Lcn4 (lipocalin 4) - Rat Genome Database

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Gene: Lcn4 (lipocalin 4) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Lcn4
Name: lipocalin 4
RGD ID: 1596715
Description: Predicted to enable small molecule binding activity. Predicted to be located in extracellular region; INTERACTS WITH acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC681375; similar to Vomeronasal secretory protein 2 precursor (Vomeronasal secretory protein II) (VNSP II) (Lipocalin-4); vomeronasal secretory protein 2
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8330,197,267 - 30,200,829 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl330,197,327 - 30,200,196 (+)EnsemblGRCr8
mRatBN7.239,799,245 - 9,802,114 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl39,799,122 - 9,814,971 (+)EnsemblmRatBN7.2
Rnor_6.035,167,685 - 5,170,554 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl35,167,685 - 5,170,545 (+)Ensemblrn6Rnor6.0
Rnor_5.0310,517,897 - 10,520,766 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.435,309,475 - 5,312,776 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera34,608,373 - 4,611,242 (+)NCBICelera
Cytogenetic Map3p13NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
acrylamide  (EXP)
bisphenol A  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

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.
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 Lcn4
19 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:137
Count of miRNA genes:112
Interacting mature miRNAs:119
Transcripts:ENSRNOT00000046109
Prediction methods:Microtar, 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.


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
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)32905627547904329Rat
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
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
10450806Scl71Serum cholesterol level QTL 715.80.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
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
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)32905627547904329Rat
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

ectoderm
endocrine system
nervous system
reproductive system
1 1 1 1

Sequence


Ensembl Acc Id: ENSRNOT00000046109   ⟹   ENSRNOP00000041973
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl39,799,122 - 9,802,759 (+)Ensembl
Rnor_6.0 Ensembl35,167,685 - 5,170,545 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000067576   ⟹   ENSRNOP00000062292
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl330,197,327 - 30,200,196 (+)Ensembl
mRatBN7.2 Ensembl39,799,193 - 9,814,971 (+)Ensembl
RefSeq Acc Id: XM_006233907   ⟹   XP_006233969
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8330,197,267 - 30,200,829 (+)NCBI
mRatBN7.239,799,245 - 9,802,114 (+)NCBI
Rnor_6.035,167,685 - 5,170,554 (+)NCBI
Rnor_5.0310,517,897 - 10,520,766 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001418660 (Get FASTA)   NCBI Sequence Viewer  
  XP_006233969 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL93470 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000041973.5
  ENSRNOP00000062292
  ENSRNOP00000062292.3
RefSeq Acc Id: XP_006233969   ⟸   XM_006233907
- Sequence:
Ensembl Acc Id: ENSRNOP00000041973   ⟸   ENSRNOT00000046109
Ensembl Acc Id: ENSRNOP00000062292   ⟸   ENSRNOT00000067576
Protein Domains
Lipocalin/cytosolic fatty-acid binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZJV7-F1-model_v2 AlphaFold D3ZJV7 1-178 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:1596715 AgrOrtholog
BioCyc Gene G2FUF-50339 BioCyc
Ensembl Genes ENSRNOG00000030708 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000043494 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000046109.5 UniProtKB/TrEMBL
  ENSRNOT00000067576 ENTREZGENE
  ENSRNOT00000067576.3 UniProtKB/TrEMBL
Gene3D-CATH 2.40.128.20 UniProtKB/TrEMBL
InterPro Calycin UniProtKB/TrEMBL
  Lipocalin UniProtKB/TrEMBL
  Lipocln_cytosolic_FA-bd UniProtKB/TrEMBL
  vonEbner_gland UniProtKB/TrEMBL
NCBI Gene 681375 ENTREZGENE
PANTHER PTHR11430 UniProtKB/TrEMBL
  VOMERONASAL SECRETORY PROTEIN 2 UniProtKB/TrEMBL
Pfam Lipocalin UniProtKB/TrEMBL
PhenoGen Lcn4 PhenoGen
PRINTS VNEBNERGLAND UniProtKB/TrEMBL
RatGTEx ENSRNOG00000030708 RatGTEx
  ENSRNOG00000043494 RatGTEx
Superfamily-SCOP Calycin UniProtKB/TrEMBL
UniProt A6JTH7 ENTREZGENE, UniProtKB/TrEMBL
  D3ZFU1_RAT UniProtKB/TrEMBL
  D3ZJV7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-05 Lcn4  lipocalin 4  LOC681375  similar to Vomeronasal secretory protein 2 precursor (Vomeronasal secretory protein II) (VNSP II) (Lipocalin-4)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC681375  similar to Vomeronasal secretory protein 2 precursor (Vomeronasal secretory protein II) (VNSP II) (Lipocalin-4)  LOC687446  similar to Vomeronasal secretory protein 2 precursor (Vomeronasal secretory protein II) (VNSP II) (Lipocalin-4)  Data merged from RGD:1585359 1643240 APPROVED
2006-11-20 LOC681375  similar to Vomeronasal secretory protein 2 precursor (Vomeronasal secretory protein II) (VNSP II) (Lipocalin-4)      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC687446  similar to Vomeronasal secretory protein 2 precursor (Vomeronasal secretory protein II) (VNSP II) (Lipocalin-4)      Symbol and Name status set to provisional 70820 PROVISIONAL