LCN2 (lipocalin 2) - Rat Genome Database

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Gene: LCN2 (lipocalin 2) Sus scrofa
Analyze
Symbol: LCN2
Name: lipocalin 2
RGD ID: 14043606
Description: ENCODES a protein that exhibits enterobactin binding (ortholog); identical protein binding (ortholog); iron ion binding (ortholog); INVOLVED IN acute-phase response (ortholog); cellular response to amyloid-beta (ortholog); cellular response to hydrogen peroxide (ortholog); ASSOCIATED WITH Abscess (ortholog); acute cystitis (ortholog); acute kidney failure (ortholog); FOUND IN cytoplasm (ortholog); cytosol (ortholog); extracellular space (ortholog)
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: neutrophil gelatinase-associated lipocalin
RGD Orthologs
Human
Mouse
Rat
Bonobo
Dog
Squirrel
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11268,609,975 - 268,614,651 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21302,600,679 - 302,609,836 (+)NCBISscrofa10.2Sscrofa10.2susScr3
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Abscess  (ISO)
acute cystitis  (ISO)
acute kidney failure  (ISO)
adult respiratory distress syndrome  (ISO)
amyotrophic lateral sclerosis  (ISO)
Animal Hepatitis  (ISO)
autosomal dominant polycystic kidney disease  (ISO)
beta thalassemia  (ISO)
Brain Injuries, Traumatic  (ISO)
calcinosis  (ISO)
celiac disease  (ISO)
Cerebral Hemorrhage  (ISO)
Chemical and Drug Induced Liver Injury  (ISO)
Chlamydophila Infections  (ISO)
chronic kidney disease  (ISO)
colon cancer  (ISO)
congenital diaphragmatic hernia  (ISO)
congenital disorder of glycosylation Iu  (ISO)
contact dermatitis  (ISO)
Contrast-Induced Nephropathy  (ISO)
COVID-19  (ISO)
developmental and epileptic encephalopathy  (ISO)
developmental and epileptic encephalopathy 31  (ISO)
Diabetic Nephropathies  (ISO)
disease of cellular proliferation  (ISO)
Drug-Related Side Effects and Adverse Reactions  (ISO)
early infantile epileptic encephalopathy  (ISO)
end stage renal disease  (ISO)
Endotoxemia  (ISO)
Escherichia Coli Infections  (ISO)
essential hypertension  (ISO)
Experimental Diabetes Mellitus  (ISO)
Experimental Liver Cirrhosis  (ISO)
Haemophilus Infections  (ISO)
heart valve disease  (ISO)
Helicobacter Infections  (ISO)
hidradenitis suppurativa  (ISO)
hydronephrosis  (ISO)
hyperuricemia  (ISO)
IgA glomerulonephritis  (ISO)
Inflammation  (ISO)
intrahepatic cholangiocarcinoma  (ISO)
kidney disease  (ISO)
Kidney Reperfusion Injury  (ISO)
Klebsiella pneumonia  (ISO)
myocardial infarction  (ISO)
myocarditis  (ISO)
Neoplasm Metastasis  (ISO)
obesity  (ISO)
oral candidiasis  (ISO)
pneumonia  (ISO)
polycystic kidney disease  (ISO)
pre-eclampsia  (ISO)
primary coenzyme Q10 deficiency 7  (ISO)
pulmonary hypertension  (ISO)
pulmonary tuberculosis  (ISO)
Radiation Injuries, Experimental  (ISO)
renal fibrosis  (ISO)
Renal Ischemia  (ISO)
renovascular hypertension  (ISO)
retinal degeneration  (ISO)
rheumatoid arthritis  (ISO)
Sepsis  (ISO)
Streptococcal Infections  (ISO)
Stroke  (ISO)
Subarachnoid Hemorrhage  (ISO)
transient cerebral ischemia  (ISO)
type 2 diabetes mellitus  (ISO)
urinary tract infection  (ISO)
uveitis  (ISO)
West Nile encephalitis  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
acute-phase response  (ISO)
cellular response to amyloid-beta  (ISO)
cellular response to hydrogen peroxide  (ISO)
cellular response to increased oxygen levels  (ISO)
cellular response to interleukin-1  (ISO)
cellular response to interleukin-6  (ISO)
cellular response to lipopolysaccharide  (ISO)
cellular response to nerve growth factor stimulus  (ISO)
cellular response to nutrient levels  (ISO)
cellular response to oxygen-glucose deprivation  (ISO)
cellular response to tumor necrosis factor  (ISO)
cellular response to X-ray  (ISO)
defense response to bacterium  (ISO)
extrinsic apoptotic signaling pathway in absence of ligand  (ISO)
innate immune response  (ISO)
long-term memory  (ISO)
negative regulation of hippocampal neuron apoptotic process  (ISO)
positive regulation of apoptotic process  (ISO)
positive regulation of cell projection organization  (ISO)
positive regulation of cold-induced thermogenesis  (ISO)
positive regulation of endothelial cell migration  (ISO)
positive regulation of endothelial tube morphogenesis  (ISO)
positive regulation of gene expression  (ISO)
positive regulation of iron ion import across plasma membrane  (ISO)
positive regulation of neuron apoptotic process  (ISO)
positive regulation of neuron death  (ISO)
positive regulation of reactive oxygen species biosynthetic process  (ISO)
positive regulation of reactive oxygen species metabolic process  (ISO)
response to bacterium  (ISO)
response to blue light  (ISO)
response to fructose  (ISO)
response to herbicide  (ISO)
response to iron(II) ion  (ISO)
response to mycotoxin  (ISO)
response to nutrient levels  (ISO)
response to oxidative stress  (ISO)
response to toxic substance  (ISO)
response to virus  (ISO)
response to xenobiotic stimulus  (ISO)
sequestering of iron ion  (ISO)
short-term memory  (ISO)
siderophore transport  (ISO)

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:14681463   PMID:18435830   PMID:19664223   PMID:23710440  


Genomics

Comparative Map Data
LCN2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11268,609,975 - 268,614,651 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21302,600,679 - 302,609,836 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LCN2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl9128,149,071 - 128,153,453 (+)EnsemblGRCh38hg38GRCh38
GRCh389128,149,453 - 128,153,453 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh379130,911,732 - 130,915,732 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369129,951,553 - 129,955,555 (+)NCBINCBI36hg18NCBI36
Build 349127,991,271 - 127,995,288NCBI
Celera9101,562,624 - 101,566,626 (+)NCBI
Cytogenetic Map9q34.11NCBI
HuRef9100,525,402 - 100,529,404 (+)NCBIHuRef
CHM1_19131,062,742 - 131,066,744 (+)NCBICHM1_1
Lcn2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39232,274,649 - 32,277,751 (-)NCBIGRCm39mm39
GRCm39 Ensembl232,274,645 - 32,278,264 (-)Ensembl
GRCm38232,384,637 - 32,387,739 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl232,384,633 - 32,388,252 (-)EnsemblGRCm38mm10GRCm38
MGSCv37232,240,157 - 32,243,259 (-)NCBIGRCm37mm9NCBIm37
MGSCv36232,206,646 - 32,209,748 (-)NCBImm8
Celera232,090,046 - 32,093,150 (-)NCBICelera
Cytogenetic Map2BNCBI
cM Map222.09NCBI
Lcn2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2315,680,688 - 15,684,033 (-)NCBI
Rnor_6.0 Ensembl311,414,186 - 11,417,546 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0311,414,189 - 11,417,534 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0316,763,059 - 16,766,404 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4311,511,402 - 11,514,747 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1311,407,773 - 11,411,119 (-)NCBI
Celera310,423,569 - 10,426,914 (-)NCBICelera
Cytogenetic Map3p12NCBI
LCN2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19127,940,799 - 127,944,798 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9127,940,799 - 127,944,798 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0999,259,278 - 99,274,494 (+)NCBIMhudiblu_PPA_v0panPan3
LCN2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1955,328,118 - 55,342,535 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl955,328,133 - 55,332,038 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha954,522,898 - 54,537,231 (-)NCBI
ROS_Cfam_1.0956,250,316 - 56,264,670 (-)NCBI
UMICH_Zoey_3.1955,010,191 - 55,024,522 (-)NCBI
UNSW_CanFamBas_1.0955,324,906 - 55,339,237 (-)NCBI
UU_Cfam_GSD_1.0955,416,588 - 55,430,934 (-)NCBI
Lcn2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947195,953,204 - 195,956,869 (+)NCBI
SpeTri2.0NW_00493648715,721,752 - 15,725,396 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LCN2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1129,976,278 - 9,981,087 (-)NCBI
ChlSab1.1 Ensembl129,976,614 - 9,980,870 (-)Ensembl
Vero_WHO_p1.0NW_0236660796,251,600 - 6,256,754 (+)NCBI


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system hemolymphoid system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 1 2 2 3
Low 10 4 3 4 2 20 2 1
Below cutoff 1

Sequence


Reference Sequences
RefSeq Acc Id: NM_001244410   ⟹   NP_001231339
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11268,610,223 - 268,614,645 (+)NCBI
Sequence:
RefSeq Acc Id: XM_021088538   ⟹   XP_020944197
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11268,609,975 - 268,614,651 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001231339 (Get FASTA)   NCBI Sequence Viewer  
  XP_020944197 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAX36897 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_020944197   ⟸   XM_021088538
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: NP_001231339   ⟸   NM_001244410
- Peptide Label: precursor
- Sequence:
Protein Domains
Lipocln_cytosolic_FA-bd_dom


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000005638 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSSSCP00000006041 ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCP00000056109 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000006200 ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCT00000065649 UniProtKB/TrEMBL
Gene3D-CATH 2.40.128.20 UniProtKB/TrEMBL
InterPro Calycin UniProtKB/TrEMBL
  LCN2/LCN12 UniProtKB/TrEMBL
  Lipocalin UniProtKB/TrEMBL
  Lipocalin_CS UniProtKB/TrEMBL
  Lipocln_cytosolic_FA-bd_dom UniProtKB/TrEMBL
NCBI Gene LCN2 ENTREZGENE
PANTHER PTHR11430 UniProtKB/TrEMBL
Pfam Lipocalin UniProtKB/TrEMBL
PRINTS NGELATINASE UniProtKB/TrEMBL
PROSITE LIPOCALIN UniProtKB/TrEMBL
Superfamily-SCOP SSF50814 UniProtKB/TrEMBL
UniProt A0A287BJ65_PIG UniProtKB/TrEMBL
  C7C1J2_PIG UniProtKB/TrEMBL
  F1RRX1_PIG UniProtKB/TrEMBL
VGNC ID VGNC:89662 ENTREZGENE