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 have transcription factor binding activity. Predicted to be involved in positive regulation of myoblast proliferation; positive regulation of nitrogen compound metabolic process; and regulation of skeletal muscle satellite cell proliferation. Predicted to localize to nucleus. Orthologous to human PAXBP1 (PAX3 and PAX7 binding protein 1); INTERACTS WITH bisphenol A; cobalt dichloride; tetrachloromethane.
Type: protein-coding
RefSeq Status: MODEL
Also 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
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21130,272,037 - 30,301,504 (-)NCBI
Rnor_6.0 Ensembl1131,185,473 - 31,213,787 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01131,184,456 - 31,213,891 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01134,795,249 - 34,824,684 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41131,001,934 - 31,030,820 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1129,938,585 - 29,968,020 (-)NCBICelera
Cytogenetic Map11q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IBA,ISO)

Molecular Function

References

Additional References at PubMed
PMID:16780588   PMID:22862948  


Genomics

Comparative Map Data
Paxbp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21130,272,037 - 30,301,504 (-)NCBI
Rnor_6.0 Ensembl1131,185,473 - 31,213,787 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01131,184,456 - 31,213,891 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01134,795,249 - 34,824,684 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41131,001,934 - 31,030,820 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1129,938,585 - 29,968,020 (-)NCBICelera
Cytogenetic Map11q11NCBI
PAXBP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2132,733,899 - 32,771,792 (-)EnsemblGRCh38hg38GRCh38
GRCh382132,733,899 - 32,771,835 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372134,106,210 - 34,144,066 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362133,028,081 - 33,066,040 (-)NCBINCBI36hg18NCBI36
Build 342133,029,001 - 33,065,869NCBI
Celera2119,289,868 - 19,327,826 (-)NCBI
Cytogenetic Map21q22.11NCBI
HuRef2119,515,579 - 19,553,535 (-)NCBIHuRef
CHM1_12133,667,852 - 33,705,826 (-)NCBICHM1_1
Paxbp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391690,810,925 - 90,841,267 (-)NCBIGRCm39mm39
GRCm39 Ensembl1690,810,925 - 90,841,431 (-)Ensembl
GRCm381691,014,037 - 91,044,379 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1691,014,037 - 91,044,543 (-)EnsemblGRCm38mm10GRCm38
MGSCv371691,014,282 - 91,044,624 (-)NCBIGRCm37mm9NCBIm37
MGSCv361690,902,895 - 90,933,369 (-)NCBImm8
Celera1692,095,885 - 92,126,049 (-)NCBICelera
Cytogenetic Map16C3.3NCBI
Paxbp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540732,179,879 - 32,210,352 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540732,178,837 - 32,210,470 (-)NCBIChiLan1.0ChiLan1.0
PAXBP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12132,472,880 - 32,510,264 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2132,472,880 - 32,511,680 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02119,094,672 - 19,132,536 (-)NCBIMhudiblu_PPA_v0panPan3
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 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3127,398,499 - 27,432,779 (-)NCBI
ROS_Cfam_1.03127,603,283 - 27,637,737 (-)NCBI
UMICH_Zoey_3.13127,470,119 - 27,504,393 (-)NCBI
UNSW_CanFamBas_1.03127,481,833 - 27,516,307 (-)NCBI
UU_Cfam_GSD_1.03127,989,512 - 28,023,735 (-)NCBI
Paxbp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440497127,986,211 - 28,020,155 (-)NCBI
SpeTri2.0NW_0049365009,447,091 - 9,481,612 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PAXBP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13196,336,955 - 196,371,175 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113196,336,952 - 196,371,258 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213206,348,599 - 206,382,973 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PAXBP1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1259,378,828 - 59,416,394 (+)NCBI
ChlSab1.1 Ensembl259,379,110 - 59,416,988 (+)Ensembl
Paxbp1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474520,988,156 - 21,019,348 (-)NCBI

Position Markers
BE117849  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21130,286,802 - 30,286,952 (+)MAPPER
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 (+)MAPPER
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


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724517Uae18Urinary albumin excretion QTL 183.7urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)111632197346583360Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111901627290463843Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112831466586994795Rat
1641927Alcrsp10Alcohol response QTL 10alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)11935127454351274Rat
1598811Bp291Blood pressure QTL 2911.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)112194422966944229Rat
1598841Memor7Memory QTL 7exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)112194422966944229Rat
1598842Glom10Glomerulus QTL 103.4kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)11133867429Rat
634341Bw121Body weight QTL 1213.56abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)112204314944444112Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)113043533986714631Rat
1300130Rf20Renal function QTL 204.44kidney glomerulus integrity trait (VT:0010546)kidney glomerulus diameter (CMO:0001166)113043533963186373Rat
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11172720192Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)1132503169342559Rat
2290451Scl58Serum cholesterol level QTL 583.48blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)111136730644444347Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112572003870720038Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112572003870720038Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112572003870720038Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112572003870720038Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112540112970401129Rat
10755497Bp388Blood pressure QTL 3882.76arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)111947517979734728Rat

miRNA Target Status

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.


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 3 41 51 35 19 35 2 2 74 35 40 11 2
Low 2 6 6 6 6 9 1 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000002800   ⟹   ENSRNOP00000002800
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1131,185,473 - 31,213,787 (-)Ensembl
RefSeq Acc Id: XM_001057305   ⟹   XP_001057305
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,272,037 - 30,301,502 (-)NCBI
Rnor_6.01131,184,456 - 31,213,891 (-)NCBI
Rnor_5.01134,795,249 - 34,824,684 (-)NCBI
RGSC_v3.41131,001,934 - 31,030,820 (-)RGD
Sequence:
RefSeq Acc Id: XM_002724693   ⟹   XP_002724739
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera1129,938,585 - 29,968,020 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039088775   ⟹   XP_038944703
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,272,037 - 30,293,042 (-)NCBI
RefSeq Acc Id: XR_005491197
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21130,280,139 - 30,301,504 (-)NCBI
Protein Sequences
Protein RefSeqs XP_001057305 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944703 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_002724739   ⟸   XM_002724693
- Sequence:
RefSeq Acc Id: XP_001057305   ⟸   XM_001057305
- Peptide Label: isoform X1
- UniProtKB: D4A8C8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000002800   ⟸   ENSRNOT00000002800
RefSeq Acc Id: XP_038944703   ⟸   XM_039088775
- Peptide Label: isoform X2
Protein Domains
GCFC

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1584739 AgrOrtholog
Ensembl Genes ENSRNOG00000002036 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000002800 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002800 UniProtKB/TrEMBL
InterPro GCFC UniProtKB/TrEMBL
  GCFC_dom UniProtKB/TrEMBL
KEGG Report rno:681004 UniProtKB/TrEMBL
NCBI Gene 681004 ENTREZGENE
PANTHER GCFC UniProtKB/TrEMBL
Pfam GCFC UniProtKB/TrEMBL
PhenoGen Paxbp1 PhenoGen
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 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