LOC102549061 (histone H2B type 1-N-like) - Rat Genome Database

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Gene: LOC102549061 (histone H2B type 1-N-like) Rattus norvegicus
Analyze
Symbol: LOC102549061
Name: histone H2B type 1-N-like
RGD ID: 7729692
Description: Predicted to be located in cytosol and nucleoplasm. Orthologous to several human genes including H2BC15 (H2B clustered histone 15) and H2BC3 (H2B clustered histone 3); INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; (+)-catechin (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: histone H2B type 1-B
RGD Orthologs
Human
Mouse
Bonobo
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21741,380,058 - 41,380,685 (+)NCBImRatBN7.2mRatBN7.2
Rnor_6.01743,627,872 - 43,628,518 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1743,627,930 - 43,628,310 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01745,482,285 - 45,482,903 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1741,011,236 - 41,011,883 (+)NCBICelera
Cytogenetic Map17p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytosol  (ISO)
nucleoplasm  (ISO)
nucleus  (ISO)

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16319397   PMID:19135898   PMID:21630459   PMID:22720776  


Genomics

Comparative Map Data
LOC102549061
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21741,380,058 - 41,380,685 (+)NCBImRatBN7.2mRatBN7.2
Rnor_6.01743,627,872 - 43,628,518 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1743,627,930 - 43,628,310 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01745,482,285 - 45,482,903 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1741,011,236 - 41,011,883 (+)NCBICelera
Cytogenetic Map17p11NCBI
H2BC3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38626,043,227 - 26,043,713 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl626,043,227 - 26,043,713 (-)EnsemblGRCh38hg38GRCh38
GRCh37626,043,455 - 26,043,941 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36626,151,434 - 26,151,864 (-)NCBINCBI36Build 36hg18NCBI36
Build 34626,151,433 - 26,151,864NCBI
Celera627,272,737 - 27,273,167 (-)NCBICelera
Cytogenetic Map6p22.2NCBI
HuRef625,986,523 - 25,986,953 (-)NCBIHuRef
CHM1_1626,045,731 - 26,046,161 (-)NCBICHM1_1
T2T-CHM13v2.0625,911,391 - 25,911,877 (-)NCBIT2T-CHM13v2.0
H2bc3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391323,930,717 - 23,931,206 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1323,930,717 - 23,931,224 (+)EnsemblGRCm39 Ensembl
GRCm381323,746,734 - 23,747,223 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1323,746,734 - 23,747,241 (+)EnsemblGRCm38mm10GRCm38
MGSCv371323,838,603 - 23,839,071 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361323,754,260 - 23,754,689 (+)NCBIMGSCv36mm8
Celera1323,978,505 - 23,978,973 (+)NCBICelera
Cytogenetic Map13A3.1NCBI
LOC100992900
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1626,536,783 - 26,537,242 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl626,536,827 - 26,537,207 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0625,878,922 - 25,879,458 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
LOC101974236
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049461,720,980 - 1,721,567 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366711,891,629 - 1,900,548 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049366711,900,150 - 1,900,560 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
H2BC3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1720,735,437 - 20,736,010 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
LOC103222019
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11746,211,585 - 46,222,696 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1746,211,652 - 46,212,029 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604425,979,231 - 25,979,737 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in LOC102549061
4 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17160781592Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17429913060781592Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17429913069599340Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17429913069599340Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17429913069599340Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17452803849528038Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17452803849528038Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17886846253868462Rat
1331765Hrtrt15Heart rate QTL 154.094heart pumping trait (VT:2000009)heart rate (CMO:0000002)171533061355836425Rat
1354640Scl32Serum cholesterol level QTL 325.4blood HDL cholesterol amount (VT:0000184)blood high density lipoprotein cholesterol level (CMO:0000052)171578159260781592Rat
1354659Scl68Serum cholesterol level QTL 683.9blood VLDL cholesterol amount (VT:0005144)blood very low density lipoprotein cholesterol level (CMO:0000648)171578159260781592Rat
7394837Memor18Memory QTL 18exploratory behavior trait (VT:0010471)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)171864018263640182Rat
1354628Stl13Serum triglyceride level QTL 133.8blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)172129303960781592Rat
70157Niddm32Non-insulin dependent diabetes mellitus QTL 324.34blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)172245492450909196Rat
61394Bp8Blood pressure QTL 82.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172308056759555013Rat
7488966Bp370Blood pressure QTL 3700.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172365318457246843Rat
12903978Cm118Cardiac mass QTL 1180.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)172365318468653184Rat
12903979Cm119Cardiac mass QTL 1190.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172365318468653184Rat
12903980Cm120Cardiac mass QTL 1200.002heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)172365318468653184Rat
12903981Am17Aortic mass QTL 170.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)172365318468653184Rat
1559055Bp278Blood pressure QTL 2780.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172365318468653184Rat
12903982Kidm70Kidney mass QTL 700.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)172365318470974005Rat
1354619Bp242Blood pressure QTL 2426.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172459934069599340Rat
1581512Cm55Cardiac mass QTL 552.80.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172702794956836890Rat
4889955Bss93Bone structure and strength QTL 934.4tibia size trait (VT:0100001)tibia cortical bone volume to tibia total bone volume ratio (CMO:0001727)172702794960463643Rat
2302377Scl61Serum cholesterol level QTL 614.36blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)172738994653481766Rat
8552928Pigfal9Plasma insulin-like growth factor 1 level QTL 99blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)172840914773409147Rat
9590107Sffal7Serum free fatty acids level QTL 74.810.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)172840914773409147Rat
10450503Bp386Blood pressure QTL 3860.28arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)173136839162109574Rat
2324621Coatc5Coat color QTL 5coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)173136839173951021Rat
2313854Bp343Blood pressure QTL 3433.9life span trait (VT:0005372)age at time of death (CMO:0001193)173199078450909196Rat
724549Niddm56Non-insulin dependent diabetes mellitus QTL 560.03blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)173199078476990784Rat
1354663Bvd5Brain ventricular dilatation QTL 53.510.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)173199078481292925Rat
1300148Bp192Blood pressure QTL 1923.47arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)173455084373951021Rat
724528Uae4Urinary albumin excretion QTL 44.90.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)173583708569599340Rat
2301412Kidm40Kidney mass QTL 400.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)173747984782479847Rat
2317054Aia12Adjuvant induced arthritis QTL 124.24joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)173828150983281509Rat
2317060Aia26Adjuvant induced arthritis QTL 263.22joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)173828150983281509Rat
1598871Memor5Memory QTL 55.3exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)174054004180387013Rat
1358295Aocep1Aortic cell protein QTL 16.10.00000071thoracic aorta cellular protein amount (VT:0010598)aortic cell percentage174099000585990005Rat
631497Bp98Blood pressure QTL 983.66arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)174135465160463643Rat


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 appendage
High 5 6
Medium 4 12 4 10 4 2 2 7 6 8 8 2
Low 3 31 28 25 3 25 6 7 48 21 31 3 6
Below cutoff 6 9 9 9 2 17 7 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000081719   ⟹   ENSRNOP00000070235
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1743,627,930 - 43,628,310 (+)Ensembl
RefSeq Acc Id: XM_006253978   ⟹   XP_006254040
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21741,380,058 - 41,380,685 (+)NCBI
Rnor_6.01743,627,872 - 43,628,518 (+)NCBI
Rnor_5.01745,482,285 - 45,482,903 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001395954 (Get FASTA)   NCBI Sequence Viewer  
  XP_006254040 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_006254040   ⟸   XM_006253978
- UniProtKB: A0A0G2JXE0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000070235   ⟸   ENSRNOT00000081719

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2JXE0-F1-model_v2 AlphaFold A0A0G2JXE0 1-126 view protein structure

Transcriptome

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

Promoters
RGD ID:13700458
Promoter ID:EPDNEW_R10980
Type:single initiation site
Name:LOC102549061_1
Description:histone H2B type 1-N-like
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_6.01743,627,889 - 43,627,949EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:7729692 AgrOrtholog
BioCyc Gene G2FUF-9382 BioCyc
Ensembl Genes ENSRNOG00000059949 Ensembl
NCBI Gene LOC102549061 ENTREZGENE
PhenoGen LOC102549061 PhenoGen
UniProt A0A0G2JXE0 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-12-18 LOC102549061  histone H2B type 1-N-like      Symbol and Name status set to provisional 70820 PROVISIONAL