H2BC13 (H2B clustered histone 13) - Rat Genome Database
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Pathways
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Gene: H2BC13 (H2B clustered histone 13) Homo sapiens
Analyze
Symbol: H2BC13
Name: H2B clustered histone 13
RGD ID: 1316667
HGNC Page HGNC
Description: Predicted to have DNA binding activity. Predicted to be involved in nucleosome assembly. Localizes to cytosol and nucleoplasm.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: dJ97D16.4; H2B histone family, member C; H2B/c; H2BFC; HIST1H2BL; histone 1, H2bl; histone cluster 1 H2B family member l; histone cluster 1, H2bl; histone H2B type 1-L; histone H2B.c
RGD Orthologs
Mouse
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 Ensembl627,807,444 - 27,807,931 (-)EnsemblGRCh38hg38GRCh38
GRCh38627,807,479 - 27,807,929 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37627,775,257 - 27,775,709 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36627,883,236 - 27,883,688 (-)NCBINCBI36hg18NCBI36
Build 34627,883,235 - 27,883,688NCBI
Celera629,381,295 - 29,381,747 (-)NCBI
Cytogenetic Map6p22.1NCBI
HuRef627,583,543 - 27,583,995 (-)NCBIHuRef
CHM1_1627,777,414 - 27,777,866 (-)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytosol  (IDA)
extracellular exosome  (HDA)
nucleoplasm  (IDA,TAS)
nucleosome  (NAS)
nucleus  (HDA,IDA)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9439656   PMID:9566873   PMID:10064132   PMID:11080476   PMID:11689053   PMID:12408966   PMID:12477932   PMID:12757711   PMID:14574404   PMID:14657027   PMID:15489334   PMID:15635413  
PMID:16283522   PMID:16307923   PMID:16319397   PMID:16627869   PMID:16713563   PMID:16916647   PMID:17314511   PMID:19615732   PMID:20458337   PMID:20800603   PMID:21081503   PMID:21113133  
PMID:21145461   PMID:21630459   PMID:21873635   PMID:22174317   PMID:22234250   PMID:22360420   PMID:22586326   PMID:22623428   PMID:23254330   PMID:23329831   PMID:23463506   PMID:25416818  
PMID:25921289   PMID:25963833   PMID:26186194   PMID:26209609   PMID:26318153   PMID:26496610   PMID:26725010   PMID:28514442   PMID:28515276   PMID:29507755   PMID:29845934   PMID:30009671  
PMID:30021884   PMID:30575818   PMID:30737378   PMID:30745168   PMID:31180492   PMID:31300519   PMID:31478661   PMID:31527615   PMID:31586073   PMID:31980649   PMID:32296183  


Genomics

Comparative Map Data
H2BC13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl627,807,444 - 27,807,931 (-)EnsemblGRCh38hg38GRCh38
GRCh38627,807,479 - 27,807,929 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37627,775,257 - 27,775,709 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36627,883,236 - 27,883,688 (-)NCBINCBI36hg18NCBI36
Build 34627,883,235 - 27,883,688NCBI
Celera629,381,295 - 29,381,747 (-)NCBI
Cytogenetic Map6p22.1NCBI
HuRef627,583,543 - 27,583,995 (-)NCBIHuRef
CHM1_1627,777,414 - 27,777,866 (-)NCBICHM1_1
H2bc7
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391323,757,934 - 23,758,381 (-)NCBIGRCm39mm39
GRCm381323,573,760 - 23,574,207 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1323,573,736 - 23,574,196 (-)EnsemblGRCm38mm10GRCm38
MGSCv371323,665,679 - 23,666,059 (-)NCBIGRCm37mm9NCBIm37
MGSCv361323,581,275 - 23,581,655 (-)NCBImm8
Celera1323,805,740 - 23,806,120 (-)NCBICelera
Cytogenetic Map13A3.1NCBI
H2BC13
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl3524,999,692 - 25,000,072 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.13524,999,666 - 25,000,124 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1

Position Markers
HIST1H2BL__6546  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37627,775,102 - 27,775,699UniSTSGRCh37
Build 36627,883,081 - 27,883,678RGDNCBI36
Celera629,381,140 - 29,381,737RGD
HuRef627,583,388 - 27,583,985UniSTS
UniSTS:480831  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37627,775,257 - 27,775,709UniSTSGRCh37
Build 36627,883,236 - 27,883,688RGDNCBI36
Celera629,381,295 - 29,381,747RGD
HuRef627,583,543 - 27,583,995UniSTS
UniSTS:490240  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37627,775,899 - 27,776,429UniSTSGRCh37
Build 36627,883,878 - 27,884,408RGDNCBI36
Celera629,381,937 - 29,382,467RGD
HuRef627,584,185 - 27,584,715UniSTS
UniSTS:483441  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37627,775,212 - 27,775,765UniSTSGRCh37
Celera629,381,250 - 29,381,803UniSTS
HuRef627,583,498 - 27,584,051UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:183
Count of miRNA genes:173
Interacting mature miRNAs:181
Transcripts:ENST00000377401
Prediction methods: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 visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High 1 2
Medium 12 10 3 32 4 8 6 2 16 6 3 1 1 3
Low 351 473 150 71 898 71 521 76 299 117 657 433 12 48 173 2 2
Below cutoff 1169 1435 697 219 678 149 1865 793 1525 143 561 667 70 461 1286 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000377401   ⟹   ENSP00000366618
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl627,807,444 - 27,807,931 (-)Ensembl
RefSeq Acc Id: NM_003519   ⟹   NP_003510
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38627,807,479 - 27,807,929 (-)NCBI
GRCh37627,775,257 - 27,775,709 (-)RGD
Build 36627,883,236 - 27,883,688 (-)NCBI Archive
Celera629,381,295 - 29,381,747 (-)RGD
HuRef627,583,543 - 27,583,995 (-)RGD
CHM1_1627,777,414 - 27,777,866 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_003510 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAN06695 (Get FASTA)   NCBI Sequence Viewer  
  BAG35050 (Get FASTA)   NCBI Sequence Viewer  
  CAB06035 (Get FASTA)   NCBI Sequence Viewer  
  EAX03106 (Get FASTA)   NCBI Sequence Viewer  
  Q99880 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_003510   ⟸   NM_003519
- UniProtKB: Q99880 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000366618   ⟸   ENST00000377401


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 6p22.1(chr6:27775494-27861432)x3 copy number gain Ductal breast carcinoma [RCV000207227] Chr6:27775494..27861432 [GRCh37]
Chr6:6p22.1		 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 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(chr6:27609423-28016099)x3 copy number gain not provided [RCV000745576] Chr6:27609423..28016099 [GRCh37]
Chr6:6p22.1		 benign
GRCh37/hg19 6p22.1(chr6:27645278-27902992)x3 copy number gain not provided [RCV000745579] Chr6:27645278..27902992 [GRCh37]
Chr6:6p22.1		 benign
GRCh37/hg19 6p22.1(chr6:27710165-27885437)x3 copy number gain not provided [RCV000745581] Chr6:27710165..27885437 [GRCh37]
Chr6:6p22.1		 benign
GRCh37/hg19 6p22.1(chr6:27713299-27872832)x3 copy number gain not provided [RCV000745582] Chr6:27713299..27872832 [GRCh37]
Chr6:6p22.1		 benign
GRCh37/hg19 6p22.1(chr6:27715243-27871553)x3 copy number gain not provided [RCV000745583] Chr6:27715243..27871553 [GRCh37]
Chr6:6p22.1		 benign
GRCh37/hg19 6p22.1(chr6:27715243-27877446)x3 copy number gain not provided [RCV000745584] Chr6:27715243..27877446 [GRCh37]
Chr6:6p22.1		 benign
GRCh37/hg19 6p22.1(chr6:27715243-27890631)x3 copy number gain not provided [RCV000745585] Chr6:27715243..27890631 [GRCh37]
Chr6:6p22.1		 benign
GRCh37/hg19 6p22.1(chr6:27715470-27886830)x3 copy number gain not provided [RCV000745586] Chr6:27715470..27886830 [GRCh37]
Chr6:6p22.1		 benign
GRCh37/hg19 6p22.1(chr6:27745142-27870358)x3 copy number gain not provided [RCV000745587] Chr6:27745142..27870358 [GRCh37]
Chr6:6p22.1		 benign
GRCh37/hg19 6p22.1(chr6:27616157-28011557)x3 copy number gain not provided [RCV001005790] Chr6:27616157..28011557 [GRCh37]
Chr6:6p22.1		 likely benign

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:4748 AgrOrtholog
COSMIC H2BC13 COSMIC
Ensembl Genes ENSG00000185130 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSP00000366618 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000377401 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.20.10 UniProtKB/Swiss-Prot
GTEx ENSG00000185130 GTEx
HGNC ID HGNC:4748 ENTREZGENE
Human Proteome Map H2BC13 Human Proteome Map
InterPro Histone-fold UniProtKB/Swiss-Prot
  Histone_H2A/H2B/H3 UniProtKB/Swiss-Prot
  Histone_H2B UniProtKB/Swiss-Prot
KEGG Report hsa:8340 UniProtKB/Swiss-Prot
NCBI Gene 8340 ENTREZGENE
OMIM 602800 OMIM
PANTHER PTHR23428 UniProtKB/Swiss-Prot
Pfam Histone UniProtKB/Swiss-Prot
PharmGKB PA29123 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.137594 ENTREZGENE
UniProt H2B1L_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary B2R5A3 UniProtKB/Swiss-Prot
  Q52LW9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-07-30 H2BC13  H2B clustered histone 13  HIST1H2BL  histone cluster 1 H2B family member l  Symbol and/or name change 5135510 APPROVED
2016-08-23 HIST1H2BL  histone cluster 1 H2B family member l    histone cluster 1, H2bl  Symbol and/or name change 5135510 APPROVED
2011-09-01 HIST1H2BL  histone cluster 1, H2bl  HIST1H2BL  histone cluster 1, H2bl  Symbol and/or name change 5135510 APPROVED