H2BC9 (H2B clustered histone 9) - Rat Genome Database
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Gene: H2BC9 (H2B clustered histone 9) Homo sapiens
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Symbol: H2BC9
Name: H2B clustered histone 9
RGD ID: 1343164
HGNC Page HGNC
Description: Exhibits STAT family protein binding activity and ubiquitin-like protein ligase binding activity. Predicted to be involved in nucleosome assembly. Localizes to cytosol; nucleoplasm; and protein-containing complex.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: H2B histone family, member J; H2B/j; H2BFJ; HIST1H2BH; histone 1, H2bh; histone cluster 1 H2B family member h; histone cluster 1, H2bh; histone H2B type 1-H; histone H2B.j
RGD Orthologs
Rat
Pig
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 Ensembl626,251,651 - 26,253,710 (+)EnsemblGRCh38hg38GRCh38
GRCh38626,251,614 - 26,252,075 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37626,251,848 - 26,261,783 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36626,359,858 - 26,360,282 (+)NCBINCBI36hg18NCBI36
Build 34626,359,857 - 26,360,282NCBI
Celera627,481,186 - 27,481,610 (+)NCBI
Cytogenetic Map6p22.2NCBI
HuRef626,194,885 - 26,195,309 (+)NCBIHuRef
CHM1_1626,254,031 - 26,254,455 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9119399   PMID:9439656   PMID:9566873   PMID:11080476   PMID:11689053   PMID:12408966   PMID:12477932   PMID:12757711   PMID:14574404   PMID:14657027   PMID:16283522   PMID:16307923  
PMID:16319397   PMID:16457587   PMID:16627869   PMID:16713563   PMID:16916647   PMID:20458337   PMID:21081503   PMID:21630459   PMID:21873635   PMID:22174317   PMID:22623428   PMID:23254330  
PMID:23463506   PMID:24705354   PMID:25963833   PMID:26318153   PMID:26479788   PMID:27976729   PMID:28977666   PMID:29507755   PMID:29845934   PMID:30021884   PMID:30745168   PMID:30804502  
PMID:31091453   PMID:31300519   PMID:31980649   PMID:32296183   PMID:32814053  


Genomics

Comparative Map Data
H2BC9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl626,251,651 - 26,253,710 (+)EnsemblGRCh38hg38GRCh38
GRCh38626,251,614 - 26,252,075 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37626,251,848 - 26,261,783 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36626,359,858 - 26,360,282 (+)NCBINCBI36hg18NCBI36
Build 34626,359,857 - 26,360,282NCBI
Celera627,481,186 - 27,481,610 (+)NCBI
Cytogenetic Map6p22.2NCBI
HuRef626,194,885 - 26,195,309 (+)NCBIHuRef
CHM1_1626,254,031 - 26,254,455 (+)NCBICHM1_1
H2bc9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01744,519,815 - 44,520,269 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1744,519,860 - 44,520,240 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01758,950,308 - 58,971,114 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41750,111,215 - 50,111,595 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1753,983,051 - 53,983,502 (+)NCBICelera
Cytogenetic Map17p11NCBI
LOC110261671
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1721,582,043 - 21,582,522 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1

Position Markers
RH77902  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37626,252,132 - 26,252,364UniSTSGRCh37
Build 36626,360,111 - 26,360,343RGDNCBI36
Celera627,481,439 - 27,481,671RGD
Cytogenetic Map6p21.3UniSTS
Cytogenetic Map6p22.2UniSTS
HuRef626,195,138 - 26,195,370UniSTS
GeneMap99-GB4 RH Map6106.35UniSTS
RH80097  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37626,252,259 - 26,252,413UniSTSGRCh37
Build 36626,360,238 - 26,360,392RGDNCBI36
Celera627,481,566 - 27,481,720RGD
Cytogenetic Map6p21.3UniSTS
Cytogenetic Map6p22.2UniSTS
HuRef626,195,265 - 26,195,419UniSTS
GeneMap99-GB4 RH Map6105.61UniSTS
HIST1H2BH_8796  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37626,251,881 - 26,252,430UniSTSGRCh37
Build 36626,359,860 - 26,360,409RGDNCBI36
Celera627,481,188 - 27,481,737RGD
HuRef626,194,887 - 26,195,436UniSTS
RH47053  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37626,250,305 - 26,250,438UniSTSGRCh37
Build 36626,358,284 - 26,358,417RGDNCBI36
Celera627,479,612 - 27,479,745RGD
Cytogenetic Map6p21.3UniSTS
Cytogenetic Map6p22.2UniSTS
HuRef626,193,311 - 26,193,444UniSTS
GeneMap99-GB4 RH Map6105.28UniSTS
UniSTS:481058  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37626,250,373 - 26,250,835UniSTSGRCh37
Build 36626,358,352 - 26,358,814RGDNCBI36
Celera627,479,680 - 27,480,142RGD
HuRef626,193,379 - 26,193,841UniSTS
UniSTS:483863  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37626,251,879 - 26,252,303UniSTSGRCh37
Build 36626,359,858 - 26,360,282RGDNCBI36
Celera627,481,186 - 27,481,610RGD
HuRef626,194,885 - 26,195,309UniSTS


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 adipose tissue appendage entire extraembryonic component
High 2 4
Medium 82 35 27 12 169 11 215 23 38 26 146 132 10 6 1 1
Low 800 903 661 187 1377 42 678 112 595 74 759 918 149 195 344 1
Below cutoff 1252 1568 703 164 198 152 2169 1237 2508 75 263 340 12 668 1465 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000619466   ⟹   ENSP00000479169
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl626,251,651 - 26,253,710 (+)Ensembl
RefSeq Acc Id: NM_003524   ⟹   NP_003515
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38626,251,614 - 26,252,075 (+)NCBI
GRCh37626,251,848 - 26,261,783 (+)NCBI
Build 36626,359,858 - 26,360,282 (+)NCBI Archive
Celera627,481,186 - 27,481,610 (+)RGD
HuRef626,194,885 - 26,195,309 (+)RGD
CHM1_1626,254,031 - 26,254,455 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_003515   ⟸   NM_003524
- UniProtKB: Q93079 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000479169   ⟸   ENST00000619466


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(chr6:26178542-26670193)x3 copy number gain not provided [RCV000682657] Chr6:26178542..26670193 [GRCh37]
Chr6:6p22.2
uncertain significance
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(chr6:25896585-26287389)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(chr6:26238509-26329714)x1 copy number loss not provided [RCV001005788] Chr6:26238509..26329714 [GRCh37]
Chr6:6p22.2
likely benign
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:4755 AgrOrtholog
COSMIC H2BC9 COSMIC
Ensembl Genes ENSG00000275713 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSP00000479169 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000619466 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.20.10 UniProtKB/Swiss-Prot
GTEx ENSG00000275713 GTEx
HGNC ID HGNC:4755 ENTREZGENE
Human Proteome Map H2BC9 Human Proteome Map
InterPro Histone-fold UniProtKB/Swiss-Prot
  Histone_H2A/H2B/H3 UniProtKB/Swiss-Prot
  Histone_H2B UniProtKB/Swiss-Prot
KEGG Report hsa:8345 UniProtKB/Swiss-Prot
NCBI Gene 8345 ENTREZGENE
OMIM 602806 OMIM
PANTHER PTHR23428 UniProtKB/Swiss-Prot
Pfam Histone UniProtKB/Swiss-Prot
PharmGKB PA29130 PharmGKB
PRINTS HISTONEH2B UniProtKB/Swiss-Prot
PROSITE HISTONE_H2B UniProtKB/Swiss-Prot
SMART H2B UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47113 UniProtKB/Swiss-Prot
UniGene Hs.247815 ENTREZGENE
UniProt H2B1H_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary B2R541 UniProtKB/Swiss-Prot
  Q4VB74 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-07-30 H2BC9  H2B clustered histone 9  HIST1H2BH  histone cluster 1 H2B family member h  Symbol and/or name change 5135510 APPROVED
2016-08-23 HIST1H2BH  histone cluster 1 H2B family member h    histone cluster 1, H2bh  Symbol and/or name change 5135510 APPROVED