Zfp560 (zinc finger protein 560) - Rat Genome Database

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Gene: Zfp560 (zinc finger protein 560) Rattus norvegicus
Analyze
Symbol: Zfp560
Name: zinc finger protein 560
RGD ID: 2323078
Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. Orthologous to human ZNF121 (zinc finger protein 121); INTERACTS WITH 17beta-estradiol (ortholog); aflatoxin B1 (ortholog); amiodarone (ortholog).
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC100359967; rCG31761-like; zinc finger protein 345
RGD Orthologs
Human
Bonobo
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8827,176,392 - 27,190,689 (-)NCBIGRCr8
mRatBN7.2818,900,142 - 18,914,444 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl818,900,528 - 18,914,442 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0821,379,447 - 21,394,804 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl821,380,504 - 21,384,131 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0821,443,219 - 21,458,566 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4819,373,913 - 19,382,145 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera820,301,398 - 20,316,761 (-)NCBICelera
Cytogenetic Map8q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleus  (IBA)

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Zfp560
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8827,176,392 - 27,190,689 (-)NCBIGRCr8
mRatBN7.2818,900,142 - 18,914,444 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl818,900,528 - 18,914,442 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0821,379,447 - 21,394,804 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl821,380,504 - 21,384,131 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0821,443,219 - 21,458,566 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4819,373,913 - 19,382,145 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera820,301,398 - 20,316,761 (-)NCBICelera
Cytogenetic Map8q13NCBI
ZNF121
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38199,560,329 - 9,584,504 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl199,560,329 - 9,584,504 (-)EnsemblGRCh38hg38GRCh38
GRCh37199,671,005 - 9,695,180 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36199,537,292 - 9,556,209 (-)NCBINCBI36Build 36hg18NCBI36
Build 34199,537,291 - 9,556,209NCBI
Celera199,571,743 - 9,590,665 (-)NCBICelera
Cytogenetic Map19p13.2NCBI
HuRef199,257,266 - 9,276,162 (-)NCBIHuRef
CHM1_1199,675,900 - 9,694,944 (-)NCBICHM1_1
T2T-CHM13v2.0199,686,517 - 9,710,677 (-)NCBIT2T-CHM13v2.0
ZNF121
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22014,474,501 - 14,499,718 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11913,452,322 - 13,484,173 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0199,092,678 - 9,117,522 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1199,785,384 - 9,804,000 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl199,785,384 - 9,804,000 (-)Ensemblpanpan1.1panPan2
ZNF121
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.168,724,345 - 8,727,719 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl68,724,568 - 8,735,991 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607411,366,512 - 11,386,561 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Zfp560
81 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:113
Count of miRNA genes:86
Interacting mature miRNAs:92
Transcripts:ENSRNOT00000071010
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8124597739Rat
2317882Alcrsp24Alcohol response QTL 243.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)8125902202Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8209764047097640Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8209764047097640Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8209764047097640Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8209764047097640Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)8470581049705810Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)8470581049705810Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)8470581049705810Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8767057852670578Rat
1354595Despr4Despair related QTL 42.160.0036locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)8768895552688955Rat
1354627Despr14Despair related QTL 140.0056locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8768895552688955Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)8873663553736635Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)8873663553736635Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)8971222053356647Rat
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
1558646Swd5Spike wave discharge measurement QTL 53.450.00036brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)81490675159906751Rat
61373Mcs4Mammary carcinoma susceptibility QTL 41.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)81629044461290444Rat

Markers in Region
D8Got17  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2818,908,948 - 18,909,131 (+)MAPPERmRatBN7.2
Rnor_6.0821,389,323 - 21,389,505NCBIRnor6.0
Rnor_5.0821,453,093 - 21,453,275UniSTSRnor5.0
RGSC_v3.4819,381,278 - 19,381,461RGDRGSC3.4
RGSC_v3.4819,381,279 - 19,381,461UniSTSRGSC3.4
RGSC_v3.1819,381,278 - 19,381,461RGD
Celera820,311,280 - 20,311,462UniSTS


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 1 47 2 11
Low 3 43 56 41 18 41 8 11 27 33 30 11 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_006226310 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006226311 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242583 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006242584 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595974 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595975 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595976 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017603578 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017603579 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017603580 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039082247 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039082248 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039082249 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039082250 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039082251 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039082253 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039082254 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473993 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211567 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000008 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000071010   ⟹   ENSRNOP00000066643
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl818,900,528 - 18,914,442 (-)Ensembl
Rnor_6.0 Ensembl821,380,504 - 21,384,131 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000105715   ⟹   ENSRNOP00000095813
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl818,900,528 - 18,914,410 (-)Ensembl
RefSeq Acc Id: XM_006242583   ⟹   XP_006242645
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8827,176,392 - 27,190,689 (-)NCBI
mRatBN7.2818,900,142 - 18,914,441 (-)NCBI
Rnor_6.0821,379,447 - 21,394,804 (-)NCBI
Rnor_5.0821,443,219 - 21,458,566 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595974   ⟹   XP_017451463
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8827,176,392 - 27,190,688 (-)NCBI
mRatBN7.2818,900,142 - 18,914,442 (-)NCBI
Rnor_6.0821,379,447 - 21,394,804 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595976   ⟹   XP_017451465
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8827,176,392 - 27,190,631 (-)NCBI
mRatBN7.2818,900,142 - 18,914,379 (-)NCBI
Rnor_6.0821,379,447 - 21,394,804 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039082247   ⟹   XP_038938175
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8827,176,392 - 27,190,688 (-)NCBI
mRatBN7.2818,900,142 - 18,914,440 (-)NCBI
RefSeq Acc Id: XM_039082248   ⟹   XP_038938176
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8827,176,392 - 27,190,689 (-)NCBI
mRatBN7.2818,900,142 - 18,914,442 (-)NCBI
RefSeq Acc Id: XM_039082249   ⟹   XP_038938177
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8827,176,392 - 27,190,688 (-)NCBI
mRatBN7.2818,900,142 - 18,914,441 (-)NCBI
RefSeq Acc Id: XM_039082250   ⟹   XP_038938178
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8827,176,392 - 27,190,689 (-)NCBI
mRatBN7.2818,900,142 - 18,914,442 (-)NCBI
RefSeq Acc Id: XM_039082251   ⟹   XP_038938179
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8827,176,392 - 27,190,661 (-)NCBI
mRatBN7.2818,900,142 - 18,914,430 (-)NCBI
RefSeq Acc Id: XM_039082253   ⟹   XP_038938181
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8827,176,392 - 27,190,626 (-)NCBI
mRatBN7.2818,900,142 - 18,914,375 (-)NCBI
RefSeq Acc Id: XM_039082254   ⟹   XP_038938182
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8827,176,392 - 27,190,688 (-)NCBI
mRatBN7.2818,900,142 - 18,914,441 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_006242645   ⟸   XM_006242583
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017451465   ⟸   XM_017595976
- Peptide Label: isoform X1
- UniProtKB: M0RAT5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017451463   ⟸   XM_017595974
- Peptide Label: isoform X1
- UniProtKB: M0RAT5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000066643   ⟸   ENSRNOT00000071010
RefSeq Acc Id: XP_038938176   ⟸   XM_039082248
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038938178   ⟸   XM_039082250
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038938177   ⟸   XM_039082249
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038938182   ⟸   XM_039082254
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038938175   ⟸   XM_039082247
- Peptide Label: isoform X2
- UniProtKB: A0A8I6API0 (UniProtKB/TrEMBL),   A6JNH8 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038938179   ⟸   XM_039082251
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038938181   ⟸   XM_039082253
- Peptide Label: isoform X5
RefSeq Acc Id: ENSRNOP00000095813   ⟸   ENSRNOT00000105715
Protein Domains
C2H2-type   KRAB

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0RAT5-F1-model_v2 AlphaFold M0RAT5 1-639 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2323078 AgrOrtholog
BioCyc Gene G2FUF-31478 BioCyc
Ensembl Genes ENSRNOG00000048394 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000071010.3 UniProtKB/TrEMBL
  ENSRNOT00000105715.1 UniProtKB/TrEMBL
Gene3D-CATH 6.10.140.140 UniProtKB/TrEMBL
  Classic Zinc Finger UniProtKB/TrEMBL
InterPro KRAB UniProtKB/TrEMBL
  KRAB_dom_sf UniProtKB/TrEMBL
  Znf_C2H2/integrase_DNA-bd UniProtKB/TrEMBL
  Znf_C2H2_sf UniProtKB/TrEMBL
NCBI Gene 100359967 ENTREZGENE
PANTHER ZINC FINGER PROTEIN UniProtKB/TrEMBL
  ZINC FINGER PROTEIN 266 UniProtKB/TrEMBL
Pfam KRAB UniProtKB/TrEMBL
  zf-C2H2 UniProtKB/TrEMBL
  zf-C2H2_6 UniProtKB/TrEMBL
PhenoGen Zfp560 PhenoGen
PROSITE KRAB UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_1 UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000048394 RatGTEx
SMART KRAB UniProtKB/TrEMBL
  ZnF_C2H2 UniProtKB/TrEMBL
Superfamily-SCOP SSF109640 UniProtKB/TrEMBL
  SSF57667 UniProtKB/TrEMBL
UniProt A0A8I6API0 ENTREZGENE, UniProtKB/TrEMBL
  A6JNH8 ENTREZGENE, UniProtKB/TrEMBL
  M0RAT5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-08-01 Zfp560  zinc finger protein 560  LOC100359967  rCG31761-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-06 LOC100359967  rCG31761-like      Symbol and Name status set to provisional 70820 PROVISIONAL