Pgap6 (post-GPI attachment to proteins 6) - Rat Genome Database

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Gene: Pgap6 (post-GPI attachment to proteins 6) Rattus norvegicus
Analyze
Symbol: Pgap6
Name: post-GPI attachment to proteins 6
RGD ID: 1311395
Description: Predicted to be located in plasma membrane. Orthologous to human PGAP6 (post-GPI attachment to proteins 6); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: M83; post-glycosylphosphatidylinositol attachment to proteins 6; post-GPI attachment to proteins factor 6; Tmem8; Tmem8a; transmembrane protein 8 (five membrane-spanning domains); transmembrane protein 8A; type I transmembrane protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81015,643,081 - 15,652,912 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1015,643,106 - 15,652,912 (+)EnsemblGRCr8
mRatBN7.21015,138,918 - 15,148,431 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1015,138,959 - 15,148,431 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1019,878,593 - 19,888,041 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01019,367,472 - 19,376,920 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01014,866,862 - 14,876,335 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01015,484,952 - 15,495,380 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1015,484,795 - 15,495,377 (+)Ensemblrn6Rnor6.0
Rnor_5.01015,298,650 - 15,309,080 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41015,384,648 - 15,394,120 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1014,806,937 - 14,816,409 (+)NCBICelera
RGSC_v3.11015,385,789 - 15,395,171 (+)NCBI
Cytogenetic Map10q12NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
membrane  (IEA)
nucleoplasm  (IEA,ISO)
plasma membrane  (IEA)

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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:17897319   PMID:23533145  


Genomics

Comparative Map Data
Pgap6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81015,643,081 - 15,652,912 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1015,643,106 - 15,652,912 (+)EnsemblGRCr8
mRatBN7.21015,138,918 - 15,148,431 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1015,138,959 - 15,148,431 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1019,878,593 - 19,888,041 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01019,367,472 - 19,376,920 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01014,866,862 - 14,876,335 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01015,484,952 - 15,495,380 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1015,484,795 - 15,495,377 (+)Ensemblrn6Rnor6.0
Rnor_5.01015,298,650 - 15,309,080 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41015,384,648 - 15,394,120 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1014,806,937 - 14,816,409 (+)NCBICelera
RGSC_v3.11015,385,789 - 15,395,171 (+)NCBI
Cytogenetic Map10q12NCBI
PGAP6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3816370,788 - 386,979 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl16370,788 - 387,113 (-)Ensemblhg38GRCh38
GRCh3716420,788 - 431,978 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3616360,777 - 371,951 (-)NCBIBuild 36Build 36hg18NCBI36
Build 3416361,860 - 371,908NCBI
Celera16621,328 - 632,498 (-)NCBICelera
Cytogenetic Map16p13.3NCBI
HuRef16339,818 - 350,835 (-)NCBIHuRef
CHM1_116420,861 - 458,154 (-)NCBICHM1_1
T2T-CHM13v2.016366,436 - 382,868 (-)NCBIT2T-CHM13v2.0
Pgap6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391726,332,290 - 26,342,228 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1726,332,273 - 26,342,228 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381726,112,752 - 26,123,254 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1726,113,299 - 26,123,254 (+)Ensemblmm10GRCm38
MGSCv371726,250,261 - 26,260,199 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361725,840,917 - 25,850,854 (+)NCBIMGSCv36mm8
Celera1726,647,061 - 26,657,000 (+)NCBICelera
Cytogenetic Map17A3.3NCBI
cM Map1713.06NCBI
Pgap6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495544216,821,275 - 16,830,275 (+)NCBIChiLan1.0ChiLan1.0
PGAP6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v218598,412 - 609,789 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1164,388,759 - 4,400,126 (-)NCBINHGRI_mPanPan1
PanPan1.116361,783 - 378,207 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl16361,783 - 378,207 (-)EnsemblpanPan2panpan1.1
PGAP6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1640,139,259 - 40,144,957 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl640,136,561 - 40,144,957 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha641,399,491 - 41,408,248 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0640,478,213 - 40,486,979 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl640,477,826 - 40,487,762 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1640,166,539 - 40,175,293 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0640,126,755 - 40,135,506 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0640,606,010 - 40,614,776 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Pgap6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344112,473,410 - 112,482,762 (+)NCBIHiC_Itri_2
SpeTri2.0NW_004936501564,963 - 580,617 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PGAP6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl341,318,889 - 41,330,273 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1341,318,569 - 41,330,430 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2341,097,604 - 41,109,203 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PGAP6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.15311,625 - 322,355 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl5311,334 - 322,243 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366606830,850,448 - 30,861,205 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pgap6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249131,210,631 - 1,219,111 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Pgap6
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v193,377,442 - 3,387,654 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Pgap6
71 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:138
Count of miRNA genes:104
Interacting mature miRNAs:129
Transcripts:ENSRNOT00000027609
Prediction methods: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
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10666111835509383Rat
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)10666092373950353Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10589381150893811Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10125055464349221Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10589381150893811Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101499153586964295Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014991535107713808Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)101465354159653541Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101553301273695498Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10687714251877142Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135730538Rat
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10130004247Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10686461896620484Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1092219745922197Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014991535107556066Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)10210370847103708Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10589381150893811Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10117749933Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138832698Rat

Markers in Region
AW490096  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21015,147,280 - 15,147,376 (+)MAPPERmRatBN7.2
Rnor_6.01015,494,227 - 15,494,322NCBIRnor6.0
Rnor_5.01015,307,927 - 15,308,022UniSTSRnor5.0
RGSC_v3.41015,392,970 - 15,393,065UniSTSRGSC3.4
Celera1014,815,259 - 14,815,354UniSTS
Cytogenetic Map10q12UniSTS


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
16 12 67 162 91 90 59 91 59 6 355 191 11 141 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000027609   ⟹   ENSRNOP00000027609
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1015,643,440 - 15,652,912 (+)Ensembl
mRatBN7.2 Ensembl1015,138,959 - 15,148,431 (+)Ensembl
Rnor_6.0 Ensembl1015,485,905 - 15,495,377 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000079826   ⟹   ENSRNOP00000069297
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1015,643,440 - 15,652,912 (+)Ensembl
mRatBN7.2 Ensembl1015,138,959 - 15,148,431 (+)Ensembl
Rnor_6.0 Ensembl1015,484,795 - 15,494,572 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000110211   ⟹   ENSRNOP00000082896
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1015,643,106 - 15,652,912 (+)Ensembl
mRatBN7.2 Ensembl1015,139,284 - 15,148,431 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000148752   ⟹   ENSRNOP00000107924
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1015,646,241 - 15,652,912 (+)Ensembl
RefSeq Acc Id: NM_001106991   ⟹   NP_001100461
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81015,643,440 - 15,652,912 (+)NCBI
mRatBN7.21015,138,959 - 15,148,431 (+)NCBI
Rnor_6.01015,485,905 - 15,495,377 (+)NCBI
Rnor_5.01015,298,650 - 15,309,080 (+)NCBI
RGSC_v3.41015,384,648 - 15,394,120 (+)RGD
Celera1014,806,937 - 14,816,409 (+)RGD
Sequence:
RefSeq Acc Id: XM_063268946   ⟹   XP_063125016
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81015,643,081 - 15,652,024 (+)NCBI
RefSeq Acc Id: XM_063268947   ⟹   XP_063125017
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81015,644,237 - 15,652,024 (+)NCBI
RefSeq Acc Id: XR_010055170
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81015,643,406 - 15,650,103 (+)NCBI
RefSeq Acc Id: NP_001100461   ⟸   NM_001106991
- Peptide Label: precursor
- UniProtKB: D3ZKI8 (UniProtKB/TrEMBL),   A6HD88 (UniProtKB/TrEMBL),   A0A0G2JV00 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000069297   ⟸   ENSRNOT00000079826
Ensembl Acc Id: ENSRNOP00000027609   ⟸   ENSRNOT00000027609
Ensembl Acc Id: ENSRNOP00000082896   ⟸   ENSRNOT00000110211
RefSeq Acc Id: XP_063125016   ⟸   XM_063268946
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZVT8 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063125017   ⟸   XM_063268947
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZVT8 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000107924   ⟸   ENSRNOT00000148752
Protein Domains
EGF-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZKI8-F1-model_v2 AlphaFold D3ZKI8 1-772 view protein structure

Transcriptome

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

Promoters
RGD ID:13697071
Promoter ID:EPDNEW_R7595
Type:initiation region
Name:Tmem8a_1
Description:transmembrane protein 8A
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_6.01015,485,916 - 15,485,976EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311395 AgrOrtholog
BioCyc Gene G2FUF-25729 BioCyc
Ensembl Genes ENSRNOG00000020374 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000027609 ENTREZGENE
  ENSRNOT00000027609.7 UniProtKB/TrEMBL
  ENSRNOT00000079826.3 UniProtKB/TrEMBL
  ENSRNOT00000110211 ENTREZGENE
  ENSRNOT00000110211.2 UniProtKB/TrEMBL
  ENSRNOT00000148752.1 UniProtKB/TrEMBL
InterPro DUF3522 UniProtKB/TrEMBL
  EGF_3 UniProtKB/TrEMBL
KEGG Report rno:303004 UniProtKB/TrEMBL
NCBI Gene 303004 ENTREZGENE
PANTHER POST-GPI ATTACHMENT TO PROTEINS FACTOR 6 UniProtKB/TrEMBL
  PTHR14319 UniProtKB/TrEMBL
Pfam DUF3522 UniProtKB/TrEMBL
PhenoGen Pgap6 PhenoGen
PROSITE EGF_1 UniProtKB/TrEMBL
  EGF_2 UniProtKB/TrEMBL
  EGF_3 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000020374 RatGTEx
UniProt A0A0G2JV00 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZVT8 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0LS45_RAT UniProtKB/TrEMBL
  A6HD88 ENTREZGENE, UniProtKB/TrEMBL
  D3ZKI8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-03-22 Pgap6  post-GPI attachment to proteins 6  Pgap6  post-glycosylphosphatidylinositol attachment to proteins 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2019-09-30 Pgap6  post-glycosylphosphatidylinositol attachment to proteins 6  Tmem8a  transmembrane protein 8A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-25 Tmem8a  transmembrane protein 8A  Tmem8  transmembrane protein 8 (five membrane-spanning domains)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Tmem8  transmembrane protein 8 (five membrane-spanning domains)   Tmem8_predicted  transmembrane protein 8 (five membrane-spanning domains) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Tmem8_predicted  transmembrane protein 8 (five membrane-spanning domains) (predicted)      Symbol and Name status set to approved 70820 APPROVED