Hmgb2l1 (high mobility group box 2-like 1) - Rat Genome Database

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Gene: Hmgb2l1 (high mobility group box 2-like 1) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Hmgb2l1 (Ensembl: Hmgb2-ps6)
Name: high mobility group box 2-like 1 (Ensembl:high mobility group box 2, pseudogene 6)
RGD ID: 1564519
Description: Predicted to enable DNA binding activity. Predicted to be involved in several processes, including DNA topological change; regulation of gene expression; and response to bacterium. Predicted to be located in several cellular components, including chromosome; extracellular space; and perinuclear region of cytoplasm. Orthologous to human HMGB2 (high mobility group box 2); INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; alpha-Zearalanol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: high mobility group protein B2; HMG2; LOC498072; RGD1564519; similar to High mobility group protein 2 (HMG-2)
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81160,721,545 - 60,722,608 (-)NCBIGRCr8
mRatBN7.21147,252,583 - 47,253,646 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl119,409,539 - 19,410,168 (-)EnsemblmRatBN7.2 Ensembl
mRatBN7.2 Ensembl1147,252,569 - 47,253,669 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1636,312,191 - 36,314,676 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01639,723,520 - 39,726,005 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01635,943,321 - 35,945,805 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01149,708,038 - 49,709,128 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1636,077,617 - 36,080,191 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1149,708,407 - 49,709,039 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01152,886,262 - 52,887,348 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41148,276,349 - 48,277,406 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1146,954,912 - 46,955,998 (-)NCBICelera
Cytogenetic Map11q12NCBI
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

Cellular Component

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
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Comprehensive gene review and curation RGD comprehensive gene curation

Genomics

Variants

.
Variants in Hmgb2l1
3 total Variants

QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11169446234Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113491804179918041Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
4889859Pur28Proteinuria QTL 2819.50.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)114545932375190161Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
10755497Bp388Blood pressure QTL 3882.76arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)111945620576331918Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112295940367959403Rat
1300130Rf20Renal function QTL 204.44kidney glomerulus integrity trait (VT:0010546)kidney glomerulus diameter (CMO:0001166)112952841860324829Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)11104193166113562Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113123913478851519Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114094618882566702Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114428575982566702Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112767241082846715Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112328045668280456Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112328045668280456Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)112952841882566702Rat
1641927Alcrsp10Alcohol response QTL 10alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)11843667453436674Rat


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSRNOT00000017635   ⟹   ENSRNOP00000017635
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1632,710,658 - 32,713,140 (-)Ensembl
Rnor_6.0 Ensembl1636,077,617 - 36,080,191 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000036049   ⟹   ENSRNOP00000060587
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl119,409,539 - 19,410,168 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000046874   ⟹   ENSRNOP00000039358
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1147,252,569 - 47,253,669 (-)Ensembl
Rnor_6.0 Ensembl1149,708,407 - 49,709,039 (-)Ensembl
RefSeq Acc Id: NM_001329881   ⟹   NP_001316810
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81160,721,545 - 60,722,608 (-)NCBI
mRatBN7.21147,252,583 - 47,253,646 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001316810 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAA12350 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000017635.4
  ENSRNOP00000039358.2
  ENSRNOP00000060587.2
  ENSRNOP00055016856
  ENSRNOP00060008407
  ENSRNOP00065004563
Ensembl Acc Id: ENSRNOP00000039358   ⟸   ENSRNOT00000046874
Ensembl Acc Id: ENSRNOP00000017635   ⟸   ENSRNOT00000017635
RefSeq Acc Id: NP_001316810   ⟸   NM_001329881
- UniProtKB: Q5FVP0 (UniProtKB/Swiss-Prot),   P52925 (UniProtKB/Swiss-Prot),   A6KIU7 (UniProtKB/TrEMBL),   D3ZN59 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000060587   ⟸   ENSRNOT00000036049
Protein Domains
HMG box

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P52925-F1-model_v2 AlphaFold P52925 1-210 view protein structure

Transcriptome

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

Promoters
RGD ID:13698124
Promoter ID:EPDNEW_R8643
Type:single initiation site
Name:Hmgb2_1
Description:high mobility group box 2
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_6.01149,709,127 - 49,709,187EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564519 AgrOrtholog
BioCyc Gene G2FUF-21481 BioCyc
Ensembl Genes ENSRNOG00000013167 Ensembl, UniProtKB/Swiss-Prot
  ENSRNOG00000026462 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000033321 Ensembl, UniProtKB/Swiss-Prot
  ENSRNOG00055012275 UniProtKB/Swiss-Prot
  ENSRNOG00060006879 UniProtKB/Swiss-Prot
  ENSRNOG00065004463 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000017635.7 UniProtKB/Swiss-Prot
  ENSRNOT00000036049.7 UniProtKB/TrEMBL
  ENSRNOT00000046874.3 UniProtKB/Swiss-Prot
  ENSRNOT00055020881 UniProtKB/Swiss-Prot
  ENSRNOT00060011259 UniProtKB/Swiss-Prot
  ENSRNOT00065006504 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.30.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro HMG_box_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMG_box_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMG_boxA_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMGB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29395 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  rno:498072 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 498072 ENTREZGENE
PANTHER HIGH MOBILITY GROUP PROTEIN B2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HIGH MOBILITY GROUP PROTEIN DSP1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam HMG_box UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMG_box_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Hmgb2l1 PhenoGen
PRINTS HIGHMOBLTY12 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE HMG_BOX_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMG_BOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000013167 RatGTEx
  ENSRNOG00000026462 RatGTEx
  ENSRNOG00000033321 RatGTEx
  ENSRNOG00055012275 RatGTEx
  ENSRNOG00060006879 RatGTEx
  ENSRNOG00065004463 RatGTEx
SMART HMG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP HMG-box UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
UniProt A6KIU7 ENTREZGENE, UniProtKB/TrEMBL
  D3ZN59 ENTREZGENE, UniProtKB/TrEMBL
  HMGB2_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q5FVP0 ENTREZGENE
UniProt Secondary Q5FVP0 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-11-25 Hmgb2l1  high mobility group box 2-like 1  RGD1564519  similar to High mobility group protein 2 (HMG-2)  Name and Symbol changed 629549 APPROVED
2008-04-30 RGD1564519  similar to High mobility group protein 2 (HMG-2)   RGD1564519_predicted  similar to High mobility group protein 2 (HMG-2) (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1564519_predicted  similar to High mobility group protein 2 (HMG-2) (predicted)  LOC498072  similar to High mobility group protein 2 (HMG-2)  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC498072  similar to High mobility group protein 2 (HMG-2)      Symbol and Name status set to provisional 70820 PROVISIONAL