Hmgn2-ps4 (high mobility group nucleosomal binding domain 2, pseudogene 4) - Rat Genome Database

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Gene: Hmgn2-ps4 (high mobility group nucleosomal binding domain 2, pseudogene 4) Rattus norvegicus
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Symbol: Hmgn2-ps4
Name: high mobility group nucleosomal binding domain 2, pseudogene 4
RGD ID: 2322336
Description: Predicted to enable nucleosomal DNA binding activity. Predicted to be located in nucleus. Predicted to be part of chromatin; INTERACTS WITH 17beta-estradiol; bisphenol A.
Type: pseudo (Ensembl: protein-coding)
RefSeq Status: INFERRED
Previously known as: hypothetical protein LOC100360316; LOC100360316; non-histone chromosomal protein HMG-17
Related Functional Gene: Hmgn2  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81635,644,108 - 35,645,333 (+)NCBIGRCr8
mRatBN7.21630,633,287 - 30,634,512 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1630,622,845 - 30,634,512 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01633,942,592 - 33,943,784 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5152,195,361 - 152,198,813 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01633,775,171 - 33,776,361 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41633,979,260 - 33,979,532 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1630,616,185 - 30,617,377 (+)NCBICelera
Cytogenetic Map16p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
chromatin  (IEA)
nucleus  (IEA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Variants

.
Variants in Hmgn2-ps4
13 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16130836262Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16132139025Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133418960Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139533930Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139533930Rat
631561Hcuc2Hepatic copper content QTL 22.8liver copper amount (VT:0003065)liver total copper weight (CMO:0001507)16139533949Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16143534949Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16144588133Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16144977551Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683223646053497Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683223659492508Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683223659492508Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683223659492508Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683223659492508Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16338015043025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760943025077Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16422760943025077Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16422760946975965Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16422760948972724Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16422760949227609Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16422760960252231Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)161900443575226532Rat
2302057Pia29Pristane induced arthritis QTL 293.60.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)162173597566735975Rat
8694453Bw172Body weight QTL 1728.330.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)162432551369325513Rat
6903294Stl30Serum triglyceride level QTL 302.60.0013blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)162515279370152793Rat


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000082953   ⟹   ENSRNOP00000074978
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5146,192,126 - 146,194,873 (-)Ensembl
Rnor_6.0 Ensembl5152,195,361 - 152,198,813 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000095450   ⟹   ENSRNOP00000082813
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5146,192,130 - 146,195,521 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000096926   ⟹   ENSRNOP00000078282
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1630,622,845 - 30,634,512 (+)Ensembl
RefSeq Acc Id: XM_003751587   ⟹   XP_003751635
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21630,633,338 - 30,634,512 (+)NCBI
Rnor_6.01633,942,592 - 33,943,784 (+)NCBI
Rnor_5.01633,775,171 - 33,776,361 (+)NCBI
Sequence:
Protein Sequences
Ensembl Protein ENSRNOP00000074978.2
Reference Protein Sequences
RefSeq Acc Id: XP_003751635   ⟸   XM_003751587
- Sequence:
RefSeq Acc Id: ENSRNOP00000074978   ⟸   ENSRNOT00000082953
RefSeq Acc Id: ENSRNOP00000082813   ⟸   ENSRNOT00000095450
RefSeq Acc Id: ENSRNOP00000078282   ⟸   ENSRNOT00000096926

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2322336 AgrOrtholog
BioCyc Gene G2FUF-11559 BioCyc
Ensembl Genes ENSRNOG00000051615 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000066721 Ensembl
Ensembl Transcript ENSRNOT00000082953.2 UniProtKB/TrEMBL
InterPro HMGN_fam UniProtKB/TrEMBL
NCBI Gene 100360316 ENTREZGENE
PANTHER NON-HISTONE CHROMOSOMAL PROTEIN HMG-17 UniProtKB/TrEMBL
  NONHISTONE CHROMOSOMAL PROTEIN HMG UniProtKB/TrEMBL
Pfam HMG14_17 UniProtKB/TrEMBL
PhenoGen Hmgn2-ps4 PhenoGen
PRINTS NONHISHMG17 UniProtKB/TrEMBL
PROSITE HMG14_17 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000051615 RatGTEx
  ENSRNOG00000066721 RatGTEx
SMART HMG17 UniProtKB/TrEMBL
UniProt A0A0G2K9F6_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-07-15 Hmgn2-ps4  high mobility group nucleosomal binding domain 2, pseudogene 4  LOC100360316  hypothetical protein LOC100360316  Name and Symbol changed 629549 APPROVED
2010-05-06 LOC100360316  hypothetical protein LOC100360316      Symbol and Name status set to provisional 70820 PROVISIONAL