Lcn6 (lipocalin 6) - Rat Genome Database

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Gene: Lcn6 (lipocalin 6) Rattus norvegicus
Analyze
Symbol: Lcn6
Name: lipocalin 6
RGD ID: 1302986
Description: Predicted to enable small molecule binding activity. Predicted to be located in extracellular region. Orthologous to human LCN6 (lipocalin 6); INTERACTS WITH bisphenol A; copper atom; copper(0).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: epididymal-specific lipocalin ELP16; epididymal-specific lipocalin-6
RGD Orthologs
Human
Mouse
Chinchilla
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8328,882,133 - 28,887,697 (+)NCBIGRCr8
mRatBN7.238,484,013 - 8,489,577 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,484,013 - 8,489,574 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx311,589,395 - 11,594,959 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0320,175,629 - 20,181,193 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0318,365,471 - 18,371,035 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.032,888,103 - 2,893,498 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl32,888,103 - 2,893,495 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.032,869,516 - 2,874,911 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.433,836,357 - 3,841,922 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.133,836,356 - 3,841,919 (+)NCBI
Celera33,308,865 - 3,314,429 (+)NCBICelera
Cytogenetic Map3p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


1 to 11 of 11 rows
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Lcn6RatAdams-Oliver Syndrome 5  ISOLCN6 (Homo sapiens)8554872ClinVar Annotator: match by term: Adams-Oliver syndrome 5ClinVarPMID:16025100 more ...
Lcn6Ratautosomal dominant intellectual developmental disorder 8  ISOLCN6 (Homo sapiens)8554872ClinVar Annotator: match by term: Neurodevelopmental disorder with or without hyperkinetic movements and seizures and autosomal dominantClinVarPMID:28492532
Lcn6Ratautosomal dominant nocturnal frontal lobe epilepsy 5  ISOLCN6 (Homo sapiens)8554872ClinVar Annotator: match by term: Autosomal dominant nocturnal frontal lobe epilepsy 5ClinVarPMID:28492532
Lcn6Ratdevelopmental and epileptic encephalopathy 14  ISOLCN6 (Homo sapiens)8554872ClinVar more ...ClinVarPMID:19264732 more ...
Lcn6Ratdevelopmental and epileptic encephalopathy 14  ISOLCN6 (Homo sapiens)8554872ClinVar more ...ClinVarPMID:16025100 more ...
Lcn6RatJoubert syndrome 1  ISOLCN6 (Homo sapiens)8554872ClinVar Annotator: match by term: Familial aplasia of the vermisClinVarPMID:16025100 more ...
Lcn6RatKleefstra syndrome 1  ISOLCN6 (Homo sapiens)8554872ClinVar Annotator: match by term: Kleefstra syndrome 1ClinVarPMID:19264732 more ...
Lcn6RatLeigh disease  ISOLCN6 (Homo sapiens)8554872ClinVar Annotator: match by term: Leigh syndromeClinVarPMID:28492532
Lcn6Ratprimary coenzyme Q10 deficiency 7  ISOLCN6 (Homo sapiens)8554872ClinVar Annotator: match by term: Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndromeClinVarPMID:28492532
Lcn6RatRafiq syndrome  ISOLCN6 (Homo sapiens)8554872ClinVar Annotator: match by term: Rafiq syndromeClinVarPMID:24566669 more ...
Lcn6Rattuberous sclerosis 1  ISOLCN6 (Homo sapiens)8554872ClinVar Annotator: match by term: Tuberous sclerosis 1ClinVarPMID:28492532
1 to 11 of 11 rows

1 to 12 of 12 rows

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Lcn6Rat1,2-dichloroethane increases expressionISOLcn6 (Mus musculus)6480464ethylene dichloride results in increased expression of LCN6 mRNACTDPMID:28960355
Lcn6Ratall-trans-retinoic acid decreases expressionISOLCN6 (Homo sapiens)6480464Tretinoin results in decreased expression of LCN6 mRNACTDPMID:33167477
Lcn6Ratbenzo[a]pyrene affects methylationISOLCN6 (Homo sapiens)6480464Benzo(a)pyrene affects the methylation of LCN6 promoterCTDPMID:27901495
Lcn6Ratbisphenol A decreases expressionEXP 6480464bisphenol A results in decreased expression of LCN6 mRNACTDPMID:25181051
Lcn6Ratcopper atom increases expressionEXP 6480464Copper deficiency results in increased expression of LCN6 mRNACTDPMID:26033743
Lcn6Ratcopper(0) increases expressionEXP 6480464Copper deficiency results in increased expression of LCN6 mRNACTDPMID:26033743
Lcn6Ratfolic acid decreases expressionISOLcn6 (Mus musculus)6480464Folic Acid results in decreased expression of LCN6 mRNACTDPMID:25629700
Lcn6Ratozone multiple interactionsISOLcn6 (Mus musculus)6480464[Air Pollutants results in increased abundance of Ozone] which results in decreased expression of LCN6 mRNACTDPMID:27106289
Lcn6Ratparacetamol decreases expressionISOLCN6 (Homo sapiens)6480464Acetaminophen results in decreased expression of LCN6 mRNACTDPMID:26690555
Lcn6Ratsilver atom increases expressionISOLcn6 (Mus musculus)6480464Silver results in increased expression of LCN6 mRNACTDPMID:27131904
Lcn6Ratsilver(0) increases expressionISOLcn6 (Mus musculus)6480464Silver results in increased expression of LCN6 mRNACTDPMID:27131904
Lcn6Ratvalproic acid increases methylationISOLCN6 (Homo sapiens)6480464Valproic Acid results in increased methylation of LCN6 geneCTDPMID:29154799

1 to 12 of 12 rows

Biological Process
1 to 10 of 10 rows

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Lcn6Ratacrosome reaction acts_upstream_of_or_withinISOLcn6 (Mus musculus)1624291 PMID:29045572RGDPMID:29045572
Lcn6Ratacrosome reaction acts_upstream_of_or_withinIEAUniProtKB:A2AJB9 and ensembl:ENSMUSP000001098371600115GO_REF:0000107EnsemblGO_REF:0000107
Lcn6Ratcalcium ion homeostasis acts_upstream_of_or_withinIEAUniProtKB:A2AJB9 and ensembl:ENSMUSP000001098371600115GO_REF:0000107EnsemblGO_REF:0000107
Lcn6Ratcalcium ion homeostasis acts_upstream_of_or_withinISOLcn6 (Mus musculus)1624291 PMID:29045572RGDPMID:29045572
Lcn6Ratcell maturation acts_upstream_of_or_withinISOLcn6 (Mus musculus)1624291 PMID:29045572RGDPMID:29045572
Lcn6Ratcell maturation acts_upstream_of_or_withinIEAUniProtKB:A2AJB9 and ensembl:ENSMUSP000001098371600115GO_REF:0000107EnsemblGO_REF:0000107
Lcn6Ratcellular homeostasis acts_upstream_of_or_withinISOLcn6 (Mus musculus)1624291 PMID:29045572RGDPMID:29045572
Lcn6Ratcellular homeostasis acts_upstream_of_or_withinIEAUniProtKB:A2AJB9 and ensembl:ENSMUSP000001098371600115GO_REF:0000107EnsemblGO_REF:0000107
Lcn6Ratresponse to calcium ion acts_upstream_of_or_withinISOLcn6 (Mus musculus)1624291 PMID:29045572RGDPMID:29045572
Lcn6Ratresponse to calcium ion acts_upstream_of_or_withinIEAUniProtKB:A2AJB9 and ensembl:ENSMUSP000001098371600115GO_REF:0000107EnsemblGO_REF:0000107
1 to 10 of 10 rows

Cellular Component

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Lcn6Ratextracellular region located_inIEAUniProtKB-SubCell:SL-02431600115GO_REF:0000044UniProtGO_REF:0000044
Lcn6Ratextracellular region located_inIEAUniProtKB-KW:KW-09641600115GO_REF:0000043UniProtGO_REF:0000043

Molecular Function

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Lcn6Ratsmall molecule binding enablesIEAInterPro:IPR0023451600115GO_REF:0000002InterProGO_REF:0000002


#
Reference Title
Reference Citation
1. LCN6, a novel human epididymal lipocalin. Hamil KG, etal., Reprod Biol Endocrinol 2003 Nov 14;1(1):112.
2. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions


Lcn6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8328,882,133 - 28,887,697 (+)NCBIGRCr8
mRatBN7.238,484,013 - 8,489,577 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,484,013 - 8,489,574 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx311,589,395 - 11,594,959 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0320,175,629 - 20,181,193 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0318,365,471 - 18,371,035 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.032,888,103 - 2,893,498 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl32,888,103 - 2,893,495 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.032,869,516 - 2,874,911 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.433,836,357 - 3,841,922 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.133,836,356 - 3,841,919 (+)NCBI
Celera33,308,865 - 3,314,429 (+)NCBICelera
Cytogenetic Map3p13NCBI
LCN6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389136,744,017 - 136,748,525 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9136,744,017 - 136,748,525 (-)EnsemblGRCh38hg38GRCh38
GRCh379139,638,469 - 139,642,977 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369138,758,290 - 138,762,801 (-)NCBINCBI36Build 36hg18NCBI36
Build 349136,914,308 - 136,918,817NCBI
Celera9110,151,587 - 110,156,098 (-)NCBICelera
Cytogenetic Map9q34.3NCBI
HuRef9109,097,648 - 109,102,120 (-)NCBIHuRef
CHM1_19139,787,050 - 139,791,503 (-)NCBICHM1_1
T2T-CHM13v2.09148,977,195 - 148,981,703 (-)NCBIT2T-CHM13v2.0
Lcn6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39225,566,650 - 25,571,620 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl225,566,798 - 25,571,620 (+)EnsemblGRCm39 Ensembl
GRCm38225,676,638 - 25,681,608 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl225,676,786 - 25,681,608 (+)EnsemblGRCm38mm10GRCm38
MGSCv37225,532,306 - 25,537,128 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36225,498,795 - 25,503,330 (+)NCBIMGSCv36mm8
Celera225,404,979 - 25,409,801 (+)NCBICelera
Cytogenetic Map2A3NCBI
cM Map217.73NCBI
Lcn6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555134,860,662 - 4,863,648 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555134,860,420 - 4,863,716 (-)NCBIChiLan1.0ChiLan1.0
LCN6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1948,800,699 - 48,805,946 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha948,014,314 - 48,019,558 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0949,678,843 - 49,684,086 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl949,678,859 - 49,684,086 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1948,454,986 - 48,460,230 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0948,753,645 - 48,758,888 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0948,800,675 - 48,805,909 (+)NCBIUU_Cfam_GSD_1.0
Lcn6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947202,228,597 - 202,231,218 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366691,143,840 - 1,146,529 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366691,143,840 - 1,146,461 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LCN6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa10.21313,834,487 - 313,839,782 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LCN6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1121,446,886 - 1,451,406 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl121,447,137 - 1,451,087 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660583,819,192 - 3,823,240 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lcn6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247601,066,532 - 1,070,083 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

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Variants in Lcn6
19 total Variants

Predicted Target Of
Summary Value
Count of predictions:176
Count of miRNA genes:147
Interacting mature miRNAs:161
Transcripts:ENSRNOT00000029655
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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.


1 to 10 of 13 rows
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat

1 to 10 of 13 rows



alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
1 2 1 16 6 11 7 10 1 16


RefSeq Transcripts NM_001001519 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF303086 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000029655   ⟹   ENSRNOP00000033421
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl38,484,013 - 8,489,574 (+)Ensembl
Rnor_6.0 Ensembl32,888,103 - 2,893,495 (+)Ensembl
RefSeq Acc Id: NM_001001519   ⟹   NP_001001519
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8328,882,133 - 28,887,697 (+)NCBI
mRatBN7.238,484,013 - 8,489,577 (+)NCBI
Rnor_6.032,888,103 - 2,893,498 (+)NCBI
Rnor_5.032,869,516 - 2,874,911 (+)NCBI
RGSC_v3.433,836,357 - 3,841,922 (+)RGD
Celera33,308,865 - 3,314,429 (+)RGD
Sequence:
Protein RefSeqs NP_001001519 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAQ14496 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000033421
  ENSRNOP00000033421.4
RefSeq Acc Id: NP_001001519   ⟸   NM_001001519
- Peptide Label: precursor
- UniProtKB: Q6KGV4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000033421   ⟸   ENSRNOT00000029655
Lipocalin/cytosolic fatty-acid binding

Name Modeler Protein Id AA Range Protein Structure
AF-Q6KGV4-F1-model_v2 AlphaFold Q6KGV4 1-181 view protein structure


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



1 to 19 of 19 rows
Database
Acc Id
Source(s)
BioCyc Gene G2FUF-50428 BioCyc
Ensembl Genes ENSRNOG00000028095 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000029655 ENTREZGENE
  ENSRNOT00000029655.5 UniProtKB/TrEMBL
Gene3D-CATH 2.40.128.20 UniProtKB/TrEMBL
InterPro Calycin UniProtKB/TrEMBL
  Lipocalin UniProtKB/TrEMBL
  Lipocalin_CS UniProtKB/TrEMBL
  Lipocln_cytosolic_FA_bd UniProtKB/TrEMBL
KEGG Report rno:414138 UniProtKB/TrEMBL
NCBI Gene 414138 ENTREZGENE
PANTHER EPIDIDYMAL-SPECIFIC LIPOCALIN-6 UniProtKB/TrEMBL
  PTHR11430 UniProtKB/TrEMBL
Pfam Lipocalin UniProtKB/TrEMBL
PhenoGen Lcn6 PhenoGen
PROSITE LIPOCALIN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000028095 RatGTEx
Superfamily-SCOP Calycin UniProtKB/TrEMBL
UniProt Q6KGV4 ENTREZGENE, UniProtKB/TrEMBL
1 to 19 of 19 rows


Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-11-17 Lcn6  lipocalin 6      Symbol and Name status set to approved 1299863 APPROVED
2005-02-14 Lcn6  lipocalin 6      Symbol and Name status set to provisional 70820 PROVISIONAL