Hmgb4l2 (high-mobility group box 4 like 2) - Rat Genome Database

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Gene: Hmgb4l2 (high-mobility group box 4 like 2) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Hmgb4l2 (Ensembl: LOC681067)
Name: high-mobility group box 4 like 2 (Ensembl:similar to RIKEN cDNA 1700001F22)
RGD ID: 1584677
Description: Predicted to enable DNA binding activity, bending. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Orthologous to human HMGB4 (high mobility group box 4).
Type: protein-coding
RefSeq Status: MODEL
Previously known as: high mobility group protein B4-like; LOC681067; similar to RIKEN cDNA 1700001F22
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X129,666,588 - 129,667,301 (-)NCBIGRCr8
mRatBN7.2X124,788,553 - 124,789,270 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX124,788,552 - 124,789,212 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0X132,424,185 - 132,424,955 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX132,424,240 - 132,424,746 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X132,506,466 - 132,507,176 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X131,865,573 - 131,866,118 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX123,810,170 - 123,810,940 (-)NCBICelera
Cytogenetic MapXq35NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleus  (IEA)

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. GOA pipeline RGD automated data pipeline

Genomics

Variants

.
Variants in Hmgb4l2
2 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
5685004Bss104Bone structure and strength QTL 1043.9tibia area (VT:1000281)tibia area measurement (CMO:0001382)X113805422126975220Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX100567703150256146Rat
738029Stresp2Stress response QTL 23.40.0004stress-related behavior trait (VT:0010451)defensive burying - approachX112934952138400867Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X113937816152453651Rat
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
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
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X103312877148312877Rat
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


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

reproductive system
High
Medium 5
Low 2
Below cutoff 1

Sequence


RefSeq Acc Id: ENSRNOT00000087819   ⟹   ENSRNOP00000069361
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX132,424,240 - 132,424,746 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000104674   ⟹   ENSRNOP00000086397
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX124,788,552 - 124,789,212 (-)Ensembl
RefSeq Acc Id: XM_006257516   ⟹   XP_006257578
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X129,666,588 - 129,667,301 (-)NCBI
mRatBN7.2X124,788,553 - 124,789,270 (-)NCBI
Rnor_6.0X132,424,185 - 132,424,955 (-)NCBI
Rnor_5.0X132,506,466 - 132,507,176 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_006257578 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000086397
  ENSRNOP00000086397.1
  ENSRNOP00000087272.1
RefSeq Acc Id: XP_006257578   ⟸   XM_006257516
- UniProtKB: A0A8I6A255 (UniProtKB/TrEMBL),   A0A8I6A6Y4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000069361   ⟸   ENSRNOT00000087819
RefSeq Acc Id: ENSRNOP00000086397   ⟸   ENSRNOT00000104674
Protein Domains
HMG box

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2JV60-F1-model_v2 AlphaFold A0A0G2JV60 1-168 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:1584677 AgrOrtholog
BioCyc Gene G2FUF-1198 BioCyc
Ensembl Genes ENSRNOG00000057013 Ensembl
  ENSRNOG00000063745 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000067113 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000103726.1 UniProtKB/TrEMBL
  ENSRNOT00000104674.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.30.10 UniProtKB/TrEMBL
InterPro HMG_box_dom UniProtKB/TrEMBL
  HMG_box_dom_sf UniProtKB/TrEMBL
KEGG Report rno:681067 UniProtKB/TrEMBL
NCBI Gene 681067 ENTREZGENE
PANTHER HIGH MOBILITY GROUP PROTEIN B4 UniProtKB/TrEMBL
  HIGH MOBILITY GROUP PROTEIN DSP1 UniProtKB/TrEMBL
Pfam HMG_box UniProtKB/TrEMBL
  HMG_box_2 UniProtKB/TrEMBL
PhenoGen Hmgb4l2 PhenoGen
PRINTS HIGHMOBLTY12 UniProtKB/TrEMBL
PROSITE HMG_BOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000057013 RatGTEx
  ENSRNOG00000063745 RatGTEx
  ENSRNOG00000067113 RatGTEx
SMART HMG UniProtKB/TrEMBL
Superfamily-SCOP SSF47095 UniProtKB/TrEMBL
UniProt A0A8I6A255 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6A6Y4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-09-19 Hmgb4l2  high-mobility group box 4 like 2  LOC681067  similar to RIKEN cDNA 1700001F22  Symbol and Name Changed 1299863 APPROVED
2008-01-09 LOC681067  similar to RIKEN cDNA 1700001F22  LOC683784  similar to RIKEN cDNA 1700001F22  Data merged from RGD:1583311 1643240 APPROVED
2006-11-19 LOC681067  similar to RIKEN cDNA 1700001F22      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC683784  similar to RIKEN cDNA 1700001F22      Symbol and Name status set to provisional 70820 PROVISIONAL