Lcn3 (lipocalin 3) - Rat Genome Database

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Gene: Lcn3 (lipocalin 3) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Lcn3
Name: lipocalin 3
RGD ID: 1562745
Description: Predicted to enable small molecule binding activity. Predicted to be located in extracellular region. Predicted to be active in extracellular space.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC502611; RGD1562745; similar to VNSP I; vomeronasal secretory protein 1
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8328,937,851 - 28,941,097 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl328,938,901 - 28,940,921 (-)EnsemblGRCr8
mRatBN7.238,539,260 - 8,542,792 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,539,737 - 8,544,201 (-)EnsemblmRatBN7.2
Rnor_6.032,945,312 - 2,947,318 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl32,945,504 - 2,947,318 (-)Ensemblrn6Rnor6.0
Rnor_5.032,925,667 - 2,928,731 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.433,892,990 - 3,895,010 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera33,365,290 - 3,367,296 (-)NCBICelera
Cytogenetic Map3p13NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

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

Genomics

Variants

.
Variants in Lcn3
6 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:89
Count of miRNA genes:58
Interacting mature miRNAs:58
Transcripts:ENSRNOT00000061847
Prediction methods:Microtar, 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
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)32267715050766390Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
10450811Scl73Serum cholesterol level QTL 734.70.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3655634751556347Rat
10450808Scl72Serum cholesterol level QTL 724.40.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
10450806Scl71Serum cholesterol level QTL 715.80.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)32862533967641995Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)3612543751125437Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3136721849Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)31141509147Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3655634751556347Rat
1558657Cm43Cardiac mass QTL 436.63e-08heart mass (VT:0007028)heart wet weight (CMO:0000069)32267715050766390Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)31527234860272348Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35675975141509147Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3655634751556347Rat


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
5 42 14 15 17 11 1 11 6 64 45 2 6 3 25 6

Sequence


Ensembl Acc Id: ENSRNOT00000061847   ⟹   ENSRNOP00000058562
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl32,945,504 - 2,947,318 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000108727   ⟹   ENSRNOP00000092215
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl38,539,737 - 8,544,201 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000125677   ⟹   ENSRNOP00000104174
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl328,939,066 - 28,940,921 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000131655   ⟹   ENSRNOP00000108541
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl328,938,901 - 28,940,921 (-)Ensembl
RefSeq Acc Id: XM_063284814   ⟹   XP_063140884
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8328,937,851 - 28,941,097 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001417738 (Get FASTA)   NCBI Sequence Viewer  
  XP_063140884 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL93541 (Get FASTA)   NCBI Sequence Viewer  
  EDL93542 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000104174.1
  ENSRNOP00000108541
  ENSRNOP00000108541.1
Ensembl Acc Id: ENSRNOP00000058562   ⟸   ENSRNOT00000061847
Ensembl Acc Id: ENSRNOP00000092215   ⟸   ENSRNOT00000108727
RefSeq Acc Id: XP_063140884   ⟸   XM_063284814
Ensembl Acc Id: ENSRNOP00000108541   ⟸   ENSRNOT00000131655
Ensembl Acc Id: ENSRNOP00000104174   ⟸   ENSRNOT00000125677
Protein Domains
Lipocalin/cytosolic fatty-acid binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZK46-F1-model_v2 AlphaFold D3ZK46 1-172 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:1562745 AgrOrtholog
BioCyc Gene G2FUF-50422 BioCyc
Ensembl Genes ENSRNOG00000040188 Ensembl
  ENSRNOG00000063072 Ensembl
  ENSRNOG00000074882 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000125677.1 UniProtKB/TrEMBL
  ENSRNOT00000131655 ENTREZGENE
  ENSRNOT00000131655.1 UniProtKB/TrEMBL
Gene3D-CATH 2.40.128.20 UniProtKB/TrEMBL
InterPro Calycin UniProtKB/TrEMBL
  Lipocalin UniProtKB/TrEMBL
  Lipocln_cytosolic_FA-bd_dom UniProtKB/TrEMBL
  von_Ebner_gland UniProtKB/TrEMBL
NCBI Gene 502611 ENTREZGENE
PANTHER PTHR11430 UniProtKB/TrEMBL
  VOMERONASAL SECRETORY PROTEIN 1 UniProtKB/TrEMBL
Pfam Lipocalin UniProtKB/TrEMBL
PhenoGen Lcn3 PhenoGen
PRINTS VNEBNERGLAND UniProtKB/TrEMBL
RatGTEx ENSRNOG00000040188 RatGTEx
  ENSRNOG00000063072 RatGTEx
  ENSRNOG00000074882 RatGTEx
Superfamily-SCOP SSF50814 UniProtKB/TrEMBL
UniProt A0ABK0LHA9_RAT UniProtKB/TrEMBL
  A0ABK0M440_RAT UniProtKB/TrEMBL
  A6JTA6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-02 Lcn3  lipocalin 3  Lcn3  lipocalin 3  Data merged from RGD:149736180 737654 PROVISIONAL
2021-08-09 Lcn3  lipocalin 3      Symbol and Name status set to provisional 45752 PROVISIONAL
2008-02-29 Lcn3  lipocalin 3  RGD1562745_predicted  similar to VNSP I (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1562745_predicted  similar to VNSP I (predicted)  LOC502611  similar to VNSP I  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC502611  similar to VNSP I      Symbol and Name status set to provisional 70820 PROVISIONAL