Hmgn5 (high mobility group nucleosome binding domain 5) - Rat Genome Database

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Gene: Hmgn5 (high mobility group nucleosome binding domain 5) Rattus norvegicus
Analyze
Symbol: Hmgn5
Name: high mobility group nucleosome binding domain 5
RGD ID: 6497694
Description: Predicted to enable chromatin binding activity. Predicted to be involved in negative regulation of apoptotic process; positive regulation of cell population proliferation; and positive regulation of gene expression. Predicted to act upstream of or within chromatin organization; glutathione metabolic process; and regulation of transcription by RNA polymerase II. Predicted to be located in mitochondrion and nucleoplasm. Predicted to be part of chromatin. Orthologous to human HMGN5 (high mobility group nucleosome binding domain 5); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 5-aza-2'-deoxycytidine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: high mobility group nucleosome-binding domain-containing protein 5; high mobility group nucleosome-binding domain-containing protein 5-like; LOC100910616; Nsbp1; nucleosome-binding protein 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X78,161,439 - 78,170,613 (-)NCBIGRCr8
mRatBN7.2X74,085,871 - 74,094,488 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX74,085,875 - 74,094,441 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX75,599,179 - 75,607,745 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X79,072,736 - 79,081,073 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X76,638,296 - 76,646,633 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X80,134,557 - 80,142,902 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX80,134,557 - 80,142,902 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X80,311,866 - 80,320,211 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
CeleraX75,355,864 - 75,364,432 (-)NCBICelera
Cytogenetic MapXq22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
chromatin  (IEA)
mitochondrion  (ISO)
nucleoplasm  (ISO)
nucleus  (IEA,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:8889548   PMID:10692437   PMID:12477932   PMID:15489334   PMID:19160411   PMID:20531280   PMID:21278158   PMID:22681889   PMID:24392144  


Genomics

Comparative Map Data
Hmgn5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X78,161,439 - 78,170,613 (-)NCBIGRCr8
mRatBN7.2X74,085,871 - 74,094,488 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX74,085,875 - 74,094,441 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX75,599,179 - 75,607,745 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X79,072,736 - 79,081,073 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X76,638,296 - 76,646,633 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X80,134,557 - 80,142,902 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX80,134,557 - 80,142,902 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X80,311,866 - 80,320,211 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
CeleraX75,355,864 - 75,364,432 (-)NCBICelera
Cytogenetic MapXq22NCBI
HMGN5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X81,113,699 - 81,201,913 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX81,113,699 - 81,201,913 (-)EnsemblGRCh38hg38GRCh38
GRCh37X80,369,198 - 80,457,412 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X80,255,856 - 80,263,772 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X80,175,344 - 80,183,261NCBI
CeleraX80,609,351 - 80,697,598 (-)NCBICelera
Cytogenetic MapXq21.1NCBI
HuRefX73,949,827 - 74,038,119 (-)NCBIHuRef
CHM1_1X80,262,599 - 80,350,840 (-)NCBICHM1_1
T2T-CHM13v2.0X79,547,434 - 79,635,633 (-)NCBIT2T-CHM13v2.0
Hmgn5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X108,048,143 - 108,056,986 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX108,048,140 - 108,057,010 (-)EnsemblGRCm39 Ensembl
GRCm38X109,004,537 - 109,013,380 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX109,004,534 - 109,013,404 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X106,199,876 - 106,208,719 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X105,207,254 - 105,216,078 (-)NCBIMGSCv36mm8
CeleraX95,826,022 - 95,834,509 (-)NCBICelera
Cytogenetic MapXDNCBI
cM MapX47.92NCBI
Hmgn5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555291,118,706 - 1,125,596 (-)NCBIChiLan1.0ChiLan1.0
HMGN5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X80,580,338 - 80,668,236 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X80,583,949 - 80,671,847 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X70,180,585 - 70,268,545 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X80,285,151 - 80,373,078 (-)NCBIpanpan1.1PanPan1.1panPan2
Hmgn5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X56,287,079 - 56,341,448 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049365472,607,491 - 2,614,037 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HMGN5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1X64,541,310 - 64,617,345 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
HMGN5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X70,103,170 - 70,201,472 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX70,102,034 - 70,111,019 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606710,969,170 - 11,056,590 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hmgn5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462483630,417 - 38,253 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Hmgn5
21 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:46
Count of miRNA genes:40
Interacting mature miRNAs:40
Transcripts:ENSRNOT00000048744, ENSRNOT00000071650
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat


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 musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium
Low 2 1 1 1
Below cutoff 1 5 12 12 3 12 2 21 18 11 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000071650   ⟹   ENSRNOP00000064623
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX80,134,557 - 80,142,902 (-)Ensembl
RefSeq Acc Id: NM_001276434   ⟹   NP_001263363
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X78,161,439 - 78,170,007 (-)NCBI
mRatBN7.2X74,085,871 - 74,094,441 (-)NCBI
Rnor_6.0X80,134,557 - 80,142,902 (-)NCBI
Rnor_5.0X80,311,866 - 80,320,211 (-)NCBI
CeleraX75,355,864 - 75,364,432 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099388   ⟹   XP_038955316
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X78,161,439 - 78,170,613 (-)NCBI
mRatBN7.2X74,085,871 - 74,094,488 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001263363 (Get FASTA)   NCBI Sequence Viewer  
  XP_038955316 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI68165 (Get FASTA)   NCBI Sequence Viewer  
  B4F777 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000047671.5
  ENSRNOP00000064623
  ENSRNOP00000064623.2
  ENSRNOP00000082504.1
Reference Protein Sequences
RefSeq Acc Id: NP_001263363   ⟸   NM_001276434
- UniProtKB: A0A8I5ZU29 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000064623   ⟸   ENSRNOT00000071650
RefSeq Acc Id: XP_038955316   ⟸   XM_039099388
- Peptide Label: isoform X1
- UniProtKB: B4F777 (UniProtKB/Swiss-Prot),   A6IV78 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R5F8-F1-model_v2 AlphaFold M0R5F8 1-402 view protein structure

Transcriptome

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

Promoters
RGD ID:13701909
Promoter ID:EPDNEW_R12433
Type:multiple initiation site
Name:Hmgn5_1
Description:high mobility group nucleosome binding domain 5
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_6.0X80,142,808 - 80,142,868EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:6497694 AgrOrtholog
BioCyc Gene G2FUF-1878 BioCyc
Ensembl Genes ENSRNOG00000029078 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000049192 Ensembl
  ENSRNOG00000065214 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000048744.6 UniProtKB/TrEMBL
  ENSRNOT00000071650.3 UniProtKB/TrEMBL
  ENSRNOT00000099107.1 UniProtKB/TrEMBL
InterPro HMGN5 UniProtKB/TrEMBL
  HMGN_fam UniProtKB/TrEMBL
NCBI Gene LOC100910616 ENTREZGENE
PANTHER HIGH MOBILITY GROUP NUCLEOSOME-BINDING DOMAIN-CONTAINING PROTEIN 5 UniProtKB/TrEMBL
  PTHR23145 UniProtKB/TrEMBL
Pfam HMG14_17 UniProtKB/TrEMBL
PhenoGen Hmgn5 PhenoGen
PRINTS NONHISHMG17 UniProtKB/TrEMBL
PROSITE HMG14_17 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000029078 RatGTEx
  ENSRNOG00000049192 RatGTEx
  ENSRNOG00000065214 RatGTEx
SMART HMG17 UniProtKB/TrEMBL
UniProt A0A8I5ZU29 ENTREZGENE, UniProtKB/TrEMBL
  A0A8L2UM24_RAT UniProtKB/TrEMBL
  A6IV78 ENTREZGENE, UniProtKB/TrEMBL
  B4F777 ENTREZGENE
  M0R5F8_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-08-05 Hmgn5  high mobility group nucleosome-binding domain-containing protein 5-like  LOC100910616  high mobility group nucleosome-binding domain-containing protein 5-like  Symbol changed 629549 APPROVED
2013-08-05 Hmgn5  high mobility group nucleosome binding domain 5  Hmgn5  high mobility group nucleosome-binding domain-containing protein 5-like  Name changed 629549 APPROVED
2012-07-05 LOC100910616  high mobility group nucleosome-binding domain-containing protein 5-like      Symbol and Name status set to provisional 70820 PROVISIONAL