Lcn12 (lipocalin 12) - Rat Genome Database

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Gene: Lcn12 (lipocalin 12) Rattus norvegicus
Analyze
Symbol: Lcn12 (Ensembl: C8g)
Name: lipocalin 12 (Ensembl:complement C8 gamma chain)
RGD ID: 1589474
Description: Enables retinoic acid binding activity. Predicted to be located in extracellular region. Predicted to be active in extracellular space. Orthologous to human LCN12 (lipocalin 12); INTERACTS WITH (+)-schisandrin B; 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: epididymal-specific lipocalin-12; LOC680602; similar to lipocalin 12
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Pig
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8328,710,557 - 28,713,537 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl328,707,042 - 28,720,501 (-)EnsemblGRCr8
mRatBN7.238,312,412 - 8,315,392 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,305,920 - 8,323,495 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx311,417,553 - 11,420,533 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0320,003,777 - 20,006,757 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0318,193,621 - 18,196,601 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.032,716,547 - 2,719,135 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl32,716,534 - 2,719,513 (-)Ensemblrn6Rnor6.0
Rnor_5.032,697,960 - 2,700,548 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.433,663,213 - 3,665,801 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera33,137,530 - 3,140,118 (-)NCBICelera
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. Conformational and biochemical characterization of a rat epididymis-specific lipocalin 12 expressed in Escherichia coli. Peng Y, etal., Biochim Biophys Acta. 2010 Nov;1804(11):2102-10. doi: 10.1016/j.bbapap.2010.07.020. Epub 2010 Aug 6.
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:21538546  


Genomics

Comparative Map Data
Lcn12
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8328,710,557 - 28,713,537 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl328,707,042 - 28,720,501 (-)EnsemblGRCr8
mRatBN7.238,312,412 - 8,315,392 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,305,920 - 8,323,495 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx311,417,553 - 11,420,533 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0320,003,777 - 20,006,757 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0318,193,621 - 18,196,601 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.032,716,547 - 2,719,135 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl32,716,534 - 2,719,513 (-)Ensemblrn6Rnor6.0
Rnor_5.032,697,960 - 2,700,548 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.433,663,213 - 3,665,801 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera33,137,530 - 3,140,118 (-)NCBICelera
Cytogenetic Map3p13NCBI
LCN12
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389136,949,197 - 136,956,538 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9136,949,551 - 136,955,497 (+)Ensemblhg38GRCh38
GRCh379139,846,725 - 139,849,949 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369138,966,589 - 138,969,770 (+)NCBIBuild 36Build 36hg18NCBI36
Build 349137,122,604 - 137,125,785NCBI
Celera9110,361,011 - 110,364,149 (+)NCBICelera
Cytogenetic Map9q34.3NCBI
HuRef9109,306,267 - 109,309,405 (+)NCBIHuRef
CHM1_19139,995,456 - 139,998,637 (+)NCBICHM1_1
T2T-CHM13v2.09149,183,558 - 149,189,824 (+)NCBIT2T-CHM13v2.0
Lcn12
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39225,380,857 - 25,384,073 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl225,380,857 - 25,383,923 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38225,490,845 - 25,494,061 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl225,490,845 - 25,493,911 (-)Ensemblmm10GRCm38
MGSCv37225,346,365 - 25,349,431 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36225,312,854 - 25,315,920 (-)NCBIMGSCv36mm8
Celera225,218,373 - 25,221,438 (-)NCBICelera
Cytogenetic Map2A3NCBI
cM Map217.3NCBI
Lcn12
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555134,998,288 - 5,003,691 (+)Ensembl
ChiLan1.0NW_0049555134,997,015 - 5,003,691 (+)NCBIChiLan1.0ChiLan1.0
LCN12
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2112,445,484 - 2,448,894 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan192,447,811 - 2,451,229 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09108,008,222 - 108,014,028 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19136,981,665 - 136,984,643 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9136,981,665 - 136,984,643 (+)EnsemblpanPan2panpan1.1
LCN12
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1948,663,181 - 48,669,264 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl948,665,943 - 48,668,859 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha947,876,681 - 47,882,740 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0949,541,123 - 49,547,182 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl949,543,885 - 49,546,802 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1948,317,334 - 48,323,393 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0948,616,049 - 48,622,108 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0948,663,213 - 48,669,262 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
LCN12
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa10.21313,750,073 - 313,755,254 (-)NCBISscrofa10.2Sscrofa10.2susScr3

Variants

.
Variants in Lcn12
8 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:138
Count of miRNA genes:110
Interacting mature miRNAs:119
Transcripts:ENSRNOT00000020997
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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
13 12 60 153 91 90 59 80 59 6 324 170 8 134 74 92 31 16 16

Sequence


Ensembl Acc Id: ENSRNOT00000020997   ⟹   ENSRNOP00000020997
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl328,710,557 - 28,720,501 (-)Ensembl
mRatBN7.2 Ensembl38,312,413 - 8,315,392 (-)Ensembl
Rnor_6.0 Ensembl32,716,534 - 2,719,513 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000061904   ⟹   ENSRNOP00000058619
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl328,709,811 - 28,720,501 (-)Ensembl
mRatBN7.2 Ensembl38,320,495 - 8,323,495 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000080257   ⟹   ENSRNOP00000070671
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl38,312,426 - 8,315,014 (-)Ensembl
Rnor_6.0 Ensembl32,716,547 - 2,719,135 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000094611   ⟹   ENSRNOP00000088027
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl328,710,557 - 28,720,501 (-)Ensembl
mRatBN7.2 Ensembl38,312,422 - 8,322,492 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000095335   ⟹   ENSRNOP00000078212
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl38,305,920 - 8,322,492 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000100264   ⟹   ENSRNOP00000079763
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl328,707,042 - 28,720,501 (-)Ensembl
mRatBN7.2 Ensembl38,320,505 - 8,322,492 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000107231   ⟹   ENSRNOP00000085280
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl328,710,557 - 28,720,501 (-)Ensembl
mRatBN7.2 Ensembl38,319,713 - 8,322,492 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000119757   ⟹   ENSRNOP00000078443
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl328,709,541 - 28,720,501 (-)Ensembl
mRatBN7.2 Ensembl38,309,076 - 8,322,492 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000120022   ⟹   ENSRNOP00000092118
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl328,710,624 - 28,720,501 (-)Ensembl
mRatBN7.2 Ensembl38,312,409 - 8,322,492 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000143624   ⟹   ENSRNOP00000101822
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl328,710,624 - 28,713,537 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000155451   ⟹   ENSRNOP00000104511
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl328,710,624 - 28,720,501 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000165026   ⟹   ENSRNOP00000109083
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl328,710,624 - 28,720,501 (-)Ensembl
RefSeq Acc Id: NM_001128138   ⟹   NP_001121610
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8328,710,571 - 28,713,159 (-)NCBI
mRatBN7.238,312,426 - 8,315,014 (-)NCBI
Rnor_6.032,716,547 - 2,719,135 (-)NCBI
Rnor_5.032,697,960 - 2,700,548 (-)NCBI
RGSC_v3.433,663,213 - 3,665,801 (-)RGD
Celera33,137,530 - 3,140,118 (-)RGD
Sequence:
RefSeq Acc Id: NM_001395074   ⟹   NP_001382003
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8328,710,557 - 28,713,537 (-)NCBI
mRatBN7.238,312,412 - 8,315,392 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001121610 (Get FASTA)   NCBI Sequence Viewer  
  NP_001382003 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein ABG24235 (Get FASTA)   NCBI Sequence Viewer  
  B3EY83 (Get FASTA)   NCBI Sequence Viewer  
  EDL93574 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000020997.6
  ENSRNOP00000101822
RefSeq Acc Id: NP_001121610   ⟸   NM_001128138
- Peptide Label: isoform 2
- UniProtKB: A0A0G2JYI8 (UniProtKB/TrEMBL),   A6JT73 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000070671   ⟸   ENSRNOT00000080257
Ensembl Acc Id: ENSRNOP00000020997   ⟸   ENSRNOT00000020997
Ensembl Acc Id: ENSRNOP00000092118   ⟸   ENSRNOT00000120022
Ensembl Acc Id: ENSRNOP00000079763   ⟸   ENSRNOT00000100264
Ensembl Acc Id: ENSRNOP00000078212   ⟸   ENSRNOT00000095335
Ensembl Acc Id: ENSRNOP00000088027   ⟸   ENSRNOT00000094611
Ensembl Acc Id: ENSRNOP00000085280   ⟸   ENSRNOT00000107231
Ensembl Acc Id: ENSRNOP00000078443   ⟸   ENSRNOT00000119757
Ensembl Acc Id: ENSRNOP00000058619   ⟸   ENSRNOT00000061904
RefSeq Acc Id: NP_001382003   ⟸   NM_001395074
- Peptide Label: isoform 1 precursor
- UniProtKB: B3EY83 (UniProtKB/Swiss-Prot),   D3ZI71 (UniProtKB/Swiss-Prot),   H9KVE9 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000104511   ⟸   ENSRNOT00000155451
Ensembl Acc Id: ENSRNOP00000101822   ⟸   ENSRNOT00000143624
Ensembl Acc Id: ENSRNOP00000109083   ⟸   ENSRNOT00000165026
Protein Domains
Lipocalin/cytosolic fatty-acid binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B3EY83-F1-model_v2 AlphaFold B3EY83 1-193 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:1589474 AgrOrtholog
BioCyc Gene G2FUF-50445 BioCyc
Ensembl Genes ENSRNOG00000028701 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00000028730 Ensembl
Ensembl Transcript ENSRNOT00000020997.6 UniProtKB/Swiss-Prot
  ENSRNOT00000143624 ENTREZGENE
Gene3D-CATH 2.40.128.20 UniProtKB/Swiss-Prot
InterPro Calycin UniProtKB/Swiss-Prot
  LCN2/LCN12 UniProtKB/Swiss-Prot
  Lipocalin UniProtKB/Swiss-Prot
  Lipocln_cytosolic_FA-bd_dom UniProtKB/Swiss-Prot
NCBI Gene 680602 ENTREZGENE
PANTHER EPIDIDYMAL-SPECIFIC LIPOCALIN-12 UniProtKB/Swiss-Prot
  PTHR11430 UniProtKB/Swiss-Prot
Pfam Lipocalin UniProtKB/Swiss-Prot
PhenoGen Lcn12 PhenoGen
PRINTS NGELATINASE UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000028701 RatGTEx
  ENSRNOG00000028730 RatGTEx
Superfamily-SCOP SSF50814 UniProtKB/Swiss-Prot
UniProt A0A0G2JYI8 ENTREZGENE
  A0A8I5ZKU8_RAT UniProtKB/TrEMBL
  A0A8I6A1Y6_RAT UniProtKB/TrEMBL
  A0A8I6A491_RAT UniProtKB/TrEMBL
  A0A8I6AEX7_RAT UniProtKB/TrEMBL
  A0ABK0L9A0_RAT UniProtKB/TrEMBL
  A0ABK0LSZ1_RAT UniProtKB/TrEMBL
  A0ABK0LUP9_RAT UniProtKB/TrEMBL
  A6JT73 ENTREZGENE, UniProtKB/TrEMBL
  B3EY83 ENTREZGENE
  D3ZI71 ENTREZGENE
  D3ZPI8_RAT UniProtKB/TrEMBL
  H9KVE9 ENTREZGENE, UniProtKB/TrEMBL
  LCN12_RAT UniProtKB/Swiss-Prot
UniProt Secondary D3ZI71 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-05 Lcn12  lipocalin 12  LOC680602  similar to lipocalin 12  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC680602  similar to lipocalin 12  LOC687251  similar to lipocalin 12  Data merged from RGD:1587727 1643240 APPROVED
2006-11-19 LOC680602  similar to lipocalin 12      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC687251  similar to lipocalin 12      Symbol and Name status set to provisional 70820 PROVISIONAL