Zkscan3 (zinc finger with KRAB and SCAN domains 3) - Rat Genome Database

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Gene: Zkscan3 (zinc finger with KRAB and SCAN domains 3) Rattus norvegicus
Analyze
Symbol: Zkscan3
Name: zinc finger with KRAB and SCAN domains 3
RGD ID: 1305753
Description: Predicted to have DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chromatin binding activity. Predicted to be involved in several processes, including negative regulation of autophagy; negative regulation of cellular senescence; and regulation of transcription, DNA-templated. Predicted to localize to cytoplasm and nucleoplasm. Orthologous to several human genes including ZKSCAN3 (zinc finger with KRAB and SCAN domains 3); INTERACTS WITH 2,4-dinitrotoluene; 2,6-dinitrotoluene; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC306977; MGC108865; Zfp307; zinc finger protein 307; zinc finger protein with KRAB and SCAN domains 3
RGD Orthologs
Human
Mouse
Bonobo
Squirrel
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21743,217,168 - 43,232,828 (+)NCBI
Rnor_6.0 Ensembl1745,247,776 - 45,263,418 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01745,247,724 - 45,263,422 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01758,204,677 - 58,220,555 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41750,862,534 - 50,901,252 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11750,865,374 - 50,880,759 (+)NCBI
Celera1753,235,157 - 53,250,769 (-)NCBICelera
Cytogenetic Map17p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

Additional References at PubMed
PMID:12477932   PMID:18940803   PMID:23434374  


Genomics

Comparative Map Data
Zkscan3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21743,217,168 - 43,232,828 (+)NCBI
Rnor_6.0 Ensembl1745,247,776 - 45,263,418 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01745,247,724 - 45,263,422 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01758,204,677 - 58,220,555 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41750,862,534 - 50,901,252 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11750,865,374 - 50,880,759 (+)NCBI
Celera1753,235,157 - 53,250,769 (-)NCBICelera
Cytogenetic Map17p11NCBI
ZKSCAN3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl628,349,947 - 28,369,172 (+)EnsemblGRCh38hg38GRCh38
GRCh38628,349,913 - 28,369,174 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37628,317,724 - 28,336,949 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36628,425,738 - 28,442,503 (+)NCBINCBI36hg18NCBI36
Build 34628,425,737 - 28,442,502NCBI
Celera629,924,132 - 29,940,962 (+)NCBI
Cytogenetic Map6p22.1NCBI
HuRef628,124,766 - 28,144,005 (+)NCBIHuRef
CHM1_1628,320,076 - 28,339,339 (+)NCBICHM1_1
Zkscan3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391321,571,174 - 21,586,942 (-)NCBIGRCm39mm39
GRCm39 Ensembl1321,571,173 - 21,586,925 (-)Ensembl
GRCm381321,387,004 - 21,402,755 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1321,387,003 - 21,402,755 (-)EnsemblGRCm38mm10GRCm38
MGSCv371321,478,873 - 21,494,624 (-)NCBIGRCm37mm9NCBIm37
MGSCv361321,394,546 - 21,412,211 (-)NCBImm8
Celera1321,652,946 - 21,668,698 (-)NCBICelera
Cytogenetic Map13A3.1NCBI
ZKSCAN3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1628,828,297 - 28,847,596 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl628,828,298 - 28,847,596 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0628,157,736 - 28,174,906 (+)NCBIMhudiblu_PPA_v0panPan3
Zkscan3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494628,778,053 - 28,795,403 (+)NCBI
SpeTri2.0NW_00493677243 - 7,099 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ZKSCAN3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11744,199,513 - 44,216,456 (-)NCBI
ChlSab1.1 Ensembl1744,200,164 - 44,216,706 (-)Ensembl
Vero_WHO_p1.0NW_02366604428,042,781 - 28,062,276 (+)NCBI

Position Markers
AI132359  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21743,232,360 - 43,232,587 (+)MAPPER
Rnor_6.01745,262,950 - 45,263,180NCBIRnor6.0
Rnor_5.01758,204,917 - 58,205,147UniSTSRnor5.0
Celera1753,235,397 - 53,235,623UniSTS
Cytogenetic Map17q11UniSTS
RH143072  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21743,226,055 - 43,226,156 (+)MAPPER
Rnor_6.01745,256,635 - 45,256,735NCBIRnor6.0
Rnor_5.01758,211,556 - 58,211,656UniSTSRnor5.0
RGSC_v3.41750,871,374 - 50,871,474UniSTSRGSC3.4
Celera1753,241,828 - 53,241,928UniSTS
Cytogenetic Map17q11UniSTS
RH124729  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21743,232,557 - 43,232,654 (+)MAPPER
Rnor_6.01745,263,151 - 45,263,247NCBIRnor6.0
Rnor_5.01758,204,850 - 58,204,946UniSTSRnor5.0
Celera1753,235,330 - 53,235,426UniSTS
Cytogenetic Map17q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17163676140Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17173413148Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17173413148Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17333697263676140Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17333697273413148Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17333697273413148Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17333697273413148Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17519104750191047Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17519104750191047Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17982730454827304Rat
1331765Hrtrt15Heart rate QTL 154.094heart pumping trait (VT:2000009)heart rate (CMO:0000002)171574375561036897Rat
1354640Scl32Serum cholesterol level QTL 325.4blood HDL cholesterol amount (VT:0000184)blood high density lipoprotein cholesterol level (CMO:0000052)171867614063676140Rat
1354659Scl68Serum cholesterol level QTL 683.9blood VLDL cholesterol amount (VT:0005144)blood very low density lipoprotein cholesterol level (CMO:0000648)171867614063676140Rat
7488966Bp370Blood pressure QTL 3700.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172149095062195822Rat
1559055Bp278Blood pressure QTL 2780.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172149095066490950Rat
12903978Cm118Cardiac mass QTL 1180.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)172149095066490950Rat
12903979Cm119Cardiac mass QTL 1190.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172149095066490950Rat
12903980Cm120Cardiac mass QTL 1200.002heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)172149095066490950Rat
12903981Am17Aortic mass QTL 170.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)172149095066490950Rat
12903982Kidm70Kidney mass QTL 700.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)172149095074823273Rat
70157Niddm32Non-insulin dependent diabetes mellitus QTL 324.34blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)172213681453475276Rat
61394Bp8Blood pressure QTL 82.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172277506564946194Rat
1354628Stl13Serum triglyceride level QTL 133.8blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)172403061863676140Rat
1581512Cm55Cardiac mass QTL 552.80.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172769095961794615Rat
4889955Bss93Bone structure and strength QTL 934.4tibia size trait (VT:0100001)tibia cortical bone volume to tibia total bone volume ratio (CMO:0001727)172769095963994435Rat
2302377Scl61Serum cholesterol level QTL 614.36blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)172807358956207236Rat
1354619Bp242Blood pressure QTL 2426.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172841314873413148Rat
9590107Sffal7Serum free fatty acids level QTL 74.810.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)173097522875975228Rat
8552928Pigfal9Plasma insulin-like growth factor 1 level QTL 99blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)173097522875975228Rat
10450503Bp386Blood pressure QTL 3860.28arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)173205588258468016Rat
2324621Coatc5Coat color QTL 5coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)173205588277922655Rat
2313854Bp343Blood pressure QTL 3433.9life span trait (VT:0005372)age at time of death (CMO:0001193)173330362753475276Rat
724549Niddm56Non-insulin dependent diabetes mellitus QTL 560.03blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)173330362778303627Rat
1354663Bvd5Brain ventricular dilatation QTL 53.510.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)173330362785321557Rat
1300148Bp192Blood pressure QTL 1923.47arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)173628324577922655Rat
724528Uae4Urinary albumin excretion QTL 44.90.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)173779030673413148Rat
2317054Aia12Adjuvant induced arthritis QTL 124.24joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)174117605786176057Rat
2317060Aia26Adjuvant induced arthritis QTL 263.22joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)174117605786176057Rat
2301412Kidm40Kidney mass QTL 400.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)174173108086731080Rat
1598871Memor5Memory QTL 55.3exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)174254187285446768Rat
631497Bp98Blood pressure QTL 983.66arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)174295602163994435Rat
1358295Aocep1Aortic cell protein QTL 16.10.00000071thoracic aorta cellular protein amount (VT:0010598)aortic cell percentage174435615789356157Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:647
Count of miRNA genes:270
Interacting mature miRNAs:347
Transcripts:ENSRNOT00000024783, ENSRNOT00000066981
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 3 36 41 28 17 28 1 66 31 36 11
Low 7 16 13 2 13 8 10 8 4 5 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001012053 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006254096 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006254099 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006254101 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008771726 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600550 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600551 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017600552 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095714 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095715 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095716 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095717 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039095718 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC089847 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474072 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK602433 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000293 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000080655   ⟹   ENSRNOP00000072953
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1745,247,794 - 45,263,418 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000081063   ⟹   ENSRNOP00000069061
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1745,247,776 - 45,262,858 (+)Ensembl
RefSeq Acc Id: NM_001012053   ⟹   NP_001012053
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21743,217,215 - 43,232,827 (+)NCBI
Rnor_6.01745,247,794 - 45,263,420 (+)NCBI
Rnor_5.01758,204,677 - 58,220,555 (-)NCBI
RGSC_v3.41750,862,534 - 50,901,252 (+)RGD
Celera1753,235,157 - 53,250,769 (-)RGD
Sequence:
RefSeq Acc Id: XM_006254096   ⟹   XP_006254158
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01745,247,724 - 45,263,422 (+)NCBI
Rnor_5.01758,204,677 - 58,220,555 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006254099   ⟹   XP_006254161
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21743,217,196 - 43,232,828 (+)NCBI
Rnor_6.01745,247,749 - 45,263,422 (+)NCBI
Rnor_5.01758,204,677 - 58,220,555 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006254101   ⟹   XP_006254163
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21743,217,168 - 43,232,828 (+)NCBI
Rnor_6.01745,247,724 - 45,263,422 (+)NCBI
Rnor_5.01758,204,677 - 58,220,555 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008771726   ⟹   XP_008769948
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21743,217,196 - 43,232,828 (+)NCBI
Rnor_6.01745,247,830 - 45,263,422 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600550   ⟹   XP_017456039
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01745,247,724 - 45,263,422 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600551   ⟹   XP_017456040
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01745,247,724 - 45,263,422 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600552   ⟹   XP_017456041
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01745,247,830 - 45,263,422 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039095714   ⟹   XP_038951642
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21743,217,196 - 43,232,828 (+)NCBI
RefSeq Acc Id: XM_039095715   ⟹   XP_038951643
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21743,217,175 - 43,232,828 (+)NCBI
RefSeq Acc Id: XM_039095716   ⟹   XP_038951644
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21743,218,826 - 43,232,828 (+)NCBI
RefSeq Acc Id: XM_039095717   ⟹   XP_038951645
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21743,225,105 - 43,232,828 (+)NCBI
RefSeq Acc Id: XM_039095718   ⟹   XP_038951646
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21743,217,195 - 43,231,986 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001012053   ⟸   NM_001012053
- UniProtKB: F7DP88 (UniProtKB/TrEMBL),   Q5FVP7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006254158   ⟸   XM_006254096
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006254161   ⟸   XM_006254099
- Peptide Label: isoform X1
- UniProtKB: F7DP88 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006254163   ⟸   XM_006254101
- Peptide Label: isoform X1
- UniProtKB: F7DP88 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008769948   ⟸   XM_008771726
- Peptide Label: isoform X1
- UniProtKB: F7DP88 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456039   ⟸   XM_017600550
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017456040   ⟸   XM_017600551
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017456041   ⟸   XM_017600552
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000072953   ⟸   ENSRNOT00000080655
RefSeq Acc Id: ENSRNOP00000069061   ⟸   ENSRNOT00000081063
RefSeq Acc Id: XP_038951643   ⟸   XM_039095715
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951646   ⟸   XM_039095718
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038951642   ⟸   XM_039095714
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951644   ⟸   XM_039095716
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951645   ⟸   XM_039095717
- Peptide Label: isoform X2
Protein Domains
C2H2-type   SCAN box

Transcriptome

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

Promoters
RGD ID:13700495
Promoter ID:EPDNEW_R11018
Type:multiple initiation site
Name:Zkscan3_1
Description:zinc finger with KRAB and SCAN domains 3
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_6.01745,247,782 - 45,247,842EPDNEW

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)
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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
COP/CrCrl (MCW & UW)
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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)
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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
F344/NRrrc (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
FHH/EurMcwi (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)
FHH/EurMcwi (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
FHL/EurMcwi (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)
FHL/EurMcwi (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
GH/OmrMcwi (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)
GK/Ox (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
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305753 AgrOrtholog
Ensembl Genes ENSRNOG00000055000 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000069061 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000072953 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000080655 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000081063 UniProtKB/TrEMBL
Gene3D-CATH 1.10.4020.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7373658 IMAGE-MGC_LOAD
InterPro KRAB_dom_sf UniProtKB/TrEMBL
  Krueppel-associated_box UniProtKB/TrEMBL
  SCAN_sf UniProtKB/TrEMBL
  Tscrpt_reg_SCAN UniProtKB/TrEMBL
  Znf_C2H2/integrase_DNA-bd UniProtKB/TrEMBL
  Znf_C2H2_sf UniProtKB/TrEMBL
KEGG Report rno:306977 UniProtKB/TrEMBL
MGC_CLONE MGC:108865 IMAGE-MGC_LOAD
NCBI Gene 306977 ENTREZGENE
Pfam KRAB UniProtKB/TrEMBL
  SCAN UniProtKB/TrEMBL
  zf-C2H2 UniProtKB/TrEMBL
PhenoGen Zkscan3 PhenoGen
PROSITE SCAN_BOX UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_1 UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/TrEMBL
SMART KRAB UniProtKB/TrEMBL
  SCAN UniProtKB/TrEMBL
  ZnF_C2H2 UniProtKB/TrEMBL
Superfamily-SCOP Krueppel-associated_box UniProtKB/TrEMBL
  SSF57667 UniProtKB/TrEMBL
UniProt F7DP88 ENTREZGENE, UniProtKB/TrEMBL
  Q5FVP7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-04 Zkscan3  zinc finger with KRAB and SCAN domains 3  Zfp307  zinc finger protein 307  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Zfp307  zinc finger protein 307  Zfp307_predicted  zinc finger protein 307 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Zfp307_predicted  zinc finger protein 307 (predicted)      Symbol and Name status set to approved 70820 APPROVED