H2BC12 (H2B clustered histone 12) - Rat Genome Database
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Gene: H2BC12 (H2B clustered histone 12) Homo sapiens
Analyze
Symbol: H2BC12
Name: H2B clustered histone 12
RGD ID: 1353528
HGNC Page HGNC
Description: Predicted to have DNA binding activity. Involved in antimicrobial humoral immune response mediated by antimicrobial peptide; defense response to other organism; and killing of cells of other organism. Localizes to cytosol; extracellular space; and nucleoplasm.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: H2B histone family, member T; H2B K; H2B/S; H2BFAiii; H2BFT; H2BK; HIRA-interacting protein 1; HIST1H2BK; histone 1, H2bk; histone cluster 1 H2B family member k; histone cluster 1, H2bk; histone family member; histone H2B type 1-K; MGC131989
RGD Orthologs
Mouse
Rat
Bonobo
Dog
Green Monkey
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 Ensembl627,146,418 - 27,146,798 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl627,146,361 - 27,146,855 (-)EnsemblGRCh38hg38GRCh38
GRCh38627,138,293 - 27,146,858 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37627,106,072 - 27,114,637 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36627,214,052 - 27,222,598 (-)NCBINCBI36hg18NCBI36
Build 34627,214,051 - 27,222,598NCBI
Celera628,712,071 - 28,720,638 (-)NCBI
Cytogenetic Map6p22.1NCBI
HuRef626,914,133 - 26,922,700 (-)NCBIHuRef
CHM1_1627,108,394 - 27,116,950 (-)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
cytosol  (IDA)
extracellular space  (IDA)
nucleoplasm  (IDA,TAS)
nucleosome  (IEA)
nucleus  (HDA,IDA)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:1768865   PMID:8620898   PMID:9566873   PMID:9710638   PMID:10064132   PMID:10384058   PMID:11080476   PMID:11689053   PMID:11859126   PMID:12408966   PMID:12477932   PMID:12757711  
PMID:12860195   PMID:14574404   PMID:14657027   PMID:15019208   PMID:15489334   PMID:15635413   PMID:15951514   PMID:16283522   PMID:16307923   PMID:16319397   PMID:16344560   PMID:16457587  
PMID:16627869   PMID:16713563   PMID:16916647   PMID:19666485   PMID:19738201   PMID:21081503   PMID:21081666   PMID:21630459   PMID:21873635   PMID:21907836   PMID:22898364   PMID:23254330  
PMID:23463506   PMID:25963833   PMID:26167880   PMID:26318153   PMID:26485645   PMID:26979993   PMID:27025967   PMID:27248496   PMID:27545878   PMID:27591049   PMID:28330616   PMID:28378594  
PMID:28977666   PMID:29162697   PMID:29507755   PMID:29509190   PMID:29777862   PMID:29845934   PMID:30092116   PMID:30209976   PMID:30745168   PMID:30804502   PMID:30890647   PMID:31180492  
PMID:31239290   PMID:31253590   PMID:31300519   PMID:31586073   PMID:31732153   PMID:31759698   PMID:31980649   PMID:32529326   PMID:32780723  


Genomics

Comparative Map Data
H2BC12
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl627,146,418 - 27,146,798 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl627,146,361 - 27,146,855 (-)EnsemblGRCh38hg38GRCh38
GRCh38627,138,293 - 27,146,858 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37627,106,072 - 27,114,637 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36627,214,052 - 27,222,598 (-)NCBINCBI36hg18NCBI36
Build 34627,214,051 - 27,222,598NCBI
Celera628,712,071 - 28,720,638 (-)NCBI
Cytogenetic Map6p22.1NCBI
HuRef626,914,133 - 26,922,700 (-)NCBIHuRef
CHM1_1627,108,394 - 27,116,950 (-)NCBICHM1_1
H2bc12
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391322,219,991 - 22,220,490 (+)NCBIGRCm39mm39
GRCm381322,035,821 - 22,036,320 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1322,035,870 - 22,036,345 (+)EnsemblGRCm38mm10GRCm38
MGSCv371322,127,756 - 22,128,136 (+)NCBIGRCm37mm9NCBIm37
MGSCv361322,043,352 - 22,043,732 (+)NCBImm8
Celera1322,308,331 - 22,308,711 (+)NCBICelera
Cytogenetic Map13A3.1NCBI
H2bc12
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01744,527,421 - 44,527,801 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1744,527,421 - 44,527,801 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01758,942,757 - 58,943,137 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41750,118,776 - 50,119,156 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1753,975,515 - 53,975,895 (+)NCBICelera
Cytogenetic Map17p11NCBI
LOC100981154
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1627,633,226 - 27,641,882 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl627,641,404 - 27,641,784 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0626,971,577 - 26,980,171 (-)NCBIMhudiblu_PPA_v0panPan3
H2BC15
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl3525,031,264 - 25,031,644 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.13525,031,173 - 25,035,326 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
LOC103221972
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11745,363,038 - 45,371,506 (+)NCBI
ChlSab1.1 Ensembl1745,363,109 - 45,363,486 (+)Ensembl

Position Markers
WI-11733  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37627,106,087 - 27,106,215UniSTSGRCh37
Build 36627,214,066 - 27,214,194RGDNCBI36
Celera628,712,086 - 28,712,214RGD
Cytogenetic Map6p21.33UniSTS
HuRef626,914,148 - 26,914,276UniSTS
GeneMap99-GB4 RH Map6118.22UniSTS
Whitehead-RH Map6160.2UniSTS
NCBI RH Map6353.4UniSTS
RH79884  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37627,107,415 - 27,107,520UniSTSGRCh37
Build 36627,215,394 - 27,215,499RGDNCBI36
Celera628,713,414 - 28,713,519RGD
Cytogenetic Map6p21.33UniSTS
HuRef626,915,476 - 26,915,581UniSTS
HIST1H2AH__7487  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37627,115,017 - 27,115,546UniSTSGRCh37
Build 36627,222,996 - 27,223,525RGDNCBI36
Celera628,721,018 - 28,721,547RGD
HuRef626,923,080 - 26,923,609UniSTS
UniSTS:480645  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37627,114,908 - 27,115,344UniSTSGRCh37
Build 36627,222,887 - 27,223,323RGDNCBI36
Celera628,720,909 - 28,721,345RGD
HuRef626,922,971 - 26,923,407UniSTS
UniSTS:482788  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372144,985,120 - 44,985,500UniSTSGRCh37
GRCh37627,114,197 - 27,114,577UniSTSGRCh37
Build 36627,222,176 - 27,222,556RGDNCBI36
Celera2130,091,648 - 30,092,028UniSTS
Celera628,720,198 - 28,720,578RGD
HuRef2130,353,673 - 30,354,053UniSTS
HuRef626,922,260 - 26,922,640UniSTS
UniSTS:483466  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37627,114,861 - 27,115,317UniSTSGRCh37
Build 36627,222,840 - 27,223,296RGDNCBI36
Celera628,720,862 - 28,721,318RGD
HuRef626,922,924 - 26,923,380UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:516
Count of miRNA genes:342
Interacting mature miRNAs:356
Transcripts:ENST00000356950, ENST00000396891
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


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 1 2 2 12 1 1 34 1
Medium 2406 2643 1667 610 1928 453 3586 1140 1717 348 1404 1599 169 1202 2052 4
Low 25 339 54 12 7 11 768 1051 1985 69 8 8 1 2 736
Below cutoff 1 5 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000356950   ⟹   ENSP00000349430
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl627,146,361 - 27,146,855 (-)Ensembl
RefSeq Acc Id: NM_001312653   ⟹   NP_001299582
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38627,146,361 - 27,146,855 (-)NCBI
CHM1_1627,116,453 - 27,116,950 (-)NCBI
Sequence:
RefSeq Acc Id: NM_080593   ⟹   NP_542160
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38627,138,293 - 27,146,858 (-)NCBI
GRCh37627,106,072 - 27,114,637 (-)RGD
Build 36627,214,052 - 27,222,598 (-)NCBI Archive
Celera628,712,071 - 28,720,638 (-)RGD
HuRef626,914,133 - 26,922,700 (-)RGD
CHM1_1627,108,394 - 27,116,950 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_542160   ⟸   NM_080593
- UniProtKB: O60814 (UniProtKB/Swiss-Prot),   A0A024RCL8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001299582   ⟸   NM_001312653
- UniProtKB: O60814 (UniProtKB/Swiss-Prot),   A0A024RCL8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000349430   ⟸   ENST00000356950
Protein Domains
Histone

Promoters
RGD ID:6804304
Promoter ID:HG_KWN:52630
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:ENST00000377459,   NM_080593
Position:
Human AssemblyChrPosition (strand)Source
Build 36627,221,786 - 27,223,437 (+)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 6p22.2-22.1(chr6:26280579-28727313)x3 copy number gain See cases [RCV000133692] Chr6:26280579..28727313 [GRCh38]
Chr6:26280807..28695090 [GRCh37]
Chr6:26388786..28803069 [NCBI36]
Chr6:6p22.2-22.1		 uncertain significance
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 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 6p22.2-22.1(chr6:26545571-27115102)x3 copy number gain Ductal breast carcinoma [RCV000207103] Chr6:26545571..27115102 [GRCh37]
Chr6:6p22.2-22.1		 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 6p22.2-22.1(chr6:26928203-27344831)x3 copy number gain not provided [RCV000682658] Chr6:26928203..27344831 [GRCh37]
Chr6:6p22.2-22.1		 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 6p22.1(chr6:27093821-27158033)x3 copy number gain not provided [RCV000745567] Chr6:27093821..27158033 [GRCh37]
Chr6:6p22.1		 benign
NM_003495.3(H4C9):c.306C>T (p.Gly102=) single nucleotide variant not provided [RCV000961690] Chr6:27139614 [GRCh38]
Chr6:27107393 [GRCh37]
Chr6:6p22.1		 benign

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:13954 AgrOrtholog
COSMIC H2BC12 COSMIC
Ensembl Genes ENSG00000197903 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSP00000349430 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000356950 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.20.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000197903 GTEx
HGNC ID HGNC:13954 ENTREZGENE
Human Proteome Map H2BC12 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:85236 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 85236 ENTREZGENE
OMIM 615045 OMIM
PANTHER PTHR23428 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Histone UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA134955134 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
UniProt A0A024RCL8 ENTREZGENE, UniProtKB/TrEMBL
  H2B1K_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary A8K7P7 UniProtKB/Swiss-Prot
  Q2VPI7 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-07-30 H2BC12  H2B clustered histone 12  HIST1H2BK  histone cluster 1 H2B family member k  Symbol and/or name change 5135510 APPROVED
2016-08-23 HIST1H2BK  histone cluster 1 H2B family member k  HIST1H2BK  histone cluster 1, H2bk  Symbol and/or name change 5135510 APPROVED