Paxbp1 (PAX3 and PAX7 binding protein 1) - Rat Genome Database

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Gene: Paxbp1 (PAX3 and PAX7 binding protein 1) Rattus norvegicus
Analyze
Symbol: Paxbp1
Name: PAX3 and PAX7 binding protein 1
RGD ID: 1584739
Description: Predicted to enable histone methyltransferase binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within positive regulation of myoblast proliferation and regulation of skeletal muscle satellite cell proliferation. Predicted to be active in nucleus. Orthologous to human PAXBP1 (PAX3 and PAX7 binding protein 1); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: GC-rich sequence DNA-binding factor 1; Gcfc1; LOC681004; PAX3- and PAX7-binding protein 1; similar to GC-rich sequence DNA-binding factor homolog
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
GRCr81143,758,116 - 43,787,624 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1143,758,116 - 43,787,542 (-)EnsemblGRCr8
mRatBN7.21130,272,037 - 30,301,504 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1130,272,037 - 30,301,648 (-)EnsemblmRatBN7.2
Rnor_6.01131,184,456 - 31,213,891 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1131,185,473 - 31,213,787 (-)Ensemblrn6Rnor6.0
Rnor_5.01134,795,249 - 34,824,684 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41131,001,934 - 31,030,820 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1129,938,585 - 29,968,020 (-)NCBICelera
Cytogenetic Map11q11NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View
High Myopia  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IBA,IEA,ISO)

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16780588   PMID:22862948  


Genomics

Comparative Map Data
Paxbp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81143,758,116 - 43,787,624 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1143,758,116 - 43,787,542 (-)EnsemblGRCr8
mRatBN7.21130,272,037 - 30,301,504 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1130,272,037 - 30,301,648 (-)EnsemblmRatBN7.2
Rnor_6.01131,184,456 - 31,213,891 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1131,185,473 - 31,213,787 (-)Ensemblrn6Rnor6.0
Rnor_5.01134,795,249 - 34,824,684 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41131,001,934 - 31,030,820 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1129,938,585 - 29,968,020 (-)NCBICelera
Cytogenetic Map11q11NCBI
PAXBP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382132,733,899 - 32,771,755 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2132,733,899 - 32,771,796 (-)Ensemblhg38GRCh38
GRCh372134,106,210 - 34,144,066 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362133,028,081 - 33,066,040 (-)NCBIBuild 36Build 36hg18NCBI36
Build 342133,029,001 - 33,065,869NCBI
Celera2119,289,868 - 19,327,826 (-)NCBICelera
Cytogenetic Map21q22.11NCBI
HuRef2119,515,579 - 19,553,535 (-)NCBIHuRef
CHM1_12133,667,852 - 33,705,826 (-)NCBICHM1_1
T2T-CHM13v2.02131,099,918 - 31,138,061 (-)NCBIT2T-CHM13v2.0
Paxbp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391690,810,925 - 90,841,267 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1690,810,925 - 90,841,431 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381691,014,037 - 91,044,379 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1691,014,037 - 91,044,543 (-)Ensemblmm10GRCm38
MGSCv371691,014,282 - 91,044,624 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361690,902,895 - 90,933,369 (-)NCBIMGSCv36mm8
Celera1692,095,885 - 92,126,049 (-)NCBICelera
Cytogenetic Map16C3.3NCBI
cM Map1652.3NCBI
Paxbp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540732,179,879 - 32,210,352 (-)Ensembl
ChiLan1.0NW_00495540732,178,837 - 32,210,470 (-)NCBIChiLan1.0ChiLan1.0
PAXBP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22228,845,112 - 28,882,939 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12123,705,075 - 23,742,904 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02119,094,672 - 19,132,536 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12132,472,880 - 32,510,264 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2132,472,880 - 32,511,680 (-)EnsemblpanPan2panpan1.1
PAXBP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13127,405,547 - 27,439,839 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3127,406,492 - 27,439,844 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3127,398,499 - 27,432,779 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.03127,603,283 - 27,637,737 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3127,603,291 - 27,637,743 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13127,470,119 - 27,504,393 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03127,481,833 - 27,516,307 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03127,989,512 - 28,023,735 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Paxbp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440497127,986,211 - 28,020,155 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365009,447,424 - 9,480,550 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365009,447,091 - 9,481,612 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PAXBP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13196,336,959 - 196,371,174 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.113196,336,952 - 196,371,258 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213206,348,599 - 206,382,973 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PAXBP1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1259,378,828 - 59,416,394 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl259,379,110 - 59,416,988 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660711,918,712 - 1,956,102 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Paxbp1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474520,988,162 - 21,019,344 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462474520,988,156 - 21,019,348 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Paxbp1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1453,545,615 - 53,574,619 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Paxbp1
187 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:25
Count of miRNA genes:24
Interacting mature miRNAs:25
Transcripts:ENSRNOT00000002800
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
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)112252474682951192Rat
1598841Memor7Memory QTL 7exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)113330600878306008Rat
1598842Glom10Glomerulus QTL 103.4kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)11381815448818154Rat
1598811Bp291Blood pressure QTL 2911.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)113330600878306008Rat
634339Niddm50Non-insulin dependent diabetes mellitus QTL 503.32blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)111080612555806125Rat
634341Bw121Body weight QTL 1213.56abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)113532319955805892Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)113674945981749459Rat
10755497Bp388Blood pressure QTL 3882.76arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)113294306789836615Rat
724517Uae18Urinary albumin excretion QTL 183.7urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)112995899657754989Rat
2290451Scl58Serum cholesterol level QTL 583.48blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)112631803155806125Rat
1300130Rf20Renal function QTL 204.44kidney glomerulus integrity trait (VT:0010546)kidney glomerulus diameter (CMO:0001166)113191546976915469Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)113642841681428416Rat
1600394Edcs1Endometrial carcinoma susceptibility QTL12.90.04uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)111282315257823152Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)113461876079618760Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112019354996351019Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)113674945981749459Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)113674945981749459Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)113674945981749459Rat
631510Spl2Serum phospholipid level QTL 24.1blood phospholipid amount (VT:0006084)serum phospholipid level (CMO:0001171)112755668572556685Rat

Markers in Region
BE117849  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21130,286,802 - 30,286,952 (+)MAPPERmRatBN7.2
Rnor_6.01131,199,222 - 31,199,371NCBIRnor6.0
Rnor_5.01134,810,015 - 34,810,164UniSTSRnor5.0
RGSC_v3.41131,016,255 - 31,016,404UniSTSRGSC3.4
Celera1129,953,351 - 29,953,500UniSTS
RH 3.4 Map11181.7UniSTS
Cytogenetic Map11q11UniSTS
BQ206323  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21130,272,215 - 30,272,356 (+)MAPPERmRatBN7.2
Rnor_6.01131,184,635 - 31,184,775NCBIRnor6.0
Rnor_5.01134,795,428 - 34,795,568UniSTSRnor5.0
RGSC_v3.41131,001,668 - 31,001,808UniSTSRGSC3.4
Celera1129,938,764 - 29,938,904UniSTS
RH 3.4 Map11180.1UniSTS
Cytogenetic Map11q11UniSTS


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
23 13 84 215 91 90 59 146 59 6 479 273 22 193 116 124 31 34 34

Sequence


Ensembl Acc Id: ENSRNOT00000002800   ⟹   ENSRNOP00000002800
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1143,758,116 - 43,787,542 (-)Ensembl
mRatBN7.2 Ensembl1130,272,037 - 30,301,648 (-)Ensembl
Rnor_6.0 Ensembl1131,185,473 - 31,213,787 (-)Ensembl
RefSeq Acc Id: NM_001426992   ⟹   NP_001413921
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81143,758,116 - 43,787,542 (-)NCBI
RefSeq Acc Id: XR_005491197
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81143,769,857 - 43,787,624 (-)NCBI
mRatBN7.21130,280,139 - 30,301,504 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001413921 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000002800
  ENSRNOP00000002800.5
Ensembl Acc Id: ENSRNOP00000002800   ⟸   ENSRNOT00000002800
RefSeq Acc Id: NP_001413921   ⟸   NM_001426992
- UniProtKB: D4A8C8 (UniProtKB/TrEMBL)
Protein Domains
GCF C-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A8C8-F1-model_v2 AlphaFold D4A8C8 1-918 view protein structure

Transcriptome

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

Promoters
RGD ID:13698064
Promoter ID:EPDNEW_R8576
Type:initiation region
Name:Paxbp1_1
Description:PAX3 and PAX7 binding protein 1
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_6.01131,213,828 - 31,213,888EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1584739 AgrOrtholog
BioCyc Gene G2FUF-21926 BioCyc
Ensembl Genes ENSRNOG00000002036 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002800 ENTREZGENE
  ENSRNOT00000002800.8 UniProtKB/TrEMBL
InterPro GCFC UniProtKB/TrEMBL
  GCFC_dom UniProtKB/TrEMBL
NCBI Gene 681004 ENTREZGENE
PANTHER GCFC UniProtKB/TrEMBL
  PAX3- AND PAX7-BINDING PROTEIN 1 UniProtKB/TrEMBL
Pfam GCFC UniProtKB/TrEMBL
PhenoGen Paxbp1 PhenoGen
RatGTEx ENSRNOG00000002036 RatGTEx
UniProt D4A8C8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-05-24 Paxbp1  PAX3 and PAX7 binding protein 1  LOC683880  similar to GC-rich sequence DNA-binding factor homolog  Data merged from RGD:1597800 1643240 APPROVED
2013-01-17 Paxbp1  PAX3 and PAX7 binding protein 1  Gcfc1  GC-rich sequence DNA-binding factor 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-08-02 Gcfc1  GC-rich sequence DNA-binding factor 1  LOC681004  similar to GC-rich sequence DNA-binding factor homolog  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC683880  similar to GC-rich sequence DNA-binding factor homolog      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC681004  similar to GC-rich sequence DNA-binding factor homolog      Symbol and Name status set to provisional 70820 PROVISIONAL