Hmgb1l2 (high mobility group box 1 like 2) - Rat Genome Database

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Gene: Hmgb1l2 (high mobility group box 1 like 2) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Hmgb1l2
Name: high mobility group box 1 like 2
RGD ID: 11468204
Description: Predicted to enable DNA binding activity. Predicted to be involved in DNA geometric change and regulation of transcription by RNA polymerase II. Predicted to be located in several cellular components, including chromosome; endoplasmic reticulum-Golgi intermediate compartment; and nucleus.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: high mobility group protein B1 pseudogene; high mobility group protein B1-like; LOC108349189
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X112,467,960 - 112,469,220 (+)NCBIGRCr8
mRatBN7.2X107,671,273 - 107,672,015 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX107,671,272 - 107,672,535 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0X115,351,012 - 115,351,755 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX115,351,114 - 115,351,755 (+)EnsemblRnor6.0rn6Rnor6.0
CeleraX107,067,851 - 107,068,594 (+)NCBICelera
Cytogenetic MapXq34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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.

Genomics

Variants

.
Variants in Hmgb1l2
6 total Variants

QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598872Memor14Memory QTL 144.5exploratory 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)X93956491138956491Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X103312877148312877Rat
1598809Memor15Memory QTL 154.4exploratory 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)X103312877148312877Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX100567703150256146Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
724551Glom1Glomerulus QTL 12.80.0004kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)X75294106120294106Rat
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


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 2 28 80 58 57 37 16 37 6 136 58 67 31 42 20

Sequence


Ensembl Acc Id: ENSRNOT00000047553   ⟹   ENSRNOP00000043407
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX115,351,114 - 115,351,755 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000108561   ⟹   ENSRNOP00000084450
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX107,671,272 - 107,672,535 (+)Ensembl
RefSeq Acc Id: XM_039100280   ⟹   XP_038956208
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X112,467,960 - 112,469,220 (+)NCBI
mRatBN7.2X107,671,273 - 107,672,015 (+)NCBI
Protein Sequences
Protein RefSeqs XP_038956208 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000069851.1
  ENSRNOP00000084450.1
Ensembl Acc Id: ENSRNOP00000043407   ⟸   ENSRNOT00000047553
RefSeq Acc Id: XP_038956208   ⟸   XM_039100280
- UniProtKB: A0A8I6GBU6 (UniProtKB/TrEMBL),   D3ZXR5 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000084450   ⟸   ENSRNOT00000108561
Protein Domains
HMG box

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZCR3-F1-model_v2 AlphaFold D3ZCR3 1-213 view protein structure

Transcriptome

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

Promoters
RGD ID:13701968
Promoter ID:EPDNEW_R12490
Type:multiple initiation site
Name:LOC108349189_1
Description:high mobility group protein B1 pseudogene
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_6.0X115,351,037 - 115,351,097EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:11468204 AgrOrtholog
BioCyc Gene G2FUF-1497 BioCyc
Ensembl Genes ENSRNOG00000034130 Ensembl
  ENSRNOG00000058908 UniProtKB/TrEMBL
  ENSRNOG00000067072 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000081634.2 UniProtKB/TrEMBL
  ENSRNOT00000108561.1 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 LOC108349189 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 Hmgb1l2 PhenoGen
PRINTS HIGHMOBLTY12 UniProtKB/TrEMBL
PROSITE HMG_BOX_1 UniProtKB/TrEMBL
  HMG_BOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000034130 RatGTEx
  ENSRNOG00000058908 RatGTEx
  ENSRNOG00000067072 RatGTEx
SMART HMG UniProtKB/TrEMBL
Superfamily-SCOP SSF47095 UniProtKB/TrEMBL
UniProt A0A8I6GBU6 ENTREZGENE, UniProtKB/TrEMBL
  D3ZXR5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-09-19 Hmgb1l2  high mobility group box 1 like 2  LOC108349189  high mobility group protein B1 pseudogene  Symbol and Name Changed 1299863 APPROVED
2016-08-02 LOC108349189  high mobility group protein B1 pseudogene      Symbol and Name status set to provisional 70820 PROVISIONAL