Pglyrp2 (peptidoglycan recognition protein 2) - Rat Genome Database

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Gene: Pglyrp2 (peptidoglycan recognition protein 2) Rattus norvegicus
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Symbol: Pglyrp2
Name: peptidoglycan recognition protein 2
RGD ID: 1359183
Description: Predicted to enable N-acetylmuramoyl-L-alanine amidase activity; peptidoglycan binding activity; and peptidoglycan immune receptor activity. Predicted to be involved in defense response to Gram-positive bacterium; detection of bacterium; and immune response. Predicted to act upstream of or within several processes, including negative regulation of natural killer cell differentiation involved in immune response; negative regulation of type II interferon production; and regulation of inflammatory response. Predicted to be located in membrane. Orthologous to human PGLYRP2 (peptidoglycan recognition protein 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; alpha-Zearalanol; gentamycin.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC299567; LOC691291; N-acetylmuramoyl-L-alanine amidase; similar to peptidoglycan recognition protein 2; similar to Peptidoglycan recognition protein-like
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
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
GRCr8712,069,414 - 12,082,437 (-)NCBIGRCr8
mRatBN7.2711,418,674 - 11,432,162 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl711,418,880 - 11,427,773 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx714,237,304 - 14,246,286 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0716,114,726 - 16,123,712 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0713,986,312 - 13,995,267 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0714,426,481 - 14,435,987 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl714,429,701 - 14,435,967 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0714,580,379 - 14,588,764 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4712,995,858 - 12,996,949 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera79,530,143 - 9,537,285 (-)NCBICelera
Cytogenetic Map7q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

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
5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:11461926   PMID:14506276   PMID:16930467   PMID:19218085   PMID:20709292   PMID:22048773   PMID:23376485   PMID:23533145  


Genomics

Comparative Map Data
Pglyrp2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8712,069,414 - 12,082,437 (-)NCBIGRCr8
mRatBN7.2711,418,674 - 11,432,162 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl711,418,880 - 11,427,773 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx714,237,304 - 14,246,286 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0716,114,726 - 16,123,712 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0713,986,312 - 13,995,267 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0714,426,481 - 14,435,987 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl714,429,701 - 14,435,967 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0714,580,379 - 14,588,764 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4712,995,858 - 12,996,949 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera79,530,143 - 9,537,285 (-)NCBICelera
Cytogenetic Map7q11NCBI
PGLYRP2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381915,468,645 - 15,479,501 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1915,468,645 - 15,498,956 (-)EnsemblGRCh38hg38GRCh38
GRCh371915,579,456 - 15,590,312 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361915,440,456 - 15,451,315 (-)NCBINCBI36Build 36hg18NCBI36
Build 341915,440,462 - 15,451,312NCBI
Celera1915,476,268 - 15,487,143 (-)NCBICelera
Cytogenetic Map19p13.12NCBI
HuRef1915,147,207 - 15,158,066 (-)NCBIHuRef
CHM1_11915,579,067 - 15,589,927 (-)NCBICHM1_1
T2T-CHM13v2.01915,593,641 - 15,604,523 (-)NCBIT2T-CHM13v2.0
Pglyrp2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391732,631,433 - 32,643,157 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1732,631,433 - 32,643,141 (-)EnsemblGRCm39 Ensembl
GRCm381732,412,459 - 32,424,219 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1732,412,459 - 32,424,167 (-)EnsemblGRCm38mm10GRCm38
MGSCv371732,550,045 - 32,557,920 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361732,550,306 - 32,561,112 (-)NCBIMGSCv36mm8
Celera1733,325,622 - 33,333,482 (-)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1717.56NCBI
Pglyrp2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554957,785,193 - 7,796,210 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554957,785,398 - 7,792,158 (+)NCBIChiLan1.0ChiLan1.0
PGLYRP2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22020,378,029 - 20,396,483 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11919,380,830 - 19,399,218 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01914,999,893 - 15,012,376 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11915,986,083 - 15,997,726 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1915,986,090 - 15,997,726 (-)Ensemblpanpan1.1panPan2
PGLYRP2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12046,724,906 - 46,730,227 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2046,726,224 - 46,730,321 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2046,572,665 - 46,577,974 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02047,211,739 - 47,217,048 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2047,210,950 - 47,217,128 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12046,446,615 - 46,451,923 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02046,863,271 - 46,868,579 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02047,136,764 - 47,142,073 (+)NCBIUU_Cfam_GSD_1.0
Pglyrp2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118205,489,000 - 205,495,525 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365965,038,452 - 5,044,569 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365965,038,452 - 5,043,172 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PGLYRP2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl262,134,533 - 62,140,184 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1262,135,578 - 62,140,180 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2261,567,649 - 61,572,250 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PGLYRP2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1614,072,310 - 14,084,014 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl614,072,423 - 14,082,798 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660745,424,409 - 5,435,504 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pglyrp2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249012,554,048 - 2,561,826 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249012,554,303 - 2,562,436 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pglyrp2
96 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:282
Count of miRNA genes:157
Interacting mature miRNAs:167
Transcripts:ENSRNOT00000042390, ENSRNOT00000060296, ENSRNOT00000074801
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
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat


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
8 6 12 63 91 90 59 25 59 6 165 57 43 35 50 31

Sequence


Ensembl Acc Id: ENSRNOT00000074801   ⟹   ENSRNOP00000064165
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl711,418,880 - 11,427,773 (-)Ensembl
Rnor_6.0 Ensembl714,429,701 - 14,435,967 (-)Ensembl
RefSeq Acc Id: NM_001399713   ⟹   NP_001386642
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8712,069,414 - 12,078,369 (-)NCBI
mRatBN7.2711,418,878 - 11,427,833 (-)NCBI
RefSeq Acc Id: XM_006241093   ⟹   XP_006241155
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8712,069,414 - 12,078,431 (-)NCBI
mRatBN7.2711,418,674 - 11,427,833 (-)NCBI
Rnor_6.0714,426,481 - 14,435,987 (-)NCBI
Rnor_5.0714,580,379 - 14,588,764 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039080048   ⟹   XP_038935976
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8712,069,414 - 12,082,414 (-)NCBI
mRatBN7.2711,418,951 - 11,432,162 (-)NCBI
RefSeq Acc Id: XM_063263155   ⟹   XP_063119225
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8712,069,414 - 12,082,437 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001386642 (Get FASTA)   NCBI Sequence Viewer  
  XP_006241155 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935976 (Get FASTA)   NCBI Sequence Viewer  
  XP_063119225 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH88306 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000064165.3
RefSeq Acc Id: XP_006241155   ⟸   XM_006241093
- Peptide Label: isoform X2
- Sequence:
Ensembl Acc Id: ENSRNOP00000064165   ⟸   ENSRNOT00000074801
RefSeq Acc Id: XP_038935976   ⟸   XM_039080048
- Peptide Label: isoform X1
- UniProtKB: M0R485 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001386642   ⟸   NM_001399713
- Peptide Label: precursor
- UniProtKB: M0R485 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063119225   ⟸   XM_063263155
- Peptide Label: isoform X1
- UniProtKB: M0R485 (UniProtKB/TrEMBL)
Protein Domains
N-acetylmuramoyl-L-alanine amidase   Peptidoglycan recognition protein family

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R485-F1-model_v2 AlphaFold M0R485 1-435 view protein structure

Transcriptome

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

Promoters
RGD ID:13695071
Promoter ID:EPDNEW_R5594
Type:initiation region
Name:Pglyrp2_1
Description:peptidoglycan recognition protein 2
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_6.0714,435,933 - 14,435,993EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359183 AgrOrtholog
BioCyc Gene G2FUF-34825 BioCyc
Ensembl Genes ENSRNOG00000042318 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000074801.4 UniProtKB/TrEMBL
Gene3D-CATH 3.40.80.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7324182 IMAGE-MGC_LOAD
InterPro Amidase_domain UniProtKB/TrEMBL
  Amidase_sf UniProtKB/TrEMBL
  PGRP UniProtKB/TrEMBL
  PGRP_domain_met/bac UniProtKB/TrEMBL
MGC_CLONE MGC:109520 IMAGE-MGC_LOAD
NCBI Gene 299567 ENTREZGENE
PANTHER N-ACETYLMURAMOYL-L-ALANINE AMIDASE UniProtKB/TrEMBL
  PTHR11022 UniProtKB/TrEMBL
Pfam Amidase_2 UniProtKB/TrEMBL
PhenoGen Pglyrp2 PhenoGen
RatGTEx ENSRNOG00000042318 RatGTEx
SMART Ami_2 UniProtKB/TrEMBL
  PGRP UniProtKB/TrEMBL
Superfamily-SCOP Amidase_2 UniProtKB/TrEMBL
UniProt M0R485 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-29 Pglyrp2  peptidoglycan recognition protein 2  LOC691291  similar to peptidoglycan recognition protein 2  Data merged from RGD:1586220 737654 PROVISIONAL
2013-08-09 Pglyrp2  peptidoglycan recognition protein 2  LOC299567  similar to Peptidoglycan recognition protein-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC691291  similar to peptidoglycan recognition protein 2      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-07-29 LOC299567  similar to Peptidoglycan recognition protein-like      Symbol and Name status set to provisional 70820 PROVISIONAL