H2bl1 (H2B.L histone variant 1) - Rat Genome Database

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Gene: H2bl1 (H2B.L histone variant 1) Rattus norvegicus
Analyze
No known orthologs.
Symbol: H2bl1 (Ensembl: LOC684444)
Name: H2B.L histone variant 1 (Ensembl:similar to HIStone family member (his-41))
RGD ID: 1590323
Description: Predicted to enable DNA binding activity. Predicted to be located in nucleus. Predicted to be part of nucleosome.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: histone H2B subacrosomal; histone H2B subacrosomal variant; LOC684444; similar to HIStone family member (his-41); uncharacterized protein LOC684444
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8232,121,294 - 32,121,769 (-)NCBIGRCr8
mRatBN7.2230,387,109 - 30,387,584 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl230,386,982 - 30,387,633 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0229,247,748 - 29,248,259 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl229,247,803 - 29,248,174 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0248,419,221 - 48,419,717 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera226,417,122 - 26,417,633 (-)NCBICelera
Cytogenetic Map2q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleosome  (IEA)
nucleus  (IEA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. GOA pipeline RGD automated data pipeline

Genomics

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:106
Count of miRNA genes:95
Interacting mature miRNAs:99
Transcripts:ENSRNOT00000071167
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631682Bp115Blood pressure QTL 1154.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2137410502Rat
738010Lnnr3Liver neoplastic nodule remodeling QTL 32.94liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)2141244106Rat
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)25873687102844969Rat
1600379Mcs18Mammary carcinoma susceptibility QTL 182.6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2788777242804738Rat
738012Anxrr3Anxiety related response QTL 33.8exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)2902351954023519Rat
10755430Coatc6Coat color QTL 60.02576coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)21159110056591100Rat
1578664Bmd9Bone mineral QTL density 95femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)21185206249003364Rat
731184Mamtr4Mammary tumor resistance QTL 40.0003mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)21649174061491740Rat
1357990Ael1Aortic elastin QTL 13.10.00091aorta elastin amount (VT:0003905)aortic elastin21907682564076825Rat
731167Glom4Glomerulus QTL 42.40.0082kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)22030467265304672Rat
2300168Bmd47Bone mineral density QTL 476.60.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)22066244865662448Rat
10402051Gdil2Gastrointestinal dilation QTL 2enteric ganglion morphology trait (VT:0001045)length of intestine affected by colonic aganglionosis to total length of colon ratio (CMO:0001836)22490385374786777Rat
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)225413423143657569Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)22691781781754745Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)22691781781754745Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)22691781781754745Rat
1354603Bp243Blood pressure QTL 2433.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)226917817127469484Rat
2290453Scl55Serum cholesterol level QTL 552.83blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)226917817136917119Rat
1331764Bp205Blood pressure QTL 2053.476arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)22699957143154682Rat
1643006Pain1Pain QTL 13.630.005mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)22699957148268661Rat
9590095Sffal3Serum free fatty acids level QTL 36.780.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)22715716072157160Rat
1300160Hrtrt3Heart rate QTL 33.62heart pumping trait (VT:2000009)absolute change in heart rate (CMO:0000534)22997159351729300Rat


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

circulatory system endocrine system hemolymphoid system integumental system musculoskeletal system nervous system reproductive system respiratory system appendage
High
Medium 7
Low 1 1
Below cutoff 1 1 1 3 5 1 6 1 3

Sequence


RefSeq Acc Id: ENSRNOT00000071167   ⟹   ENSRNOP00000065543
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl230,386,982 - 30,387,633 (-)Ensembl
Rnor_6.0 Ensembl229,247,803 - 29,248,174 (-)Ensembl
RefSeq Acc Id: NM_001409105   ⟹   NP_001396034
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8232,121,294 - 32,121,769 (-)NCBI
mRatBN7.2230,387,109 - 30,387,584 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001396034 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM10160 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000065543
  ENSRNOP00000065543.1
RefSeq Acc Id: ENSRNOP00000065543   ⟸   ENSRNOT00000071167
RefSeq Acc Id: NP_001396034   ⟸   NM_001409105
- UniProtKB: M0R7V6 (UniProtKB/TrEMBL),   A6I552 (UniProtKB/TrEMBL)
Protein Domains
Histone H2A/H2B/H3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R7V6-F1-model_v2 AlphaFold M0R7V6 1-123 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13691101
Promoter ID:EPDNEW_R1619
Type:multiple initiation site
Name:LOC684444_1
Description:similar to HIStone family member (his-41)
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0229,248,207 - 29,248,267EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1590323 AgrOrtholog
BioCyc Gene G2FUF-54704 BioCyc
Ensembl Genes ENSRNOG00000045818 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000071167 ENTREZGENE
  ENSRNOT00000071167.2 UniProtKB/TrEMBL
Gene3D-CATH 1.10.20.10 UniProtKB/TrEMBL
InterPro Histone-fold UniProtKB/TrEMBL
  Histone_core_D UniProtKB/TrEMBL
  Histone_H2B UniProtKB/TrEMBL
KEGG Report rno:684444 UniProtKB/TrEMBL
NCBI Gene 684444 ENTREZGENE
PANTHER HISTONE H2B VARIANT L1 UniProtKB/TrEMBL
  PTHR23428 UniProtKB/TrEMBL
Pfam Histone UniProtKB/TrEMBL
PhenoGen H2bl1 PhenoGen
PRINTS HISTONEH2B UniProtKB/TrEMBL
RatGTEx ENSRNOG00000045818 RatGTEx
SMART H2B UniProtKB/TrEMBL
Superfamily-SCOP Histone-fold UniProtKB/TrEMBL
UniProt A6I552 ENTREZGENE, UniProtKB/TrEMBL
  M0R7V6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-09-19 H2bl1  H2B.L histone variant 1  LOC684444  similar to HIStone family member (his-41)  Symbol and Name Changed 1299863 APPROVED
2006-11-20 LOC684444  similar to HIStone family member (his-41)      Symbol and Name status set to provisional 70820 PROVISIONAL