Lcn1 (lipocalin 1) - Rat Genome Database

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Gene: Lcn1 (lipocalin 1) Rattus norvegicus
Analyze
Symbol: Lcn1
Name: lipocalin 1
RGD ID: 619872
Description: Predicted to enable several functions, including chloride ion binding activity; identical protein binding activity; and zinc ion binding activity. Predicted to be involved in sensory perception of taste. Predicted to be located in extracellular region. Predicted to be active in extracellular space. Orthologous to several human genes including LCN1 (lipocalin 1); INTERACTS WITH 1,2-dimethylhydrazine; 2,3,7,8-tetrachlorodibenzodioxine; aflatoxin B1.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Lcn1p1; lipocalin 1 pseudogene 1; VEG protein 1; Vegp1; von Ebner gland protein 1; von Ebners gland protein 1
RGD Orthologs
Human
Mouse
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8329,930,943 - 29,935,418 (+)NCBIGRCr8GRCr8GRCr8
mRatBN7.239,532,860 - 9,537,859 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl39,532,915 - 9,536,577 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx312,590,063 - 12,594,538 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0321,175,443 - 21,179,918 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0319,430,763 - 19,435,238 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.034,233,111 - 4,236,960 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl34,233,111 - 4,236,960 (+)Ensemblrn6Rnor6.0
Rnor_5.039,591,615 - 9,595,715 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.434,879,048 - 4,883,523 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera34,345,110 - 4,349,585 (+)NCBICelera
RGSC_v3.134,879,047 - 4,883,523 (+)NCBI
Cytogenetic Map3p13NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

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. Structural organization of the genes for rat von Ebner's gland proteins 1 and 2 reveals their close relationship to lipocalins. Kock K, etal., Eur J Biochem 1994 May 1;221(3):905-16.
3. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Possible role for salivary gland protein in taste reception indicated by homology to lipophilic-ligand carrier proteins. Schmale H, etal., Nature 1990 Jan 25;343(6256):366-9.
7. mRNAs encoding a von Ebner's-like protein and the Huntington disease protein are induced in rat male germ cells by Sertoli cells. Syed V, etal., J Biol Chem 1999 Apr 16;274(16):10737-42.
Additional References at PubMed
PMID:7813422   PMID:8999869   PMID:11287427   PMID:15489503   PMID:21805676   PMID:22664934   PMID:23376485   PMID:23580065  


Genomics

Comparative Map Data
Lcn1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8329,930,943 - 29,935,418 (+)NCBIGRCr8GRCr8GRCr8
mRatBN7.239,532,860 - 9,537,859 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl39,532,915 - 9,536,577 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx312,590,063 - 12,594,538 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0321,175,443 - 21,179,918 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0319,430,763 - 19,435,238 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.034,233,111 - 4,236,960 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl34,233,111 - 4,236,960 (+)Ensemblrn6Rnor6.0
Rnor_5.039,591,615 - 9,595,715 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.434,879,048 - 4,883,523 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera34,345,110 - 4,349,585 (+)NCBICelera
RGSC_v3.134,879,047 - 4,883,523 (+)NCBI
Cytogenetic Map3p13NCBI
LCN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389135,521,440 - 135,526,540 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9135,521,438 - 135,526,540 (+)Ensemblhg38GRCh38
GRCh379138,413,286 - 138,418,386 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369137,553,107 - 137,558,199 (+)NCBIBuild 36Build 36hg18NCBI36
Build 349135,639,230 - 135,644,323NCBI
Celera9108,930,399 - 108,935,455 (+)NCBICelera
Cytogenetic Map9q34.3NCBI
HuRef9107,875,074 - 107,880,176 (+)NCBIHuRef
CHM1_19138,561,863 - 138,566,965 (+)NCBICHM1_1
T2T-CHM13v2.09147,749,482 - 147,754,582 (+)NCBIT2T-CHM13v2.0
Lcn3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39225,655,545 - 25,658,110 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl225,655,581 - 25,658,111 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38225,765,533 - 25,768,098 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl225,765,569 - 25,768,099 (+)Ensemblmm10GRCm38
MGSCv37225,621,089 - 25,623,619 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36225,587,578 - 25,590,108 (+)NCBIMGSCv36mm8
Celera225,491,663 - 25,494,194 (+)NCBICelera
Cytogenetic Map2A3NCBI
cM Map217.99NCBI

Variants

.
Variants in Lcn1
32 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:52
Count of miRNA genes:51
Interacting mature miRNAs:52
Transcripts:ENSRNOT00000042910
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.


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
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
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)32905627547904329Rat
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
ectoderm
endocrine system
endoderm
hemolymphoid system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
1 5 6 9 6 1 10 6 4 3 34 9 1 1

Sequence


Ensembl Acc Id: ENSRNOT00000042910   ⟹   ENSRNOP00000041023
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl39,516,457 - 9,521,081 (-)Ensembl
Rnor_6.0 Ensembl34,233,111 - 4,236,960 (+)Ensembl
RefSeq Acc Id: NM_022945   ⟹   NP_075234
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8329,930,943 - 29,935,418 (+)NCBI
mRatBN7.239,532,860 - 9,537,335 (+)NCBI
Rnor_6.034,233,111 - 4,236,960 (+)NCBI
Rnor_5.039,591,615 - 9,595,715 (+)NCBI
RGSC_v3.434,879,048 - 4,883,523 (+)RGD
Celera34,345,110 - 4,349,585 (+)RGD
Sequence:
RefSeq Acc Id: XM_039105817   ⟹   XP_038961745
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8329,932,215 - 29,935,418 (+)NCBI
mRatBN7.239,532,955 - 9,537,859 (+)NCBI
Protein Sequences
Protein RefSeqs NP_075234 (Get FASTA)   NCBI Sequence Viewer  
  XP_038961745 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAA36263 (Get FASTA)   NCBI Sequence Viewer  
  CAA52809 (Get FASTA)   NCBI Sequence Viewer  
  EDL93473 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000043245
  ENSRNOP00000043245.5
GenBank Protein P20289 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_075234   ⟸   NM_022945
- Peptide Label: precursor
- UniProtKB: P20289 (UniProtKB/Swiss-Prot),   A6JTH4 (UniProtKB/TrEMBL),   R9PXY4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000041023   ⟸   ENSRNOT00000042910
RefSeq Acc Id: XP_038961745   ⟸   XM_039105817
- Peptide Label: isoform X1
Protein Domains
Lipocalin/cytosolic fatty-acid binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P20289-F1-model_v2 AlphaFold P20289 1-177 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:619872 AgrOrtholog
BioCyc Gene G2FUF-50343 BioCyc
Ensembl Genes ENSRNOG00000033020 Ensembl, UniProtKB/Swiss-Prot
  ENSRNOG00000033761 Ensembl
  ENSRNOG00000085594 ENTREZGENE
Ensembl Transcript ENSRNOT00000041399 ENTREZGENE
  ENSRNOT00000041399.5 UniProtKB/Swiss-Prot
Gene3D-CATH 2.40.128.20 UniProtKB/Swiss-Prot
InterPro Calycin UniProtKB/Swiss-Prot
  Lipocalin UniProtKB/Swiss-Prot
  Lipocln_cytosolic_FA-bd_dom UniProtKB/Swiss-Prot
  von_Ebner_gland UniProtKB/Swiss-Prot
KEGG Report rno:65039 UniProtKB/Swiss-Prot
NCBI Gene 65039 ENTREZGENE
PANTHER LIPOCALIN 1-LIKE PROTEIN 1-RELATED UniProtKB/Swiss-Prot
  PTHR11430 UniProtKB/Swiss-Prot
Pfam Lipocalin UniProtKB/Swiss-Prot
PhenoGen Lcn1 PhenoGen
PRINTS VNEBNERGLAND UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000033020 RatGTEx
  ENSRNOG00000033761 RatGTEx
  ENSRNOG00000085594 RatGTEx
Superfamily-SCOP SSF50814 UniProtKB/Swiss-Prot
UniProt A6JTH4 ENTREZGENE, UniProtKB/TrEMBL
  P20289 ENTREZGENE
  R9PXY4 ENTREZGENE, UniProtKB/TrEMBL
  VEGP1_RAT UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-07-30 Lcn1-ps1  lipocalin 1, pseudogene 1  Lcn1p1  lipocalin 1 pseudogene 1  Name and Symbol changed 629549 APPROVED
2014-07-30 Lcn1  lipocalin 1  Lcn1-ps1  lipocalin 1, pseudogene 1  Name and Symbol changed 629549 APPROVED
2014-07-25 Lcn1p1  lipocalin 1 pseudogene 1  Vegp1  von Ebners gland protein 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-11-17 Vegp1  von Ebners gland protein 1      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Vegp1  von Ebners gland protein 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression highly expressed in the von Egner's salivary glands of the tongue 730165
gene_product member of the lipocalin superfamily of lipophilic-ligand carrier proteins 730111