H2BC4 (H2B clustered histone 4) - Rat Genome Database
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Gene: H2BC4 (H2B clustered histone 4) Homo sapiens
Analyze
Symbol: H2BC4
Name: H2B clustered histone 4
RGD ID: 1344863
HGNC Page HGNC
Description: Exhibits identical protein binding activity. Involved in antimicrobial humoral immune response mediated by antimicrobial peptide and defense response to other organism. Localizes to cytosol; extracellular space; and nucleoplasm.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: dJ221C16.3; H2B histone family, member L; H2B.1; H2B/a; H2B/g; H2B/h; H2B/k; H2B/l; H2BC10; H2BC6; H2BC7; H2BC8; H2BFL; HIST1H2BC; HIST1H2BE; HIST1H2BF; HIST1H2BG; HIST1H2BI; histone 1, H2bc; histone cluster 1 H2B family member c; histone cluster 1, H2bc; histone H2B type 1-C/E/F/G/I; histone H2B.1 A; histone H2B.a; histone H2B.g; histone H2B.h; histone H2B.k; histone H2B.l; MGC104246
RGD Orthologs
Mouse
Bonobo
Dog
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl626,114,873 - 26,123,926 (-)EnsemblGRCh38hg38GRCh38
GRCh38626,113,170 - 26,123,926 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37626,113,389 - 26,124,266 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36626,231,674 - 26,232,111 (-)NCBINCBI36hg18NCBI36
Build 34626,231,673 - 26,232,111NCBI
Celera627,352,959 - 27,353,396 (-)NCBI
Cytogenetic Map6p22.2NCBI
HuRef626,066,734 - 26,067,171 (-)NCBIHuRef
CHM1_1626,125,932 - 26,126,369 (-)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Pipeline to import KEGG annotations from KEGG into RGD
2. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:422550   PMID:9119399   PMID:9149941   PMID:9439656   PMID:9566873   PMID:11080476   PMID:11689053   PMID:12408966   PMID:12477932   PMID:12860195   PMID:14657027   PMID:16522924  
PMID:17353931   PMID:19343720   PMID:19414484   PMID:20348541   PMID:20458337   PMID:21081503   PMID:21630459   PMID:21873635   PMID:21907836   PMID:22082156   PMID:22174317   PMID:22623428  
PMID:23084401   PMID:23376485   PMID:25416956   PMID:25609649   PMID:25954010   PMID:25963833   PMID:26237645   PMID:26318153   PMID:26381412   PMID:26496610   PMID:27402160   PMID:27462807  
PMID:28031328   PMID:28190768   PMID:29104064   PMID:29128334   PMID:29229926   PMID:29507755   PMID:29735542   PMID:29845934   PMID:29859926   PMID:30532072   PMID:30745168   PMID:30997501  
PMID:31239290   PMID:31586073   PMID:32296183  


Genomics

Comparative Map Data
H2BC4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl626,114,873 - 26,123,926 (-)EnsemblGRCh38hg38GRCh38
GRCh38626,113,170 - 26,123,926 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37626,113,389 - 26,124,266 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36626,231,674 - 26,232,111 (-)NCBINCBI36hg18NCBI36
Build 34626,231,673 - 26,232,111NCBI
Celera627,352,959 - 27,353,396 (-)NCBI
Cytogenetic Map6p22.2NCBI
HuRef626,066,734 - 26,067,171 (-)NCBIHuRef
CHM1_1626,125,932 - 26,126,369 (-)NCBICHM1_1
H2bc4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391323,868,182 - 23,876,805 (+)NCBIGRCm39mm39
GRCm381323,684,199 - 23,692,480 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1323,684,199 - 23,692,908 (+)EnsemblGRCm38mm10GRCm38
MGSCv371323,776,068 - 23,784,349 (+)NCBIGRCm37mm9NCBIm37
MGSCv361323,691,664 - 23,699,945 (+)NCBImm8
Celera1323,915,492 - 23,923,779 (+)NCBICelera
Cytogenetic Map13A3.1NCBI
LOC100989841
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1626,606,149 - 26,616,991 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl626,616,435 - 26,616,815 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0625,948,480 - 25,959,296 (-)NCBIMhudiblu_PPA_v0panPan3
H2BC4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl3524,066,399 - 24,066,779 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.13524,062,068 - 24,066,934 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1

Position Markers
RH46761  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37626,124,438 - 26,124,576UniSTSGRCh37
Build 36626,232,417 - 26,232,555RGDNCBI36
Celera627,353,702 - 27,353,840RGD
Cytogenetic Map6p22.1UniSTS
HuRef626,067,477 - 26,067,615UniSTS
GeneMap99-GB4 RH Map6105.5UniSTS
A008J29  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37626,124,435 - 26,124,699UniSTSGRCh37
Build 36626,232,414 - 26,232,678RGDNCBI36
Celera627,353,699 - 27,353,963RGD
Cytogenetic Map6p22.1UniSTS
HuRef626,067,474 - 26,067,738UniSTS
GeneMap99-GB4 RH Map6105.5UniSTS
UniSTS:486876  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37626,123,702 - 26,124,132UniSTSGRCh37
Build 36626,231,681 - 26,232,111RGDNCBI36
Celera627,352,966 - 27,353,396RGD
HuRef626,066,741 - 26,067,171UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system visual system appendage entire extraembryonic component pharyngeal arch
High 7 10
Medium 105 48 113 79 392 80 79 53 72 75 287 221 17 2 4 11 4
Low 350 63 299 233 1581 241 738 146 347 343 375 526 17 1 4
Below cutoff 73 13 37 23 255 26 69 32 64 56 56 155 3 3

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000314332   ⟹   ENSP00000321744
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl626,114,873 - 26,123,910 (-)Ensembl
RefSeq Acc Id: ENST00000396984   ⟹   ENSP00000380180
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl626,123,356 - 26,123,926 (-)Ensembl
RefSeq Acc Id: NM_001381989   ⟹   NP_001368918
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38626,113,170 - 26,123,926 (-)NCBI
RefSeq Acc Id: NM_003526   ⟹   NP_003517
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38626,123,467 - 26,123,926 (-)NCBI
GRCh37626,123,695 - 26,124,132 (-)RGD
Build 36626,231,674 - 26,232,111 (-)NCBI Archive
Celera627,352,959 - 27,353,396 (-)RGD
HuRef626,066,734 - 26,067,171 (-)RGD
CHM1_1626,125,932 - 26,126,369 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_003517   ⟸   NM_003526
- UniProtKB: P62807 (UniProtKB/Swiss-Prot),   B2R4S9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001368918   ⟸   NM_001381989
RefSeq Acc Id: ENSP00000321744   ⟸   ENST00000314332
RefSeq Acc Id: ENSP00000380180   ⟸   ENST00000396984
Protein Domains
Histone

Promoters
RGD ID:6872248
Promoter ID:EPDNEW_H9289
Type:initiation region
Name:HIST1H2BC_1
Description:histone cluster 1 H2B family member c
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38626,123,926 - 26,123,986EPDNEW
RGD ID:6804325
Promoter ID:HG_KWN:52581
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:ENST00000396980,   UC003NGK.2,   UC003NGN.1,   UC003NGO.1,   UC003NGP.1
Position:
Human AssemblyChrPosition (strand)Source
Build 36626,231,281 - 26,233,277 (-)MPROMDB

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 6p22.3-21.33(chr6:18120520-30767516)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052180]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052180]|See cases [RCV000052180] Chr6:18120520..30767516 [GRCh38]
Chr6:18120751..30735293 [GRCh37]
Chr6:18228730..30843272 [NCBI36]
Chr6:6p22.3-21.33
pathogenic
GRCh38/hg38 6p25.2-21.33(chr6:3224310-30657190)x3 copy number gain See cases [RCV000138956] Chr6:3224310..30657190 [GRCh38]
Chr6:3224544..30624967 [GRCh37]
Chr6:3169543..30732946 [NCBI36]
Chr6:6p25.2-21.33
pathogenic
GRCh38/hg38 6p22.2(chr6:25991402-26280693)x3 copy number gain See cases [RCV000139521] Chr6:25991402..26280693 [GRCh38]
Chr6:25991630..26280921 [GRCh37]
Chr6:26099609..26388900 [NCBI36]
Chr6:6p22.2
likely benign
GRCh38/hg38 6p25.3-12.3(chr6:156974-46789291)x3 copy number gain See cases [RCV000143497] Chr6:156974..46789291 [GRCh38]
Chr6:156974..46757028 [GRCh37]
Chr6:101974..46864987 [NCBI36]
Chr6:6p25.3-12.3
pathogenic
GRCh37/hg19 6p22.2(chr6:26104332-26365573)x4 copy number gain Ductal breast carcinoma [RCV000207323] Chr6:26104332..26365573 [GRCh37]
Chr6:6p22.2
uncertain significance
GRCh37/hg19 6p22.2(chr6:25839165-26536884)x4 copy number gain See cases [RCV000447433] Chr6:25839165..26536884 [GRCh37]
Chr6:6p22.2
uncertain significance
GRCh37/hg19 6p25.3-q27(chr6:156975-170919482)x3 copy number gain See cases [RCV000512067] Chr6:156975..170919482 [GRCh37]
Chr6:6p25.3-q27
pathogenic
GRCh37/hg19 6p25.3-q27(chr6:156975-170919482) copy number gain See cases [RCV000510595] Chr6:156975..170919482 [GRCh37]
Chr6:6p25.3-q27
pathogenic
GRCh37/hg19 6p22.2(chr6:25851789-26319486)x3 copy number gain not provided [RCV000682656] Chr6:25851789..26319486 [GRCh37]
Chr6:6p22.2
uncertain significance
GRCh37/hg19 6p25.3-q27(chr6:108666-170980171)x3 copy number gain not provided [RCV000745403] Chr6:108666..170980171 [GRCh37]
Chr6:6p25.3-q27
pathogenic
GRCh37/hg19 6p25.3-q27(chr6:60107-171054786)x3 copy number gain not provided [RCV000745400] Chr6:60107..171054786 [GRCh37]
Chr6:6p25.3-q27
pathogenic
GRCh37/hg19 6p25.3-q27(chr6:165632-170919470)x3 copy number gain not provided [RCV000745404] Chr6:165632..170919470 [GRCh37]
Chr6:6p25.3-q27
pathogenic
GRCh37/hg19 6p22.2(chr6:26110314-26338056)x3 copy number gain not provided [RCV000745546] Chr6:26110314..26338056 [GRCh37]
Chr6:6p22.2
benign
GRCh37/hg19 6p22.2(chr6:26110961-26219744)x3 copy number gain not provided [RCV000745547] Chr6:26110961..26219744 [GRCh37]
Chr6:6p22.2
benign
GRCh38/hg38 6p22.2(chr6:25991391-26116829)x3 copy number gain See cases [RCV000140950] Chr6:25991391..26116829 [GRCh38]
Chr6:25991619..26117057 [GRCh37]
Chr6:26099598..26225036 [NCBI36]
Chr6:6p22.2
likely benign
GRCh37/hg19 6p22.2(chr6:26067079-26207758)x1 copy number loss not provided [RCV000849592] Chr6:26067079..26207758 [GRCh37]
Chr6:6p22.2
uncertain significance
GRCh37/hg19 6p22.2(chr6:25896585-26287389)x4 copy number gain not provided [RCV000845790] Chr6:25896585..26287389 [GRCh37]
Chr6:6p22.2
uncertain significance
GRCh37/hg19 6p22.2(chr6:25996066-26303969)x3 copy number gain not provided [RCV000847447] Chr6:25996066..26303969 [GRCh37]
Chr6:6p22.2
uncertain significance
GRCh37/hg19 6p22.2(chr6:26067580-26306202)x3 copy number gain not provided [RCV000849663] Chr6:26067580..26306202 [GRCh37]
Chr6:6p22.2
uncertain significance
GRCh37/hg19 6p22.2(chr6:26046566-26670193)x3 copy number gain not provided [RCV001258882] Chr6:26046566..26670193 [GRCh37]
Chr6:6p22.2
uncertain significance
GRCh37/hg19 6p22.2(chr6:26090243-26265667)x3 copy number gain not provided [RCV001258883] Chr6:26090243..26265667 [GRCh37]
Chr6:6p22.2
uncertain significance

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:4757 AgrOrtholog
COSMIC H2BC4 COSMIC
Ensembl Genes ENSG00000180596 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSG00000273802 UniProtKB/Swiss-Prot
  ENSG00000274290 UniProtKB/Swiss-Prot
  ENSG00000277224 UniProtKB/Swiss-Prot
  ENSG00000278588 UniProtKB/Swiss-Prot
Ensembl Protein ENSP00000321744 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000348924 UniProtKB/Swiss-Prot
  ENSP00000366962 UniProtKB/Swiss-Prot
  ENSP00000380180 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000445633 UniProtKB/Swiss-Prot
  ENSP00000483237 UniProtKB/Swiss-Prot
  ENSP00000489317 UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000314332 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000356530 UniProtKB/Swiss-Prot
  ENST00000377733 UniProtKB/Swiss-Prot
  ENST00000396984 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000541790 UniProtKB/Swiss-Prot
  ENST00000614097 UniProtKB/Swiss-Prot
  ENST00000634910 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.20.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000180596 GTEx
  ENSG00000273802 GTEx
  ENSG00000274290 GTEx
  ENSG00000277224 GTEx
  ENSG00000278588 GTEx
HGNC ID HGNC:4757 ENTREZGENE
Human Proteome Map H2BC4 Human Proteome Map
InterPro Histone-fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Histone_H2A/H2B/H3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Histone_H2B UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:3017 UniProtKB/Swiss-Prot
  hsa:8339 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  hsa:8343 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  hsa:8344 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  hsa:8346 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  hsa:8347 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 8347 ENTREZGENE
OMIM 602847 OMIM
PANTHER PTHR23428 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Histone UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA29132 PharmGKB
PRINTS HISTONEH2B UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE HISTONE_H2B UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART H2B UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47113 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Hs.658713 ENTREZGENE
  Hs.726509 ENTREZGENE
UniProt B2R4S9 ENTREZGENE, UniProtKB/TrEMBL
  H2B1C_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary P02278 UniProtKB/Swiss-Prot
  Q3B872 UniProtKB/Swiss-Prot
  Q4VB69 UniProtKB/Swiss-Prot
  Q93078 UniProtKB/Swiss-Prot
  Q93080 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-07-30 H2BC4  H2B clustered histone 4  HIST1H2BC  histone cluster 1 H2B family member c  Symbol and/or name change 5135510 APPROVED
2016-08-23 HIST1H2BC  histone cluster 1 H2B family member c    histone cluster 1, H2bc  Symbol and/or name change 5135510 APPROVED