Hmgb1l5 (high mobility group box 1 like 5) - Rat Genome Database

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Gene: Hmgb1l5 (high mobility group box 1 like 5) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Hmgb1l5 (Ensembl: AABR07029613.1)
Name: high mobility group box 1 like 5
RGD ID: 1563668
Description: Predicted to be involved in chromatin remodeling. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in amyotrophic lateral sclerosis. Orthologous to human HMGB1 (high mobility group box 1) and HMGB1P1 (high mobility group box 1 pseudogene 1); PARTICIPATES IN base excision repair pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: high mobility group protein B1-like; LOC497907; RGD1563668; similar to High mobility group protein 1 (HMG-1)
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81040,269,191 - 40,270,053 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1040,268,954 - 40,270,059 (-)EnsemblGRCr8
GRCr8 Ensembl1971,943,082 - 71,944,278 (-)EnsemblGRCr8
mRatBN7.21039,768,658 - 39,769,408 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1955,045,869 - 55,047,145 (-)EnsemblmRatBN7.2
mRatBN7.2 Ensembl1039,768,658 - 39,769,293 (-)EnsemblmRatBN7.2
Rnor_6.01040,994,237 - 40,994,990 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01040,824,637 - 40,825,387 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41041,063,864 - 41,092,666 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1039,096,330 - 39,097,083 (-)NCBICelera
Cytogenetic Map10q22NCBI
JBrowse:




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

Cellular Component
chromosome  (IEA)
nucleus  (IBA,IEA)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
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 Hmgb1l5
57 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:495
Count of miRNA genes:229
Interacting mature miRNAs:267
Transcripts:ENSRNOT00000058640
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61441Btemp1Thermal response to stress QTL 14body temperature trait (VT:0005535)core body temperature (CMO:0001036)103589345164140567Rat
152025229Scl83Serum cholesterol level QTL 834.33blood cholesterol amount (VT:0000180)103621155669161158Rat
1578779Tcas10Tongue tumor susceptibility QTL 103.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)103179628176796281Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101577675460776754Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102702353598502431Rat
2293669Bmd33Bone mineral density QTL 334.50.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)102744378772443787Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)103550938391417879Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10125055464349221Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
2293679Bmd30Bone mineral density QTL 303.50.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)102744378772443787Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10687714251877142Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)101993920764939207Rat
61332Eau3Experimental allergic uveoretinitis QTL 30.004uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)101803578263035782Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1092219745922197Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)10210370847103708Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101866841963668419Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102183375861843633Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102895035373950353Rat
1358897Stresp6Stress response QTL 64.170.022blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)103589326364653589Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102980091064653589Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102744378772443787Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101499153586964295Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014991535107556066Rat
2293652Bmd22Bone mineral density QTL 224.90.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)102744378772443787Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102293137391127454Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10666092373950353Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10589381150893811Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10589381150893811Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)101465354159653541Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101553301273695498Rat
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)102466212373695339Rat
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102702353561843633Rat
2298480Eau7Experimental allergic uveoretinitis QTL 70.0049uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)103550938380509383Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10589381150893811Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)102980091091417879Rat
2298495Eae23Experimental allergic encephalomyelitis QTL 2316.93nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis duration (CMO:0001424)101617552561175525Rat
2313087Bmd80Bone mineral density QTL 803.20.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)102011061465110614Rat
1354614Hpcl1Hepatic cholesterol level QTL 13.3liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)103589326352293000Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)102758722696099902Rat
2289985Bp305Blood pressure QTL 305arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102907697874076978Rat
631532Cm50Cardiac mass QTL 506.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)101803578263035782Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
2293705Bmd25Bone mineral density QTL 257.10.0001femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)102744378772443787Rat
1600371Mcs21Mammary carcinoma susceptibility QTL 213mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)102937704652699134Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014991535107713808Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103112911376129113Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10686461896620484Rat
12880050Am10Aortic mass QTL 100.016aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)103950348784503487Rat
6893342Cm78Cardiac mass QTL 780.10.88heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)103550938388177745Rat
2313055Bw96Body weight QTL 963.60.0001body mass (VT:0001259)body weight (CMO:0000012)102011061465110614Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102702353599451848Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
7 8 38 32 28 16 10 16 6 79 30 28 26 26 12 3 3

Sequence


Ensembl Acc Id: ENSRNOT00000058640   ⟹   ENSRNOP00000055435
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1040,268,954 - 40,270,059 (-)Ensembl
mRatBN7.2 Ensembl1039,768,658 - 39,769,293 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000086591   ⟹   ENSRNOP00000073890
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1971,943,082 - 71,944,278 (-)Ensembl
mRatBN7.2 Ensembl1955,045,869 - 55,047,145 (-)Ensembl
RefSeq Acc Id: XM_039087830   ⟹   XP_038943758
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81040,269,191 - 40,270,053 (-)NCBI
mRatBN7.21039,768,658 - 39,769,408 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001417261 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943758 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000055435
  ENSRNOP00000055435.3
  ENSRNOP00000073890.1
RefSeq Acc Id: XP_038943758   ⟸   XM_039087830
Ensembl Acc Id: ENSRNOP00000055435   ⟸   ENSRNOT00000058640
Ensembl Acc Id: ENSRNOP00000073890   ⟸   ENSRNOT00000086591
Protein Domains
HMG box

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZC69-F1-model_v2 AlphaFold D3ZC69 1-211 view protein structure

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:1563668 AgrOrtholog
BioCyc Gene G2FUF-25072 BioCyc
Ensembl Genes ENSRNOG00000038478 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000051482 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000058640 ENTREZGENE
  ENSRNOT00000058640.6 UniProtKB/TrEMBL
  ENSRNOT00000086591.3 UniProtKB/TrEMBL
Gene3D-CATH 1.10.30.10 UniProtKB/TrEMBL
InterPro HMG_box_dom UniProtKB/TrEMBL
  HMG_box_dom_sf UniProtKB/TrEMBL
  HMG_boxA_CS UniProtKB/TrEMBL
  HMGB UniProtKB/TrEMBL
NCBI Gene 497907 ENTREZGENE
PANTHER HIGH MOBILITY GROUP PROTEIN B1 UniProtKB/TrEMBL
  HIGH MOBILITY GROUP PROTEIN B1 UniProtKB/TrEMBL
  HIGH MOBILITY GROUP PROTEIN DSP1 UniProtKB/TrEMBL
Pfam HMG_box UniProtKB/TrEMBL
  HMG_box_2 UniProtKB/TrEMBL
PhenoGen Hmgb1l5 PhenoGen
PRINTS HIGHMOBLTY12 UniProtKB/TrEMBL
PROSITE HMG_BOX_1 UniProtKB/TrEMBL
  HMG_BOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000038478 RatGTEx
  ENSRNOG00000051482 RatGTEx
SMART HMG UniProtKB/TrEMBL
Superfamily-SCOP SSF47095 UniProtKB/TrEMBL
UniProt A0A0G2K6P4 ENTREZGENE, UniProtKB/TrEMBL
  A6KJ57 ENTREZGENE, UniProtKB/TrEMBL
  D3ZC69 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-09-19 Hmgb1l5  high mobility group box 1 like 5  RGD1563668  similar to High mobility group protein 1 (HMG-1)  Symbol and Name Changed 1299863 APPROVED
2008-04-30 RGD1563668  similar to High mobility group protein 1 (HMG-1)   RGD1563668_predicted  similar to High mobility group protein 1 (HMG-1) (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-10 RGD1563668_predicted  similar to High mobility group protein 1 (HMG-1) (predicted)    similar to High mobility group protein 1 (HMG-1) (Amphoterin) (Heparin-binding protein p30) (predicted)  Name updated 1299863 APPROVED
2006-03-07 RGD1563668_predicted  similar to High mobility group protein 1 (HMG-1) (Amphoterin) (Heparin-binding protein p30) (predicted)  LOC497907  similar to High mobility group protein 1 (HMG-1) (Amphoterin) (Heparin-binding protein p30)  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC497907  similar to High mobility group protein 1 (HMG-1) (Amphoterin) (Heparin-binding protein p30)      Symbol and Name status set to provisional 70820 PROVISIONAL