Lcn9 (lipocalin 9) - Rat Genome Database

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Gene: Lcn9 (lipocalin 9) Rattus norvegicus
Analyze
Symbol: Lcn9
Name: lipocalin 9
RGD ID: 1306341
Description: Predicted to enable small molecule binding activity. Predicted to be located in extracellular region. Predicted to be active in extracellular space. Orthologous to human LCN9 (lipocalin 9); INTERACTS WITH bisphenol A; cadmium dichloride; trichloroethene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: epididymal-specific lipocalin-9; LOC296578; RGD1306341; similar to Putative MUP-like lipocalin precursor
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8329,041,710 - 29,050,677 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl329,041,133 - 29,044,895 (+)EnsemblGRCr8
mRatBN7.238,644,427 - 8,646,782 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,636,548 - 8,652,200 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx311,698,621 - 11,700,973 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0320,281,832 - 20,284,184 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0318,537,153 - 18,539,505 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.033,272,150 - 3,274,792 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl33,272,193 - 3,274,547 (+)Ensemblrn6Rnor6.0
Rnor_5.038,634,275 - 8,636,629 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.433,996,496 - 3,998,850 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera33,467,437 - 3,469,791 (+)NCBICelera
RGSC_v3.133,996,506 - 3,998,233 (+)NCBI
Cytogenetic Map3p13NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

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. 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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:23017836  


Genomics

Comparative Map Data
Lcn9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8329,041,710 - 29,050,677 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl329,041,133 - 29,044,895 (+)EnsemblGRCr8
mRatBN7.238,644,427 - 8,646,782 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,636,548 - 8,652,200 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx311,698,621 - 11,700,973 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0320,281,832 - 20,284,184 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0318,537,153 - 18,539,505 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.033,272,150 - 3,274,792 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl33,272,193 - 3,274,547 (+)Ensemblrn6Rnor6.0
Rnor_5.038,634,275 - 8,636,629 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.433,996,496 - 3,998,850 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera33,467,437 - 3,469,791 (+)NCBICelera
RGSC_v3.133,996,506 - 3,998,233 (+)NCBI
Cytogenetic Map3p13NCBI
LCN9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389135,663,309 - 135,666,961 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9135,663,309 - 135,666,961 (+)Ensemblhg38GRCh38
GRCh379138,555,155 - 138,558,807 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369137,694,989 - 137,697,770 (+)NCBIBuild 36Build 36hg18NCBI36
Build 349135,781,112 - 135,783,700NCBI
Celera9109,072,999 - 109,075,781 (+)NCBICelera
Cytogenetic Map9q34.3NCBI
HuRef9108,017,019 - 108,019,760 (+)NCBIHuRef
CHM1_19138,703,687 - 138,706,468 (+)NCBICHM1_1
T2T-CHM13v2.09147,889,683 - 147,893,335 (+)NCBIT2T-CHM13v2.0
Lcn9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39225,713,100 - 25,715,558 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl225,713,165 - 25,715,549 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38225,823,088 - 25,825,546 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl225,823,153 - 25,825,537 (+)Ensemblmm10GRCm38
MGSCv37225,678,673 - 25,681,057 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36225,645,162 - 25,647,546 (+)NCBIMGSCv36mm8
Celera225,542,705 - 25,545,089 (+)NCBICelera
Cytogenetic Map2A3NCBI
cM Map218.15NCBI
Lcn9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555134,787,222 - 4,788,768 (-)Ensembl
ChiLan1.0NW_0049555134,786,615 - 4,788,768 (-)NCBIChiLan1.0ChiLan1.0
LCN9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2113,720,888 - 3,724,539 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan193,723,221 - 3,726,872 (-)NCBINHGRI_mPanPan1
LCN9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1949,632,813 - 49,636,854 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl949,632,799 - 49,637,517 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha948,885,218 - 48,889,279 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0950,511,967 - 50,516,033 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl950,513,262 - 50,515,241 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1949,291,922 - 49,295,114 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0949,586,426 - 49,590,488 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0949,635,077 - 49,638,824 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Lcn9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947201,443,005 - 201,444,836 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366691,930,272 - 1,932,167 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366691,930,222 - 1,932,053 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LCN9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa10.21308,696,220 - 308,698,468 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LCN9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1122,526,003 - 2,530,175 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660582,631,001 - 2,634,529 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lcn9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247601,143,457 - 1,145,561 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Lcn9
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1511,258,902 - 11,261,203 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Lcn9
21 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:184
Count of miRNA genes:114
Interacting mature miRNAs:130
Transcripts:ENSRNOT00000044284
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.


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
nervous system
renal system
reproductive system
respiratory system
2 5 1 10 8 8 1 12 1 3 42 22 4 14 37 7

Sequence


Ensembl Acc Id: ENSRNOT00000044284   ⟹   ENSRNOP00000047057
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl329,042,541 - 29,044,895 (+)Ensembl
mRatBN7.2 Ensembl38,644,427 - 8,646,782 (+)Ensembl
Rnor_6.0 Ensembl33,272,193 - 3,274,547 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000107186   ⟹   ENSRNOP00000092390
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl38,636,548 - 8,652,200 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000109099   ⟹   ENSRNOP00000086331
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl329,041,133 - 29,044,342 (+)Ensembl
mRatBN7.2 Ensembl38,636,548 - 8,646,783 (+)Ensembl
RefSeq Acc Id: NM_001106560   ⟹   NP_001100030
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8329,042,541 - 29,044,895 (+)NCBI
mRatBN7.238,644,427 - 8,646,782 (+)NCBI
Rnor_6.033,272,193 - 3,274,547 (+)NCBI
Rnor_5.038,634,275 - 8,636,629 (+)NCBI
RGSC_v3.433,996,496 - 3,998,850 (+)RGD
Celera33,467,437 - 3,469,791 (+)RGD
Sequence:
RefSeq Acc Id: XM_063283465   ⟹   XP_063139535
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8329,041,710 - 29,050,677 (+)NCBI
RefSeq Acc Id: XM_063283466   ⟹   XP_063139536
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8329,041,710 - 29,050,677 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001100030 (Get FASTA)   NCBI Sequence Viewer  
  XP_063139535 (Get FASTA)   NCBI Sequence Viewer  
  XP_063139536 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein ABG24239 (Get FASTA)   NCBI Sequence Viewer  
  EDL93536 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000047057
  ENSRNOP00000047057.2
  ENSRNOP00000086331.2
RefSeq Acc Id: NP_001100030   ⟸   NM_001106560
- Peptide Label: precursor
- UniProtKB: B3EY87 (UniProtKB/TrEMBL),   A6JTB1 (UniProtKB/TrEMBL),   F7FKU6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000047057   ⟸   ENSRNOT00000044284
Ensembl Acc Id: ENSRNOP00000092390   ⟸   ENSRNOT00000107186
Ensembl Acc Id: ENSRNOP00000086331   ⟸   ENSRNOT00000109099
RefSeq Acc Id: XP_063139535   ⟸   XM_063283465
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063139536   ⟸   XM_063283466
- Peptide Label: isoform X2
Protein Domains
Lipocalin/cytosolic fatty-acid binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B3EY87-F1-model_v2 AlphaFold B3EY87 1-179 view protein structure

Transcriptome

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

Promoters
RGD ID:13691893
Promoter ID:EPDNEW_R2417
Type:single initiation site
Name:Lcn9_1
Description:lipocalin 9
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_6.033,272,197 - 3,272,257EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306341 AgrOrtholog
BioCyc Gene G2FUF-50411 BioCyc
Ensembl Genes ENSRNOG00000027821 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000044284 ENTREZGENE
  ENSRNOT00000044284.4 UniProtKB/TrEMBL
  ENSRNOT00000109099.2 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
  Maj_urinary UniProtKB/TrEMBL
KEGG Report rno:296578 UniProtKB/TrEMBL
NCBI Gene 296578 ENTREZGENE
PANTHER EPIDIDYMAL-SPECIFIC LIPOCALIN-9 UniProtKB/TrEMBL
  PTHR11430 UniProtKB/TrEMBL
Pfam Lipocalin UniProtKB/TrEMBL
PhenoGen Lcn9 PhenoGen
PRINTS LIPOCALIN UniProtKB/TrEMBL
  MAJORURINARY UniProtKB/TrEMBL
PROSITE LIPOCALIN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000027821 RatGTEx
Superfamily-SCOP Calycin UniProtKB/TrEMBL
UniProt A0A8I6GET9_RAT UniProtKB/TrEMBL
  A6JTB1 ENTREZGENE, UniProtKB/TrEMBL
  B3EY87 ENTREZGENE
  F7FKU6 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary B3EY87 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Lcn9  lipocalin 9   Lcn9_predicted  lipocalin 9 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Lcn9_predicted  lipocalin 9 (predicted)  RGD1306341_predicted  similar to Putative MUP-like lipocalin precursor (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1306341_predicted  similar to Putative MUP-like lipocalin precursor (predicted)  LOC296578_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC296578_predicted  similar to Putative MUP-like lipocalin precursor (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL