Zbp1 (Z-DNA binding protein 1) - Rat Genome Database
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Gene: Zbp1 (Z-DNA binding protein 1) Rattus norvegicus
Analyze
Symbol: Zbp1
Name: Z-DNA binding protein 1
RGD ID: 619956
Description: Predicted to have double-stranded RNA binding activity; identical protein binding activity; and left-handed Z-DNA binding activity. Predicted to be involved in several processes, including positive regulation of defense response; positive regulation of programmed cell death; and regulation of interleukin-1-mediated signaling pathway. Predicted to localize to cytosol and nucleus. Orthologous to human ZBP1 (Z-DNA binding protein 1); INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Dlm1; tumor stroma and activated macrophage protein DLM-1; Z-DNA-binding protein 1
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
mRatBN7.23161,993,351 - 162,009,297 (-)NCBI
Rnor_6.0 Ensembl3171,276,062 - 171,286,537 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03171,276,062 - 171,292,062 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03177,340,450 - 177,356,357 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43164,078,444 - 164,088,795 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13163,984,480 - 163,994,831 (-)NCBI
Celera3161,180,812 - 161,191,132 (-)NCBICelera
Cytogenetic Map3q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (ISO)
cytosol  (ISO)
nucleus  (IBA,ISO,ISS)

Molecular Function

References

Additional References at PubMed
PMID:11524677   PMID:17618271   PMID:19095800   PMID:19158679   PMID:23586486   PMID:26152301   PMID:28500298  


Genomics

Comparative Map Data
Zbp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23161,993,351 - 162,009,297 (-)NCBI
Rnor_6.0 Ensembl3171,276,062 - 171,286,537 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03171,276,062 - 171,292,062 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03177,340,450 - 177,356,357 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43164,078,444 - 164,088,795 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13163,984,480 - 163,994,831 (-)NCBI
Celera3161,180,812 - 161,191,132 (-)NCBICelera
Cytogenetic Map3q42NCBI
ZBP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2057,603,846 - 57,620,576 (-)EnsemblGRCh38hg38GRCh38
GRCh382057,603,852 - 57,620,480 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372056,178,908 - 56,195,482 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362055,612,308 - 55,628,935 (-)NCBINCBI36hg18NCBI36
Build 342055,612,309 - 55,628,935NCBI
Celera2052,919,278 - 52,936,016 (-)NCBI
Cytogenetic Map20q13.31NCBI
HuRef2052,960,880 - 52,977,617 (-)NCBIHuRef
CHM1_12056,079,953 - 56,096,848 (-)NCBICHM1_1
Zbp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392173,048,405 - 173,060,715 (-)NCBIGRCm39mm39
GRCm39 Ensembl2173,048,405 - 173,060,716 (-)Ensembl
GRCm382173,206,612 - 173,218,959 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2173,206,612 - 173,218,923 (-)EnsemblGRCm38mm10GRCm38
MGSCv372173,032,113 - 173,044,423 (-)NCBIGRCm37mm9NCBIm37
MGSCv362172,849,551 - 172,861,829 (-)NCBImm8
Celera2179,174,441 - 179,186,462 (-)NCBICelera
Cytogenetic Map2H3NCBI
Zbp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554451,866,376 - 1,881,948 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554451,867,436 - 1,878,132 (+)NCBIChiLan1.0ChiLan1.0
ZBP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12055,222,405 - 55,239,136 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2055,222,405 - 55,239,130 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02053,944,224 - 53,961,362 (-)NCBIMhudiblu_PPA_v0panPan3
ZBP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12442,583,674 - 42,589,857 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2442,584,083 - 42,589,753 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2441,824,727 - 41,836,590 (-)NCBI
ROS_Cfam_1.02443,442,817 - 43,454,678 (-)NCBI
UMICH_Zoey_3.12442,527,583 - 42,539,421 (-)NCBI
UNSW_CanFamBas_1.02442,667,206 - 42,679,124 (-)NCBI
UU_Cfam_GSD_1.02443,325,535 - 43,337,462 (-)NCBI
Zbp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640182,896,282 - 182,907,707 (+)NCBI
SpeTri2.0NW_004936530398,980 - 408,798 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ZBP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1757,973,096 - 57,986,136 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11757,975,982 - 57,986,117 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21765,133,675 - 65,147,101 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ZBP1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.126,494,410 - 6,510,928 (+)NCBI
Zbp1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474124,022,433 - 24,033,090 (-)NCBI

Position Markers
D3Mco78  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03171,277,123 - 171,277,347NCBIRnor6.0
Rnor_5.03177,341,511 - 177,341,735UniSTSRnor5.0
RGSC_v3.43164,079,505 - 164,079,729UniSTSRGSC3.4
Celera3161,181,873 - 161,182,097UniSTS
Cytogenetic Map3q42UniSTS
RH135435  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03171,276,244 - 171,276,460NCBIRnor6.0
Rnor_5.03177,340,632 - 177,340,848UniSTSRnor5.0
RGSC_v3.43164,078,626 - 164,078,842UniSTSRGSC3.4
Celera3161,180,994 - 161,181,210UniSTS
RH 3.4 Map31496.8UniSTS
Cytogenetic Map3q42UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)3103141814176418101Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)3103141814176418101Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3103141814176418101Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3150368003177699992Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3139578365177699992Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3153412455177699992Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3129787213177699992Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3148034701177699992Rat
1300161Rf10Renal function QTL 103.57renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)3170428815177699992Rat
1331726Bp208Blood pressure QTL 2083.129arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3148348517171467264Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3138374177177699992Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)345406058177699992Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3138374177177699992Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3128986468173986468Rat
1578666Vnigr1Vascular neointimal growth QTL 14.6artery morphology trait (VT:0002191)artery lumen area (CMO:0001409)3156381661176418101Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)330846101172879276Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3146232777177699992Rat
2301411Bp320Blood pressure QTL 3200.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3153381237174632112Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3132875075176418101Rat
12879874Cm98Cardiac mass QTL 980.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)3153381237174632112Rat
12879875Kidm64Kidney mass QTL 640.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3153381237174632112Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3130006659175006659Rat
12879871Am7Aortic mass QTL 70.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)3153381237174632112Rat
2317883Alcrsp26Alcohol response QTL 261.80.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)3153918022177699992Rat
12879872Cm97Cardiac mass QTL 970.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3153381237174632112Rat
12879873Cm96Cardiac mass QTL 960.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)3153381237174632112Rat
12879876Bw182Body weight QTL 1820.003body mass (VT:0001259)body weight (CMO:0000012)3153381237174632112Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:195
Count of miRNA genes:134
Interacting mature miRNAs:149
Transcripts:ENSRNOT00000008365
Prediction methods:Microtar, 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 1 6 15 1
Low 2 5 23 15 4 15 15 12 11
Below cutoff 12 22 20 20 8 9 27 6 11 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000008365   ⟹   ENSRNOP00000008365
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3171,276,062 - 171,286,413 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000081036   ⟹   ENSRNOP00000071089
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3171,276,130 - 171,286,537 (-)Ensembl
RefSeq Acc Id: NM_133564   ⟹   NP_598248
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23161,993,351 - 162,003,706 (-)NCBI
Rnor_6.03171,276,062 - 171,286,413 (-)NCBI
Rnor_5.03177,340,450 - 177,356,357 (-)NCBI
Celera3161,180,812 - 161,191,132 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006235674   ⟹   XP_006235736
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23161,993,351 - 162,009,296 (-)NCBI
Rnor_6.03171,276,062 - 171,292,062 (-)NCBI
Rnor_5.03177,340,450 - 177,356,357 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039104189   ⟹   XP_038960117
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23161,993,351 - 162,009,297 (-)NCBI
RefSeq Acc Id: XM_039104190   ⟹   XP_038960118
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23161,993,351 - 162,009,297 (-)NCBI
RefSeq Acc Id: XM_039104191   ⟹   XP_038960119
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23161,993,351 - 162,009,297 (-)NCBI
RefSeq Acc Id: XM_039104192   ⟹   XP_038960120
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23161,993,351 - 162,009,296 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_598248   ⟸   NM_133564
- UniProtKB: G3V6S4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006235736   ⟸   XM_006235674
- Peptide Label: isoform X1
- UniProtKB: G3V6S4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000008365   ⟸   ENSRNOT00000008365
RefSeq Acc Id: ENSRNOP00000071089   ⟸   ENSRNOT00000081036
RefSeq Acc Id: XP_038960119   ⟸   XM_039104191
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038960117   ⟸   XM_039104189
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038960118   ⟸   XM_039104190
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038960120   ⟸   XM_039104192
- Peptide Label: isoform X1
Protein Domains
Z-binding   Zalpha

Transcriptome

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

Promoters
RGD ID:13692718
Promoter ID:EPDNEW_R3237
Type:initiation region
Name:Zbp1_1
Description:Z-DNA 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_6.03171,286,535 - 171,286,595EPDNEW

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)
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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
3 177350773 177350774 G A snv RCS/Kyo (KyushuU), HWY/Slc (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 171286385 171286386 G A snv CDR


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619956 AgrOrtholog
Ensembl Genes ENSRNOG00000006314 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000008365 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000071089 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008365 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000081036 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro RHIM_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Zalpha_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZBP1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:171091 UniProtKB/TrEMBL
NCBI Gene 171091 ENTREZGENE
PANTHER PTHR14966 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam RHIM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  z-alpha UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Zbp1 PhenoGen
PROSITE Z_BINDING UniProtKB/Swiss-Prot
SMART Zalpha UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46785 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt G3V6S4 ENTREZGENE, UniProtKB/TrEMBL
  Q8VDA5 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Zbp1  Z-DNA binding protein 1    tumor stroma and activated macrophage protein DLM-1  Name updated 1299863 APPROVED
2004-09-10 Zbp1  tumor stroma and activated macrophage protein DLM-1  Dlm1    Symbol and Name updated 1299863 APPROVED
2002-08-07 Dlm1  tumor stroma and activated macrophage protein DLM-1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_homology human homolog expressed predominantly in lymphatic tissues 632620