Nlrc3 (NLR family, CARD domain containing 3) - Rat Genome Database

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Gene: Nlrc3 (NLR family, CARD domain containing 3) Rattus norvegicus
Analyze
Symbol: Nlrc3
Name: NLR family, CARD domain containing 3
RGD ID: 1304902
Description: Predicted to enable phosphatidylinositol 3-kinase regulatory subunit binding activity. Predicted to be involved in several processes, including negative regulation of cell population proliferation; negative regulation of cytokine production; and negative regulation of intracellular signal transduction. Predicted to act upstream of or within regulation of protein ubiquitination and response to lipopolysaccharide. Predicted to be located in centriolar satellite; intracellular membrane-bounded organelle; and perinuclear region of cytoplasm. Predicted to be part of inflammasome complex. Predicted to be active in cytosol. Orthologous to human NLRC3 (NLR family CARD domain containing 3); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC287070; NLR family CARD domain-containing protein 3; NLR family, CARD domain containing 3, pseudogene 1; Nlrc3-ps1; RGD1304902; similar to NOD3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21011,551,378 - 11,585,027 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1011,551,356 - 11,584,398 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01011,809,531 - 11,844,184 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1011,810,926 - 11,842,482 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01010,565,817 - 10,600,272 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41011,828,972 - 11,850,949 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11011,830,270 - 11,850,949 (+)NCBI
Celera1010,507,188 - 10,541,841 (+)NCBICelera
Cytogenetic Map10q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:15705585   PMID:22863753   PMID:24560620   PMID:25277106   PMID:27951586   PMID:32383265  


Genomics

Comparative Map Data
Nlrc3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21011,551,378 - 11,585,027 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1011,551,356 - 11,584,398 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01011,809,531 - 11,844,184 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1011,810,926 - 11,842,482 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01010,565,817 - 10,600,272 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41011,828,972 - 11,850,949 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11011,830,270 - 11,850,949 (+)NCBI
Celera1010,507,188 - 10,541,841 (+)NCBICelera
Cytogenetic Map10q12NCBI
NLRC3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38163,539,033 - 3,577,403 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl163,539,033 - 3,577,403 (-)EnsemblGRCh38hg38GRCh38
GRCh37163,589,033 - 3,627,404 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36163,529,034 - 3,567,393 (-)NCBINCBI36Build 36hg18NCBI36
Celera163,795,793 - 3,834,163 (-)NCBICelera
Cytogenetic Map16p13.3NCBI
HuRef163,558,668 - 3,596,656 (-)NCBIHuRef
CHM1_1163,589,077 - 3,627,393 (-)NCBICHM1_1
T2T-CHM13v2.0163,566,292 - 3,604,671 (-)NCBIT2T-CHM13v2.0
Nlrc3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39163,762,871 - 3,796,881 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl163,762,871 - 3,794,496 (-)EnsemblGRCm39 Ensembl
GRCm38163,943,807 - 3,979,017 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl163,945,007 - 3,976,632 (-)EnsemblGRCm38mm10GRCm38
MGSCv37163,946,933 - 3,976,632 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36163,860,235 - 3,891,860 (-)NCBIMGSCv36mm8
Celera164,577,681 - 4,607,937 (-)NCBICelera
Cytogenetic Map16A1NCBI
Nlrc3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544213,814,434 - 13,833,222 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544213,795,322 - 13,834,362 (+)NCBIChiLan1.0ChiLan1.0
NLRC3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1163,637,607 - 3,674,210 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl163,637,612 - 3,674,088 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0162,463,940 - 2,487,961 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
NLRC3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1637,668,654 - 37,707,387 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl637,647,976 - 37,703,190 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha638,996,730 - 39,036,797 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0637,882,981 - 37,923,068 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl637,883,470 - 37,920,833 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1637,666,136 - 37,706,192 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0637,559,251 - 37,599,498 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0637,969,988 - 38,010,066 (+)NCBIUU_Cfam_GSD_1.0
Nlrc3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344105,935,890 - 105,962,779 (-)NCBIHiC_Itri_2
SpeTri2.0NW_004936694757,121 - 773,924 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NLRC3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl338,687,967 - 38,710,938 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1338,673,590 - 38,719,188 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2340,028,718 - 40,050,697 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NLRC3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.153,241,552 - 3,262,763 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl53,242,242 - 3,262,261 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606827,540,652 - 27,579,410 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nlrc3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248241,357,326 - 1,375,688 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248241,356,587 - 1,375,403 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Nlrc3
121 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:159
Count of miRNA genes:118
Interacting mature miRNAs:129
Transcripts:ENSRNOT00000036189, ENSRNOT00000036205
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
1576304Schws7Schwannoma susceptibility QTL 70.0115nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)10476552719816042Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402717245662Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402719233348Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10538701450387014Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10615418215990232Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat


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 exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 8 19
Low 1 26 17 9 9 1 1 12 33 31 11 1
Below cutoff 17 32 32 32 7 9 58 2 8 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000036189   ⟹   ENSRNOP00000032675
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1011,563,461 - 11,584,398 (+)Ensembl
Rnor_6.0 Ensembl1011,810,926 - 11,842,482 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000036205   ⟹   ENSRNOP00000033954
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1011,563,461 - 11,565,819 (+)Ensembl
Rnor_6.0 Ensembl1011,810,926 - 11,824,905 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000102487   ⟹   ENSRNOP00000079659
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1011,551,880 - 11,584,398 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000115404   ⟹   ENSRNOP00000081315
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1011,551,356 - 11,584,398 (+)Ensembl
RefSeq Acc Id: XM_006245834   ⟹   XP_006245896
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21011,551,378 - 11,585,027 (+)NCBI
Rnor_6.01011,809,531 - 11,844,184 (+)NCBI
Rnor_5.01010,565,817 - 10,600,272 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_006245896 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_006245896   ⟸   XM_006245834
- UniProtKB: A0A8I5ZRD5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000032675   ⟸   ENSRNOT00000036189
RefSeq Acc Id: ENSRNOP00000033954   ⟸   ENSRNOT00000036205
RefSeq Acc Id: ENSRNOP00000081315   ⟸   ENSRNOT00000115404
RefSeq Acc Id: ENSRNOP00000079659   ⟸   ENSRNOT00000102487
Protein Domains
NACHT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZYP9-F1-model_v2 AlphaFold D3ZYP9 1-1100 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:1304902 AgrOrtholog
BioCyc Gene G2FUF-25996 BioCyc
Ensembl Genes ENSRNOG00000024210 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000032675.6 UniProtKB/TrEMBL
  ENSRNOP00000033954.5 UniProtKB/TrEMBL
  ENSRNOP00000079659.1 UniProtKB/TrEMBL
  ENSRNOP00000081315 ENTREZGENE
  ENSRNOP00000081315.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000036189.8 UniProtKB/TrEMBL
  ENSRNOT00000036205.5 UniProtKB/TrEMBL
  ENSRNOT00000102487.1 UniProtKB/TrEMBL
  ENSRNOT00000115404 ENTREZGENE
  ENSRNOT00000115404.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.300 UniProtKB/TrEMBL
  3.80.10.10 UniProtKB/TrEMBL
InterPro L_dom-like UniProtKB/TrEMBL
  Leu-rich_rpt UniProtKB/TrEMBL
  NACHT_NTPase UniProtKB/TrEMBL
  NLRC_HD2 UniProtKB/TrEMBL
  NOD2_WH UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
NCBI Gene 287070 ENTREZGENE
PANTHER F-BOX DOMAIN-CONTAINING PROTEIN UniProtKB/TrEMBL
  NACHT, LRR AND CARD DOMAINS-CONTAINING UniProtKB/TrEMBL
  NLR FAMILY CARD DOMAIN-CONTAINING PROTEIN 3 UniProtKB/TrEMBL
  RAN GTPASE-ACTIVATING PROTEIN 1 UniProtKB/TrEMBL
Pfam LRR_6 UniProtKB/TrEMBL
  NACHT UniProtKB/TrEMBL
  NLRC4_HD2 UniProtKB/TrEMBL
  NOD2_WH UniProtKB/TrEMBL
PhenoGen Nlrc3 PhenoGen
PROSITE NACHT UniProtKB/TrEMBL
SMART LRR_RI UniProtKB/TrEMBL
Superfamily-SCOP RNI-like UniProtKB/TrEMBL
  SSF52540 UniProtKB/TrEMBL
UniProt A0A8I5ZN35_RAT UniProtKB/TrEMBL
  A0A8I5ZRD5 ENTREZGENE, UniProtKB/TrEMBL
  D3ZYP9_RAT UniProtKB/TrEMBL
  D4A8Z8_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-03-05 Nlrc3  NLR family, CARD domain containing 3  Nlrc3-ps1  NLR family, CARD domain containing 3, pseudogene 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-06-08 Nlrc3-ps1  NLR family, CARD domain containing 3, pseudogene 1  Nlrc3  NLR family, CARD domain containing 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-04 Nlrc3  NLR family, CARD domain containing 3  RGD1304902_predicted  similar to NOD3 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1304902_predicted  similar to NOD3 (predicted)  LOC287070_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC287070_predicted  similar to NOD3 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL