion20534489
esv22275CNV Gain19812545
nsv519626CNV Gain19592680
dgv2459e1CNV Complex17122850
nsv469772CNV Complex16826518
dgv2460e1CNV Complex17122850
dgv63n47OTHER Inversion21111241
dgv5n1OTHER Inversion15895083
esv1007027OTHER Inversion20482838
nsv7453OTHER Inversion18451855

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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2 diseases for H2BFM:    About MalaCards
systemic lupus erythematosus    lupus erythematosus


H2BFM for disorders           About GeneDecksing


Export disorders for H2BFM gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for H2BFM gene integrated from 10 sources:
(articles sorted by number of sources associating them with H2BFM)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (Nature 2005)
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  3. A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)2 Dephoure N.... Gygi S.P. (Proc. Natl. Acad. Sci. U.S.A. 2008)
  4. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (amp 2008)
  5. Proteomic analysis of human O6-methylguanine-DNA methyltransferase by affinity chromatography and tandem mass spectrometry. (PubMed id 16226712)1 Niture S.K....Srivenugopal K.S. (Biochem. Biophys. Res. Commun. 2005)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 286436 HGNC: 27867 AceView: LOC286436 Ensembl:ENSG00000101812 euGenes: HUgn286436
ECgene: H2BFM Kegg: 286436 H-InvDB: H2BFM

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for H2BFM Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for H2BFM gene:
Search GeneIP for patents involving H2BFM

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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