LOC108349258 (high mobility group protein B4-like) - Rat Genome Database

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Gene: LOC108349258 (high mobility group protein B4-like) Rattus norvegicus
Analyze
No known orthologs.
Symbol: LOC108349258 (Ensembl: LOC120093120)
Name: high mobility group protein B4-like
RGD ID: 11417756
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: RGD1565430; similar to RIKEN cDNA 1700001F22
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X141,326,170 - 141,326,881 (+)NCBIGRCr8
mRatBN7.2X136,290,250 - 136,290,937 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX136,290,233 - 136,290,934 (+)EnsemblmRatBN7.2 Ensembl
mRatBN7.2 EnsemblX136,154,060 - 136,154,790 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0X142,344,626 - 142,345,439 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX142,344,878 - 142,345,372 (+)EnsemblRnor6.0rn6Rnor6.0
CeleraX133,664,080 - 133,664,893 (+)NCBICelera
Cytogenetic MapXq36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model



Biological Process

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
LOC108349258Ratregulation of transcription by RNA polymerase II involved_inIBAMGI:96113 more ...1600115GO_REF:0000033GO_CentralGO_REF:0000033

Cellular Component

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
LOC108349258Ratnucleus located_inIEAUniProtKB-KW:KW-05391600115GO_REF:0000043UniProtGO_REF:0000043
LOC108349258Ratnucleus located_inIEAUniRule:UR0004008111600115GO_REF:0000104UniProtGO_REF:0000104

Molecular Function

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
LOC108349258RatDNA binding enablesIEAUniProtKB-KW:KW-02381600115GO_REF:0000043UniProtGO_REF:0000043
LOC108349258RatDNA binding enablesIEAUniRule:UR0004008111600115GO_REF:0000104UniProtGO_REF:0000104
LOC108349258RatDNA binding, bending enablesIBAFB:FBgn0004362 more ...1600115GO_REF:0000033GO_CentralGO_REF:0000033


#
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.


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Variants in LOC108349258
1 total Variants

Predicted Target Of
Summary Value
Count of predictions:33
Count of miRNA genes:32
Interacting mature miRNAs:33
Transcripts:ENSRNOT00000056621
Prediction methods: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.


The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
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
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X126975089152453651Rat
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
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




alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
1 9 10 20 17 11 2 4 2 44 24 11 9 28 9


RefSeq Transcripts XM_017588341 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602407 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JAXUCZ010000021 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000056621   ⟹   ENSRNOP00000053460
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX142,344,878 - 142,345,372 (+)Ensembl
RefSeq Acc Id: XM_017602407   ⟹   XP_017457896
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X141,326,170 - 141,326,881 (+)NCBI
mRatBN7.2X136,290,250 - 136,290,937 (+)NCBI
Rnor_6.0X142,344,626 - 142,345,439 (+)NCBI
Sequence:
Protein RefSeqs XP_017457896 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000085463.1
  ENSRNOP00000087272.1
  ENSRNOP00000109348
RefSeq Acc Id: XP_017457896   ⟸   XM_017602407
- UniProtKB: A0A8I6AIS0 (UniProtKB/TrEMBL),   A0A8I6A6Y4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000053460   ⟸   ENSRNOT00000056621
HMG box

Name Modeler Protein Id AA Range Protein Structure
AF-D3ZLG2-F1-model_v2 AlphaFold D3ZLG2 1-165 view protein structure


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



1 to 32 of 32 rows
Database
Acc Id
Source(s)
BioCyc Gene G2FUF-893 BioCyc
Ensembl Genes ENSRNOG00000047496 Ensembl
  ENSRNOG00000066398 UniProtKB/TrEMBL
  ENSRNOG00000067113 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000067936 Ensembl
  ENSRNOG00000085671 ENTREZGENE
Ensembl Transcript ENSRNOT00000097379.1 UniProtKB/TrEMBL
  ENSRNOT00000103726.1 UniProtKB/TrEMBL
  ENSRNOT00000124222 ENTREZGENE
Gene3D-CATH 1.10.30.10 UniProtKB/TrEMBL
InterPro HMG_box_dom UniProtKB/TrEMBL
  HMG_box_dom_sf UniProtKB/TrEMBL
  HMGB UniProtKB/TrEMBL
KEGG Report rno:108349258 UniProtKB/TrEMBL
NCBI Gene LOC108349258 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 LOC108349258 PhenoGen
PRINTS HIGHMOBLTY12 UniProtKB/TrEMBL
PROSITE HMG_BOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000047496 RatGTEx
  ENSRNOG00000066398 RatGTEx
  ENSRNOG00000067113 RatGTEx
  ENSRNOG00000067936 RatGTEx
  ENSRNOG00000085671 RatGTEx
SMART HMG UniProtKB/TrEMBL
Superfamily-SCOP SSF47095 UniProtKB/TrEMBL
UniProt A0A8I6A440_RAT UniProtKB/TrEMBL
  A0A8I6A6Y4 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AIS0 ENTREZGENE
1 to 32 of 32 rows


Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-02 LOC108349258  high mobility group protein B4-like  RGD1565430  similar to RIKEN cDNA 1700001F22  Data merged from RGD:149736144 737654 PROVISIONAL
2021-08-09 RGD1565430  similar to RIKEN cDNA 1700001F22      Symbol and Name status set to provisional 45752 PROVISIONAL
2016-08-02 LOC108349258  high mobility group protein B4-like      Symbol and Name status set to provisional 70820 PROVISIONAL