Zfx (zinc finger protein X-linked) - Rat Genome Database
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Gene: Zfx (zinc finger protein X-linked) Rattus norvegicus
Analyze
Symbol: Zfx
Name: zinc finger protein X-linked
RGD ID: 1562664
Description: Predicted to have chromatin insulator sequence binding activity. Predicted to be involved in several processes, including gamete generation; ovarian follicle development; and parental behavior. Predicted to localize to chromosome; nucleolus; and nucleoplasm. Orthologous to human ZFX (zinc finger protein X-linked); INTERACTS WITH ammonium chloride; bisphenol A; flutamide.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC367832; RGD1562664; similar to sex-determining protein Zfx - mouse; zinc finger X-chromosomal protein
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
mRatBN7.2X58,804,690 - 58,853,155 (-)NCBI
Rnor_6.0 EnsemblX63,158,976 - 63,204,530 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X63,158,368 - 63,204,971 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X63,749,779 - 63,797,636 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X81,430,210 - 81,477,028 (-)NCBIRGSC3.4rn4RGSC3.4
CeleraX59,240,896 - 59,287,404 (-)NCBICelera
Cytogenetic MapXq22NCBI
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
chromosome  (IBA)
nucleolus  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IEA)

Molecular Function

References

Additional References at PubMed
PMID:9187153   PMID:11214319  


Genomics

Comparative Map Data
Zfx
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X58,804,690 - 58,853,155 (-)NCBI
Rnor_6.0 EnsemblX63,158,976 - 63,204,530 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X63,158,368 - 63,204,971 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X63,749,779 - 63,797,636 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X81,430,210 - 81,477,028 (-)NCBIRGSC3.4rn4RGSC3.4
CeleraX59,240,896 - 59,287,404 (-)NCBICelera
Cytogenetic MapXq22NCBI
ZFX
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX24,149,173 - 24,216,255 (+)EnsemblGRCh38hg38GRCh38
GRCh38X24,148,982 - 24,216,255 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X24,167,099 - 24,234,372 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh37X24,167,047 - 24,234,372 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X24,077,824 - 24,142,549 (+)NCBINCBI36hg18NCBI36
Build 34X23,929,464 - 23,989,474NCBI
CeleraX28,291,063 - 28,357,675 (+)NCBI
Cytogenetic MapXp22.11NCBI
HuRefX21,911,587 - 21,977,093 (+)NCBIHuRef
CHM1_1X24,199,109 - 24,265,719 (+)NCBICHM1_1
Zfx
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X93,118,237 - 93,194,250 (-)NCBIGRCm39mm39
GRCm38X94,074,631 - 94,150,645 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX94,074,631 - 94,123,702 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X91,319,970 - 91,368,746 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X90,327,351 - 90,375,619 (-)NCBImm8
CeleraX80,975,763 - 81,039,081 (-)NCBICelera
Cytogenetic MapXC3NCBI
cM MapX41.48NCBI
Zfx
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555094,505,235 - 4,571,513 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555094,545,468 - 4,571,513 (+)NCBIChiLan1.0ChiLan1.0
ZFX
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X24,118,870 - 24,183,804 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX24,118,956 - 24,183,804 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X16,745,872 - 16,813,486 (+)NCBIMhudiblu_PPA_v0panPan3
ZFX
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 EnsemblX19,760,045 - 19,790,196 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1X19,722,172 - 19,793,059 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Zfx
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936624417,164 - 471,638 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ZFX
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1X20,220,812 - 20,273,689 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X21,713,386 - 21,749,342 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ZFX
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X22,626,683 - 22,630,119 (+)NCBI
Zfx
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624897503,741 - 550,027 (+)NCBI

Position Markers
D5Mit8  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X82,981,120 - 82,981,241NCBIRnor6.0
Rnor_5.0X82,950,219 - 82,950,340UniSTSRnor5.0
RGSC_v3.4X100,103,660 - 100,103,789UniSTSRGSC3.4
RGSC_v3.1X100,177,092 - 100,177,222RGD
CeleraX77,996,730 - 77,996,859UniSTS
RH 3.4 MapX736.2UniSTS
Cytogenetic MapXq31UniSTS
DXMit6  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X63,204,761 - 63,204,971NCBIRnor6.0
Rnor_5.0X63,797,402 - 63,797,612UniSTSRnor5.0
RGSC_v3.4X81,478,146 - 81,478,357RGDRGSC3.4
RGSC_v3.4X81,478,147 - 81,478,357UniSTSRGSC3.4
RGSC_v3.1X100,177,092 - 100,177,222RGD
CeleraX59,288,523 - 59,288,733UniSTS
RH 3.4 MapX736.2RGD
Cytogenetic MapXq31UniSTS
DXRat65  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X63,237,001 - 63,237,257NCBIRnor6.0
Rnor_5.0X63,829,641 - 63,829,897UniSTSRnor5.0
RGSC_v3.4X81,510,395 - 81,510,704RGDRGSC3.4
RGSC_v3.4X81,510,396 - 81,510,652UniSTSRGSC3.4
RGSC_v3.1X81,583,688 - 81,583,944RGD
CeleraX59,320,326 - 59,320,582UniSTS
RH 3.4 Map41029.28RGD
RH 3.4 Map41029.28UniSTS
SHRSP x BN MapX17.21UniSTS
SHRSP x BN MapX17.21RGD
Cytogenetic MapXq31UniSTS
RH132649  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X63,158,652 - 63,158,831NCBIRnor6.0
Rnor_5.0X63,750,063 - 63,750,242UniSTSRnor5.0
RGSC_v3.4X81,429,886 - 81,430,065UniSTSRGSC3.4
CeleraX59,240,572 - 59,240,751UniSTS
Cytogenetic MapXq31UniSTS
AW531358  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X63,159,299 - 63,159,491NCBIRnor6.0
Rnor_5.0X63,750,710 - 63,750,902UniSTSRnor5.0
RGSC_v3.4X81,430,533 - 81,430,725UniSTSRGSC3.4
CeleraX59,241,219 - 59,241,411UniSTS
Cytogenetic MapXq31UniSTS
mZfa  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X63,162,762 - 63,163,222NCBIRnor6.0
Rnor_5.0X63,754,173 - 63,754,633UniSTSRnor5.0
RGSC_v3.4X81,433,996 - 81,434,456UniSTSRGSC3.4
CeleraX59,244,682 - 59,245,142UniSTS
Cytogenetic MapXq31UniSTS
PMC262401P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0X63,204,756 - 63,204,979NCBIRnor6.0
Rnor_5.0X63,797,397 - 63,797,620UniSTSRnor5.0
RGSC_v3.4X81,478,142 - 81,478,365UniSTSRGSC3.4
CeleraX59,288,518 - 59,288,741UniSTS
Cytogenetic MapXq31UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X15688119127888215Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X44320616158345622Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX44557974120045269Rat
70221Bp56Blood pressure QTL 564.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X6139809770352120Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:335
Count of miRNA genes:218
Interacting mature miRNAs:273
Transcripts:ENSRNOT00000065194
Prediction methods:Miranda, Pita, 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 2 28 34 18 19 18 8 8 68 28 35 11 8
Low 1 15 23 23 23 2 6 7 6
Below cutoff 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000065194   ⟹   ENSRNOP00000060490
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX63,158,976 - 63,203,643 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000075866
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX63,165,407 - 63,165,978 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076175   ⟹   ENSRNOP00000068277
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX63,159,731 - 63,204,530 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076613   ⟹   ENSRNOP00000068137
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX63,160,839 - 63,182,385 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076765   ⟹   ENSRNOP00000068521
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX63,162,480 - 63,165,759 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076974   ⟹   ENSRNOP00000068150
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX63,178,249 - 63,203,643 (-)Ensembl
RefSeq Acc Id: NM_001109017   ⟹   NP_001102487
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X58,804,690 - 58,852,924 (-)NCBI
Rnor_6.0X63,158,976 - 63,203,643 (-)NCBI
Rnor_5.0X63,749,779 - 63,797,636 (-)NCBI
RGSC_v3.4X81,430,210 - 81,477,028 (-)RGD
CeleraX59,240,896 - 59,287,404 (-)RGD
Sequence:
RefSeq Acc Id: XM_006257030   ⟹   XP_006257092
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X58,804,690 - 58,853,155 (-)NCBI
Rnor_6.0X63,158,368 - 63,204,971 (-)NCBI
Rnor_5.0X63,749,779 - 63,797,636 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006257031   ⟹   XP_006257093
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X63,158,368 - 63,204,694 (-)NCBI
Rnor_5.0X63,749,779 - 63,797,636 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006257032   ⟹   XP_006257094
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X58,804,690 - 58,852,916 (-)NCBI
Rnor_6.0X63,158,368 - 63,204,694 (-)NCBI
Rnor_5.0X63,749,779 - 63,797,636 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008773265   ⟹   XP_008771487
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X58,804,690 - 58,852,916 (-)NCBI
Rnor_6.0X63,158,368 - 63,204,694 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017602121   ⟹   XP_017457610
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X63,158,368 - 63,182,385 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099944   ⟹   XP_038955872
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X58,804,690 - 58,851,993 (-)NCBI
RefSeq Acc Id: XM_039099945   ⟹   XP_038955873
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X58,804,690 - 58,853,155 (-)NCBI
RefSeq Acc Id: XM_039099946   ⟹   XP_038955874
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X58,804,690 - 58,852,918 (-)NCBI
RefSeq Acc Id: XM_039099947   ⟹   XP_038955875
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X58,804,690 - 58,852,918 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001102487   ⟸   NM_001109017
- Sequence:
RefSeq Acc Id: XP_006257092   ⟸   XM_006257030
- Peptide Label: isoform X1
- UniProtKB: A0A096MJV6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257093   ⟸   XM_006257031
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006257094   ⟸   XM_006257032
- Peptide Label: isoform X1
- UniProtKB: A0A096MJV6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008771487   ⟸   XM_008773265
- Peptide Label: isoform X1
- UniProtKB: A0A096MJV6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457610   ⟸   XM_017602121
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000060490   ⟸   ENSRNOT00000065194
RefSeq Acc Id: ENSRNOP00000068150   ⟸   ENSRNOT00000076974
RefSeq Acc Id: ENSRNOP00000068277   ⟸   ENSRNOT00000076175
RefSeq Acc Id: ENSRNOP00000068137   ⟸   ENSRNOT00000076613
RefSeq Acc Id: ENSRNOP00000068521   ⟸   ENSRNOT00000076765
RefSeq Acc Id: XP_038955873   ⟸   XM_039099945
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955875   ⟸   XM_039099947
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038955874   ⟸   XM_039099946
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038955872   ⟸   XM_039099944
- Peptide Label: isoform X1
Protein Domains
C2H2-type   Zfx_Zfy_act

Transcriptome

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

Promoters
RGD ID:13701842
Promoter ID:EPDNEW_R12363
Type:single initiation site
Name:Zfx_1
Description:zinc finger protein X-linked
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_6.0X63,204,520 - 63,204,580EPDNEW

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)
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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
LEW/Crl (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
LEW/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
MHS/Gib (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
MNS/Gib (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
MR/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
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/Ygl (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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
X 63754074 63754075 C T snv HWY/Slc (KyushuU), LE/OrlBarth (UDEL), RCS/Kyo (KyushuU)
X 63754167 63754168 T G snv DOB/Oda (KyushuU), F344/Jcl (KyushuU), LEC/Tj (KyushuU), LE/OrlBarth (UDEL), HWY/Slc (KyushuU), IS-Tlk/Kyo (KyushuU), Crl:SD (UDEL), RCS/Kyo (KyushuU), SDLEF7/Barth (UDEL), IS/Kyo (KyushuU), BN/SsNSlc (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), F344/NSlc (KyushuU), BUF/MNa (KyushuU), F344/DuCrlCrlj (KyushuU), NIG-III/Hok (KyushuU), LE/Stm (KyushuU), ZFDM (KyushuU)
X 63754224 63754225 C T snv NIG-III/Hok (KyushuU), BUF/MNa (KyushuU), IS/Kyo (KyushuU), SDLEF7/Barth (UDEL), F344/DuCrlCrlj (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), LEC/Tj (KyushuU), HWY/Slc (KyushuU), F344/NSlc (KyushuU), HTX/Kyo (KyushuU)
X 63754272 63754273 C G snv HTX/Kyo (KyushuU), SDLEF7/Barth (UDEL), BUF/MNa (KyushuU), DOB/Oda (KyushuU), LEC/Tj (KyushuU), LE/OrlBarth (UDEL)
X 63754274 63754275 A C snv HTX/Kyo (KyushuU), LE/OrlBarth (UDEL), BUF/MNa (KyushuU), SDLEF7/Barth (UDEL)
X 63754314 63754315 C T snv SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), HTX/Kyo (KyushuU), Crl:SD (UDEL)
X 63754547 63754548 T C snv BDIX.Cg-Tal/NemOda (KyushuU), LE/OrlBarth (UDEL), SDLEF7/Barth (UDEL)
X 63754733 63754734 A T snv SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), IS/Kyo (KyushuU), HTX/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU), LEC/Tj (KyushuU), ZF (KyushuU), ZFDM (KyushuU)
X 63754773 63754774 G T snv IS/Kyo (KyushuU), SDLEF7/Barth (UDEL)
X 63754775 63754776 C T snv IS/Kyo (KyushuU), SDLEF7/Barth (UDEL)
X 63754979 63754980 G C snv SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL), Crl:SD (UDEL)
X 63755038 63755039 C T snv Crl:SD (UDEL), SDLEF7/Barth (UDEL), LE/OrlBarth (UDEL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562664 AgrOrtholog
Ensembl Genes ENSRNOG00000005624 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000060490 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000068137 UniProtKB/TrEMBL
  ENSRNOP00000068150 UniProtKB/TrEMBL
  ENSRNOP00000068277 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000068521 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000065194 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000076175 UniProtKB/TrEMBL
  ENSRNOT00000076613 UniProtKB/TrEMBL
  ENSRNOT00000076765 UniProtKB/TrEMBL
  ENSRNOT00000076974 UniProtKB/TrEMBL
InterPro Transcrp_activ_Zfx/Zfy-dom UniProtKB/TrEMBL
  Znf_C2H2/integrase_DNA-bd UniProtKB/TrEMBL
  Znf_C2H2_sf UniProtKB/TrEMBL
KEGG Report rno:367832 UniProtKB/TrEMBL
NCBI Gene 367832 ENTREZGENE
Pfam zf-C2H2 UniProtKB/TrEMBL
  Zfx_Zfy_act UniProtKB/TrEMBL
PhenoGen Zfx PhenoGen
PROSITE ZINC_FINGER_C2H2_1 UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/TrEMBL
SMART ZnF_C2H2 UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/TrEMBL
UniProt A0A096MJI1_RAT UniProtKB/TrEMBL
  A0A096MJJ3_RAT UniProtKB/TrEMBL
  A0A096MJV6 ENTREZGENE, UniProtKB/TrEMBL
  A0A096MKH8_RAT UniProtKB/TrEMBL
  D3ZR02_RAT UniProtKB/TrEMBL
  Q99NJ3_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Zfx  zinc finger protein X-linked   Zfx_predicted  zinc finger protein X-linked (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Zfx_predicted  zinc finger protein X-linked (predicted)  RGD1562664_predicted  similar to sex-determining protein Zfx - mouse (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1562664_predicted  similar to sex-determining protein Zfx - mouse (predicted)  LOC367832  similar to sex-determining protein Zfx - mouse  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC367832  similar to sex-determining protein Zfx - mouse      Symbol and Name status set to provisional 70820 PROVISIONAL