Pnma3 (PNMA family member 3) - Rat Genome Database

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Gene: Pnma3 (PNMA family member 3) Rattus norvegicus
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Symbol: Pnma3
Name: PNMA family member 3
RGD ID: 1563752
Description: Predicted to enable nucleic acid binding activity and zinc ion binding activity. Orthologous to human PNMA3 (PNMA family member 3); INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC293840; paraneoplastic antigen MA3; paraneoplastic Ma antigen 3; RGD1563752; similar to Paraneoplastic antigen MA3
RGD Orthologs
Human
Mouse
Bonobo
Squirrel
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X155,946,428 - 155,952,761 (+)NCBIGRCr8
mRatBN7.2X150,906,080 - 150,912,674 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX150,906,278 - 150,910,839 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX153,098,983 - 153,101,971 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X156,631,329 - 156,634,317 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X154,174,455 - 154,177,445 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X153,063,276 - 153,067,500 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX153,064,028 - 153,067,500 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01148,792,196 - 148,796,525 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X159,058,220 - 159,061,212 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1131,870,973 - 131,873,962 (+)NCBICelera
Cytogenetic MapXq37NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. GOA pipeline RGD automated data pipeline
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

Genomics

Comparative Map Data
Pnma3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X155,946,428 - 155,952,761 (+)NCBIGRCr8
mRatBN7.2X150,906,080 - 150,912,674 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX150,906,278 - 150,910,839 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX153,098,983 - 153,101,971 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X156,631,329 - 156,634,317 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X154,174,455 - 154,177,445 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X153,063,276 - 153,067,500 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX153,064,028 - 153,067,500 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01148,792,196 - 148,796,525 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X159,058,220 - 159,061,212 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1131,870,973 - 131,873,962 (+)NCBICelera
Cytogenetic MapXq37NCBI
PNMA3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X153,056,470 - 153,060,462 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX153,056,409 - 153,060,467 (+)EnsemblGRCh38hg38GRCh38
GRCh37X152,224,827 - 152,228,822 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X151,975,422 - 151,979,483 (+)NCBINCBI36Build 36hg18NCBI36
Build 34X151,895,442 - 151,899,390NCBI
CeleraX152,559,961 - 152,564,021 (+)NCBICelera
Cytogenetic MapXq28NCBI
HuRefX141,026,372 - 141,030,359 (+)NCBIHuRef
CHM1_1X152,099,904 - 152,103,965 (+)NCBICHM1_1
T2T-CHM13v2.0X151,323,992 - 151,327,987 (+)NCBIT2T-CHM13v2.0
Pnma3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X72,108,393 - 72,111,797 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX72,108,393 - 72,111,797 (+)EnsemblGRCm39 Ensembl
GRCm38X73,064,787 - 73,068,191 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX73,064,787 - 73,068,191 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X70,310,126 - 70,313,530 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X69,317,507 - 69,320,911 (+)NCBIMGSCv36mm8
CeleraX63,989,352 - 63,992,616 (+)NCBICelera
Cytogenetic MapXA7.3NCBI
cM MapX37.29NCBI
PNMA3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X153,121,568 - 153,125,586 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X153,125,171 - 153,129,189 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X142,631,788 - 142,635,768 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X152,551,230 - 152,554,859 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX152,551,452 - 152,552,940 (+)Ensemblpanpan1.1panPan2
Pnma3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X118,162,618 - 118,166,310 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493671492,269 - 93,660 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493671490,133 - 93,805 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PNMA3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X127,546,571 - 127,550,588 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX127,547,198 - 127,548,589 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606565,369,831 - 65,373,811 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Pnma3
11 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:50
Count of miRNA genes:47
Interacting mature miRNAs:49
Transcripts:ENSRNOT00000022997
Prediction methods:Miranda, Rnahybrid
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
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X113937816152453651Rat
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X126975089152453651Rat

Markers in Region
UniSTS:496785  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X150,880,736 - 150,880,962 (+)MAPPERmRatBN7.2
mRatBN7.2X150,908,926 - 150,909,152 (-)MAPPERmRatBN7.2
mRatBN7.2X150,880,736 - 150,880,962 (-)MAPPERmRatBN7.2
mRatBN7.2X150,908,926 - 150,909,152 (+)MAPPERmRatBN7.2
Rnor_6.0X153,037,320 - 153,037,545NCBIRnor6.0
Rnor_6.0X153,066,466 - 153,066,691NCBIRnor6.0
Rnor_5.01148,795,491 - 148,795,716UniSTSRnor5.0
Rnor_5.01148,766,898 - 148,767,123UniSTSRnor5.0
RGSC_v3.4X159,060,178 - 159,060,403UniSTSRGSC3.4
RGSC_v3.4X159,030,352 - 159,030,577UniSTSRGSC3.4
Celera1131,845,018 - 131,845,243UniSTS
Celera1131,872,931 - 131,873,156UniSTS
Cytogenetic MapXq37UniSTS


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 53
Low 2 3 21 2 23 2
Below cutoff 3 15 27 13 15 13 8 9 24 16 8 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000079424   ⟹   ENSRNOP00000070839
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX150,906,278 - 150,910,839 (+)Ensembl
Rnor_6.0 EnsemblX153,064,028 - 153,067,500 (+)Ensembl
RefSeq Acc Id: NM_001106342   ⟹   NP_001099812
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X155,949,222 - 155,952,214 (+)NCBI
mRatBN7.2X150,906,969 - 150,909,961 (+)NCBI
Rnor_6.0X153,064,028 - 153,067,500 (+)NCBI
Rnor_5.01148,792,196 - 148,796,525 (+)NCBI
RGSC_v3.4X159,058,220 - 159,061,212 (+)RGD
Celera1131,870,973 - 131,873,962 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006229513   ⟹   XP_006229575
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X155,946,428 - 155,952,761 (+)NCBI
mRatBN7.2X150,906,080 - 150,912,674 (+)NCBI
Rnor_6.0X153,063,277 - 153,065,829 (+)NCBI
Rnor_5.01148,792,196 - 148,796,525 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001099812 (Get FASTA)   NCBI Sequence Viewer  
  XP_006229575 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL82843 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000070839
  ENSRNOP00000070839.1
Reference Protein Sequences
RefSeq Acc Id: NP_001099812   ⟸   NM_001106342
- UniProtKB: D3Z8Y9 (UniProtKB/TrEMBL),   A6KSZ0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006229575   ⟸   XM_006229513
- Peptide Label: isoform X1
- UniProtKB: D3Z8Y9 (UniProtKB/TrEMBL),   A6KSZ0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000070839   ⟸   ENSRNOT00000079424
Protein Domains
CCHC-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3Z8Y9-F1-model_v2 AlphaFold D3Z8Y9 1-465 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:1563752 AgrOrtholog
BioCyc Gene G2FUF-689 BioCyc
Ensembl Genes ENSRNOG00000052022 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000079424.2 UniProtKB/TrEMBL
InterPro PNMA UniProtKB/TrEMBL
  PNMA_C UniProtKB/TrEMBL
  PNMA_N UniProtKB/TrEMBL
  Znf_CCHC UniProtKB/TrEMBL
  Znf_CCHC_sf UniProtKB/TrEMBL
KEGG Report rno:293840 UniProtKB/TrEMBL
NCBI Gene 293840 ENTREZGENE
PANTHER PTHR23095 UniProtKB/TrEMBL
  PTHR23095:SF22 UniProtKB/TrEMBL
Pfam PNMA UniProtKB/TrEMBL
  PNMA_N UniProtKB/TrEMBL
PhenoGen Pnma3 PhenoGen
PROSITE ZF_CCHC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000052022 RatGTEx
Superfamily-SCOP SSF57756 UniProtKB/TrEMBL
UniProt A6KSZ0 ENTREZGENE, UniProtKB/TrEMBL
  D3Z8Y9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-09-28 Pnma3  PNMA family member 3  Pnma3  paraneoplastic Ma antigen 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-10 Pnma3  paraneoplastic Ma antigen 3  Pnma3  paraneoplastic antigen MA3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Pnma3  paraneoplastic antigen MA3   Pnma3_predicted  paraneoplastic antigen MA3 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Pnma3_predicted  paraneoplastic antigen MA3 (predicted)  RGD1563752_predicted  similar to Paraneoplastic antigen MA3 (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1563752_predicted  similar to Paraneoplastic antigen MA3 (predicted)  LOC293840  similar to Paraneoplastic antigen MA3  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC293840  similar to Paraneoplastic antigen MA3      Symbol and Name status set to provisional 70820 PROVISIONAL