Hdlbpl2 (high density lipoprotein binding protein like 2) - Rat Genome Database

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Gene: Hdlbpl2 (high density lipoprotein binding protein like 2) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Hdlbpl2 (Ensembl: RGD1563104)
Name: high density lipoprotein binding protein like 2 (Ensembl:similar to Vigilin (High density lipoprotein-binding protein))
RGD ID: 1563104
Description: Predicted to enable mRNA binding activity. Predicted to be active in cytoplasm and nucleus.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical protein LOC302773; LOC302773; RGD1563104; similar to Vigilin (High density lipoprotein-binding protein); similar to Vigilin (High density lipoprotein-binding protein) (HDL-binding protein); uncharacterized protein LOC302773
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X93,888,744 - 93,910,279 (+)NCBIGRCr8
mRatBN7.2X89,628,705 - 89,650,241 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX89,628,725 - 89,650,241 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX91,322,599 - 91,326,351 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X94,791,738 - 94,795,490 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X92,329,136 - 92,332,888 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X96,528,836 - 96,532,588 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX96,528,836 - 96,532,588 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X96,393,492 - 96,397,244 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X113,634,155 - 113,637,907 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX90,796,594 - 90,800,346 (+)NCBICelera
Cytogenetic MapXq31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IBA)
nucleus  (IBA)

Molecular Function
mRNA binding  (IBA)

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Variants

.
Variants in Hdlbpl2
64 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:13
Count of miRNA genes:13
Interacting mature miRNAs:13
Transcripts:ENSRNOT00000043728
Prediction methods:Miranda, Pita, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
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
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat
724551Glom1Glomerulus QTL 12.80.0004kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)X75294106120294106Rat


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

nervous system reproductive system
High
Medium 3
Low 4
Below cutoff 1 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000043728   ⟹   ENSRNOP00000054125
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX89,628,725 - 89,650,241 (+)Ensembl
Rnor_6.0 EnsemblX96,528,836 - 96,532,588 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000112716   ⟹   ENSRNOP00000090439
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX89,637,904 - 89,650,241 (+)Ensembl
RefSeq Acc Id: NM_001419543   ⟹   NP_001406472
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X93,888,744 - 93,910,279 (+)NCBI
mRatBN7.2X89,628,705 - 89,650,241 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001406472 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM07056 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000054125
  ENSRNOP00000054125.1
  ENSRNOP00000090439.1
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000054125   ⟸   ENSRNOT00000043728
RefSeq Acc Id: ENSRNOP00000090439   ⟸   ENSRNOT00000112716
RefSeq Acc Id: NP_001406472   ⟸   NM_001419543
- UniProtKB: D4A4T3 (UniProtKB/TrEMBL),   A6IVC4 (UniProtKB/TrEMBL)
Protein Domains
K Homology

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A4T3-F1-model_v2 AlphaFold D4A4T3 1-1250 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:1563104 AgrOrtholog
BioCyc Gene G2FUF-1742 BioCyc
Ensembl Genes ENSRNOG00000031294 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000043728 ENTREZGENE
  ENSRNOT00000043728.3 UniProtKB/TrEMBL
  ENSRNOT00000112716.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.1370.10 UniProtKB/TrEMBL
InterPro IPR004087 UniProtKB/TrEMBL
  KH_dom_type_1_sf UniProtKB/TrEMBL
  KH_type_1 UniProtKB/TrEMBL
KEGG Report rno:302773 UniProtKB/TrEMBL
NCBI Gene 302773 ENTREZGENE
PANTHER DODECA-SATELLITE-BINDING PROTEIN 1, ISOFORM A UniProtKB/TrEMBL
  SCP160 UniProtKB/TrEMBL
Pfam KH_1 UniProtKB/TrEMBL
PhenoGen Hdlbpl2 PhenoGen
PROSITE KH_TYPE_1 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000031294 RatGTEx
SMART SM00322 UniProtKB/TrEMBL
Superfamily-SCOP SSF54791 UniProtKB/TrEMBL
UniProt A6IVC4 ENTREZGENE, UniProtKB/TrEMBL
  D4A4T3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-09-19 Hdlbpl2  high density lipoprotein binding protein like 2  RGD1563104  similar to Vigilin (High density lipoprotein-binding protein)  Symbol and Name Changed 1299863 APPROVED
2008-04-30 RGD1563104  similar to Vigilin (High density lipoprotein-binding protein)   RGD1563104_predicted  similar to Vigilin (High density lipoprotein-binding protein) (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-10 RGD1563104_predicted  similar to Vigilin (High density lipoprotein-binding protein) (predicted)    similar to Vigilin (High density lipoprotein-binding protein) (HDL-binding protein) (predicted)  Name updated 1299863 APPROVED
2006-03-07 RGD1563104_predicted  similar to Vigilin (High density lipoprotein-binding protein) (HDL-binding protein) (predicted)  LOC302773  similar to Vigilin (High density lipoprotein-binding protein) (HDL-binding protein)  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC302773  similar to Vigilin (High density lipoprotein-binding protein) (HDL-binding protein)      Symbol and Name status set to provisional 70820 PROVISIONAL