Lcn5 (lipocalin 5) - Rat Genome Database

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Gene: Lcn5 (lipocalin 5) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Lcn5
Name: lipocalin 5
RGD ID: 69320
Description: Predicted to enable small molecule binding activity. Predicted to be located in extracellular region; INTERACTS WITH 6-propyl-2-thiouracil; ammonium chloride; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: androgen-dependent epididymal 18.5 kDa protein; E-RABP; epididymal retinoic acid-binding protein; epididymal secretory protein I; epididymal-specific lipocalin-5; Erabp; ESP-I
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8328,871,323 - 28,875,335 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl328,871,323 - 28,875,231 (+)EnsemblGRCr8
mRatBN7.238,473,196 - 8,477,208 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,473,196 - 8,477,436 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx311,578,565 - 11,582,576 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0320,164,793 - 20,168,804 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0318,354,641 - 18,358,652 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd326,434,369 - 26,438,381 (+)NCBIDahl_SR_JrHsd
Lyon_Normotensive333,383,244 - 33,387,256 (+)NCBILyon_Normotensive
Lyon_Hypertensive325,282,735 - 25,286,747 (+)NCBILyon_Hypertensive
F344_StmMcwi36,485,395 - 6,489,407 (+)NCBIF344_StmMcwi
Rnor_6.032,876,559 - 2,881,305 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl32,877,293 - 2,881,305 (+)Ensemblrn6Rnor6.0
Rnor_5.032,858,706 - 2,862,718 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.433,825,478 - 3,829,490 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera33,298,097 - 3,302,109 (+)NCBICelera
RGSC_v3.133,825,477 - 3,829,490 (+)NCBI
Cytogenetic Map3p13NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Molecular cloning of the cDNA for two major androgen-dependent secretory proteins of 18.5 kilodaltons synthesized by the rat epididymis. Brooks DE, etal., J Biol Chem 1986 Apr 15;261(11):4956-61.
2. Structure and expression of the rat epididymal secretory protein I gene. An androgen-regulated member of the lipocalin superfamily with a rare splice donor site. Girotti M, etal., Biochem J 1992 Jan 1;281 ( Pt 1):203-10.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. An 18-kDa androgen-regulated protein that modifies galactosyltransferase activity is synthesized by the rat caput epididymidis, but has no structural similarity to rat milk alphalactalbumin. Moore A, etal., Biol Reprod 1990 Sep;43(3):497-506.
5. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
6. GOA pipeline RGD automated data pipeline
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:2165489   PMID:8069623  


Genomics

Variants

.
Variants in Lcn5
21 total Variants

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
appendage
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
8 3 9 57 39 38 19 40 19 4 114 58 1 45 26 46 19

Sequence


Ensembl Acc Id: ENSRNOT00000061855   ⟹   ENSRNOP00000058570
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl38,473,196 - 8,477,118 (+)Ensembl
Rnor_6.0 Ensembl32,877,293 - 2,881,305 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000100844   ⟹   ENSRNOP00000083177
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl328,871,323 - 28,875,231 (+)Ensembl
mRatBN7.2 Ensembl38,473,196 - 8,477,436 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000104006   ⟹   ENSRNOP00000083347
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl38,473,196 - 8,477,208 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000109451   ⟹   ENSRNOP00000076959
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl328,871,323 - 28,874,578 (+)Ensembl
mRatBN7.2 Ensembl38,473,196 - 8,477,014 (+)Ensembl
RefSeq Acc Id: NM_024136   ⟹   NP_077050
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8328,871,323 - 28,875,335 (+)NCBI
mRatBN7.238,473,196 - 8,477,208 (+)NCBI
Dahl_SR_JrHsd326,434,369 - 26,438,381 (+)NCBI
Lyon_Normotensive333,383,244 - 33,387,256 (+)NCBI
Lyon_Hypertensive325,282,735 - 25,286,747 (+)NCBI
F344_StmMcwi36,485,395 - 6,489,407 (+)NCBI
Rnor_6.032,877,293 - 2,881,305 (+)NCBI
Rnor_5.032,858,706 - 2,862,718 (+)NCBI
RGSC_v3.433,825,478 - 3,829,490 (+)RGD
Celera33,298,097 - 3,302,109 (+)RGD
Sequence:
RefSeq Acc Id: NP_077050   ⟸   NM_024136
- Peptide Label: precursor
- UniProtKB: P06911 (UniProtKB/Swiss-Prot),   A6JT98 (UniProtKB/TrEMBL),   A6JT97 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000058570   ⟸   ENSRNOT00000061855
Ensembl Acc Id: ENSRNOP00000076959   ⟸   ENSRNOT00000109451
Ensembl Acc Id: ENSRNOP00000083347   ⟸   ENSRNOT00000104006
Ensembl Acc Id: ENSRNOP00000083177   ⟸   ENSRNOT00000100844
Protein Domains
Lipocalin/cytosolic fatty-acid binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P06911-F1-model_v2 AlphaFold P06911 1-188 view protein structure

Transcriptome

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

Promoters
RGD ID:13691890
Promoter ID:EPDNEW_R2414
Type:single initiation site
Name:Lcn5_1
Description:lipocalin 5
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.032,877,294 - 2,877,354EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69320 AgrOrtholog
BioCyc Gene G2FUF-50430 BioCyc
Ensembl Genes ENSRNOG00000058597 Ensembl
Gene3D-CATH 2.40.128.20 UniProtKB/Swiss-Prot
InterPro Calycin UniProtKB/Swiss-Prot
  Lipocalin UniProtKB/Swiss-Prot
  Lipocalin_CS UniProtKB/Swiss-Prot
  Lipocln_cytosolic_FA-bd_dom UniProtKB/Swiss-Prot
KEGG Report rno:29552 UniProtKB/Swiss-Prot
NCBI Gene 29552 ENTREZGENE
PANTHER EPIDIDYMAL-SPECIFIC LIPOCALIN-5 UniProtKB/Swiss-Prot
  PTHR11430 UniProtKB/Swiss-Prot
Pfam Lipocalin UniProtKB/Swiss-Prot
PhenoGen Lcn5 PhenoGen
PRINTS PGNDSYNTHASE UniProtKB/Swiss-Prot
PROSITE LIPOCALIN UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000058597 RatGTEx
Superfamily-SCOP SSF50814 UniProtKB/Swiss-Prot
UniProt A0A8I5Y105_RAT UniProtKB/TrEMBL
  A0A8I5ZWE5_RAT UniProtKB/TrEMBL
  A6JT97 ENTREZGENE, UniProtKB/TrEMBL
  A6JT98 ENTREZGENE, UniProtKB/TrEMBL
  LCN5_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-18 Lcn5  lipocalin 5  Erabp  epididymal retinoic acid-binding protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Erabp  epididymal retinoic acid-binding protein      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference