Pnma2 (PNMA family member 2) - Rat Genome Database

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Gene: Pnma2 (PNMA family member 2) Rattus norvegicus
Analyze
Symbol: Pnma2
Name: PNMA family member 2
RGD ID: 1307266
Description: Predicted to be located in nucleolus. Orthologous to human PNMA2 (PNMA family member 2); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC305977; paraneoplastic antigen MA2; paraneoplastic Ma antigen 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81545,287,445 - 45,296,340 (+)NCBIGRCr8
mRatBN7.21541,111,942 - 41,119,649 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1541,112,009 - 41,121,427 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1542,977,486 - 42,985,039 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01544,127,698 - 44,135,253 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01542,572,270 - 42,579,929 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01543,581,874 - 43,589,680 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1543,582,020 - 43,589,680 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01548,006,292 - 48,014,067 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41546,452,913 - 46,460,573 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11546,473,585 - 46,474,680 (+)NCBI
Celera1540,779,534 - 40,786,898 (+)NCBICelera
Cytogenetic Map15p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleolus  (IEA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:31505169  


Genomics

Comparative Map Data
Pnma2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81545,287,445 - 45,296,340 (+)NCBIGRCr8
mRatBN7.21541,111,942 - 41,119,649 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1541,112,009 - 41,121,427 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1542,977,486 - 42,985,039 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01544,127,698 - 44,135,253 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01542,572,270 - 42,579,929 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01543,581,874 - 43,589,680 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1543,582,020 - 43,589,680 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01548,006,292 - 48,014,067 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41546,452,913 - 46,460,573 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11546,473,585 - 46,474,680 (+)NCBI
Celera1540,779,534 - 40,786,898 (+)NCBICelera
Cytogenetic Map15p12NCBI
PNMA2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38826,504,701 - 26,513,872 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl826,504,701 - 26,514,092 (-)EnsemblGRCh38hg38GRCh38
GRCh37826,362,217 - 26,371,388 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36826,418,113 - 26,427,400 (-)NCBINCBI36Build 36hg18NCBI36
Celera825,324,618 - 25,333,902 (-)NCBICelera
Cytogenetic Map8p21.2NCBI
HuRef824,907,036 - 24,916,314 (-)NCBIHuRef
CHM1_1826,563,803 - 26,573,090 (-)NCBICHM1_1
T2T-CHM13v2.0826,781,276 - 26,790,451 (-)NCBIT2T-CHM13v2.0
Pnma2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391467,139,038 - 67,157,512 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1467,148,619 - 67,158,472 (+)EnsemblGRCm39 Ensembl
GRCm381466,901,589 - 66,920,063 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1466,911,170 - 66,921,023 (+)EnsemblGRCm38mm10GRCm38
MGSCv371467,530,045 - 67,538,898 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361465,869,515 - 65,874,167 (+)NCBIMGSCv36mm8
Celera1464,664,973 - 64,673,798 (+)NCBICelera
Cytogenetic Map14D1NCBI
cM Map1434.6NCBI
Pnma2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495540349,183,280 - 49,184,855 (-)NCBIChiLan1.0ChiLan1.0
PNMA2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2745,038,107 - 45,047,393 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1820,752,210 - 20,761,495 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0825,777,591 - 25,786,877 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1822,684,517 - 22,693,903 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl822,687,494 - 22,688,588 (-)Ensemblpanpan1.1panPan2
PNMA2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12531,038,519 - 31,045,874 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2531,042,477 - 31,043,571 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2531,626,722 - 31,634,100 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02531,238,188 - 31,245,570 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2531,238,204 - 31,245,591 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12531,172,868 - 31,180,236 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02531,043,957 - 31,051,322 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02531,210,416 - 31,217,798 (+)NCBIUU_Cfam_GSD_1.0
Pnma2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049439,170,548 - 9,176,853 (+)NCBIHiC_Itri_2
SpeTri2.0NW_004936757423,220 - 429,447 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PNMA2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1410,422,331 - 10,428,389 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11410,422,325 - 10,428,389 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21411,587,498 - 11,593,567 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PNMA2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1824,620,551 - 24,625,695 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl824,619,441 - 24,620,535 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605217,533,473 - 17,542,911 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pnma2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475821,350,675 - 21,355,715 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475821,322,368 - 21,355,720 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pnma2
50 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:713
Count of miRNA genes:269
Interacting mature miRNAs:345
Transcripts:ENSRNOT00000013001
Prediction methods:Microtar, Miranda, 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
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153361105871477291Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153361105871477291Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)154063126898288169Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
152025253Hrtrt24Heart rate QTL 243.82heart pumping trait (VT:2000009)152788577486257085Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)151985656646187442Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)153405413979054139Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
2306968Anxrr23Anxiety related response QTL 234.83reflex trait (VT:0001961)amplitude of the acoustic startle response (CMO:0001520)154063126846187442Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
7411725Strs7Sensitivity to stroke QTL 73.8cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)154028990149308583Rat


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
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000013001   ⟹   ENSRNOP00000013001
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1541,112,028 - 41,121,427 (+)Ensembl
Rnor_6.0 Ensembl1543,582,020 - 43,589,680 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000096509   ⟹   ENSRNOP00000082403
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1541,112,009 - 41,121,031 (+)Ensembl
RefSeq Acc Id: NM_001107272   ⟹   NP_001100742
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81545,287,480 - 45,295,139 (+)NCBI
mRatBN7.21541,111,990 - 41,119,649 (+)NCBI
Rnor_6.01543,582,020 - 43,589,680 (+)NCBI
Rnor_5.01548,006,292 - 48,014,067 (-)NCBI
RGSC_v3.41546,452,913 - 46,460,573 (+)RGD
Celera1540,779,534 - 40,786,898 (+)RGD
Sequence:
RefSeq Acc Id: XM_039093337   ⟹   XP_038949265
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81545,287,445 - 45,296,340 (+)NCBI
mRatBN7.21541,111,942 - 41,119,311 (+)NCBI
RefSeq Acc Id: XM_063274291   ⟹   XP_063130361
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81545,287,475 - 45,296,340 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001100742 (Get FASTA)   NCBI Sequence Viewer  
  XP_038949265 (Get FASTA)   NCBI Sequence Viewer  
  XP_063130361 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL85395 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000013001.3
  ENSRNOP00000082403.1
RefSeq Acc Id: NP_001100742   ⟸   NM_001107272
- UniProtKB: D4A068 (UniProtKB/TrEMBL),   A6K6N5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000013001   ⟸   ENSRNOT00000013001
RefSeq Acc Id: XP_038949265   ⟸   XM_039093337
- Peptide Label: isoform X1
- UniProtKB: D4A068 (UniProtKB/TrEMBL),   A6K6N5 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000082403   ⟸   ENSRNOT00000096509
RefSeq Acc Id: XP_063130361   ⟸   XM_063274291
- Peptide Label: isoform X1
- UniProtKB: A6K6N5 (UniProtKB/TrEMBL),   D4A068 (UniProtKB/TrEMBL)
Protein Domains
Paraneoplastic antigen Ma-like C-terminal   Paraneoplastic antigen Ma-like N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A068-F1-model_v2 AlphaFold D4A068 1-364 view protein structure

Transcriptome

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

Promoters
RGD ID:13699760
Promoter ID:EPDNEW_R10283
Type:single initiation site
Name:Pnma2_1
Description:PNMA family member 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_6.01543,582,050 - 43,582,110EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307266 AgrOrtholog
BioCyc Gene G2FUF-13318 BioCyc
Ensembl Genes ENSRNOG00000009815 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000013001.4 UniProtKB/TrEMBL
  ENSRNOT00000096509.1 UniProtKB/TrEMBL
InterPro PNMA UniProtKB/TrEMBL
  PNMA_C UniProtKB/TrEMBL
  PNMA_N UniProtKB/TrEMBL
KEGG Report rno:305977 UniProtKB/TrEMBL
NCBI Gene 305977 ENTREZGENE
PANTHER PTHR23095 UniProtKB/TrEMBL
  PTHR23095:SF16 UniProtKB/TrEMBL
Pfam PNMA UniProtKB/TrEMBL
  PNMA_N UniProtKB/TrEMBL
PhenoGen Pnma2 PhenoGen
RatGTEx ENSRNOG00000009815 RatGTEx
UniProt A6K6N5 ENTREZGENE, UniProtKB/TrEMBL
  D4A068 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-09-28 Pnma2  PNMA family member 2  Pnma2  paraneoplastic Ma antigen 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-10 Pnma2  paraneoplastic Ma antigen 2  Pnma2  paraneoplastic antigen MA2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Pnma2  paraneoplastic antigen MA2   Pnma2_predicted  paraneoplastic antigen MA2 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Pnma2_predicted  paraneoplastic antigen MA2 (predicted)      Symbol and Name status set to approved 70820 APPROVED