Zfp54 (zinc finger protein 54) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Zfp54 (zinc finger protein 54) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Zfp54
Name: zinc finger protein 54
RGD ID: 1307738
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.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC308232; Zfp51; zinc finger protein 51
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8169,864,213 - 69,876,881 (+)NCBIGRCr8
mRatBN7.2161,190,806 - 61,205,841 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl161,136,700 - 61,203,995 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx165,954,674 - 65,966,956 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0174,637,365 - 74,649,643 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0167,864,713 - 67,876,995 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0161,286,077 - 61,338,888 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl161,314,070 - 61,326,280 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0163,764,847 - 63,803,750 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4159,370,984 - 59,383,096 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1159,373,930 - 59,385,075 (+)NCBI
Celera157,305,324 - 57,317,883 (+)NCBICelera
Cytogenetic Map1q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932  


Genomics

Variants

.
Variants in Zfp54
98 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1165833076Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
1300167Hrtrt2Heart rate QTL 24.35heart pumping trait (VT:2000009)heart rate (CMO:0000002)11148131275088344Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)11148131282174945Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11148131282174945Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11148131282174945Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11148131282174945Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
724520Bp145Blood pressure QTL 1452.10.0024arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12078482865784828Rat
1357400Bw62Body weight QTL624.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)12234064767340647Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)122340647102268831Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)12887978078430678Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)130882023123479925Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132356093162846471Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13273727390665040Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132737458199368955Rat
1354599Bw29Body weight QTL 293.460.001body mass (VT:0001259)body weight (CMO:0000012)13344984878449848Rat
1354643Foco2Food consumption QTL 27.170.0001eating behavior trait (VT:0001431)food intake rate (CMO:0000427)13344984878449848Rat
8552900Pigfal1Plasma insulin-like growth factor 1 level QTL 17.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13483685879836858Rat
8552948Pigfal11Plasma insulin-like growth factor 1 level QTL 114.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13483685879836858Rat
9589820Insglur3Insulin/glucose ratio QTL 310.750.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)13483685879836858Rat
1331732Srn4Serum renin concentration QTL 44.467renin activity (VT:0005581)plasma renin activity level (CMO:0000116)13523959878430678Rat
1331792Rf29Renal function QTL 294.589urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)13523959878430678Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143284731118944897Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143284731118944897Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143284731118944897Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)143284731118944897Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143284731118944897Rat
2302059Pia36Pristane induced arthritis QTL 363.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)14333300288333002Rat
1331778Rf28Renal function QTL 284.66urine potassium amount (VT:0010539)urine potassium excretion rate (CMO:0000761)14580314078430678Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)148963584144267916Rat
4889962Bss94Bone structure and strength QTL 943.8tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)14936146582174945Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)14939317294393172Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149393172159356837Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149393289199050459Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)15386304190532583Rat
4889919Bss86Bone structure and strength QTL 864.1tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)15389511782174945Rat
4889929Bss87Bone structure and strength QTL 876.7tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)15389511782174945Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)15673266898773277Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)156949932101949932Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)157336763151090257Rat


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 5 12 12 7
Low 3 43 52 41 7 41 8 10 72 35 29 4 8
Below cutoff 1 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000077642   ⟹   ENSRNOP00000072743
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl161,191,746 - 61,203,995 (+)Ensembl
Rnor_6.0 Ensembl161,314,070 - 61,326,280 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000082730   ⟹   ENSRNOP00000072773
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl161,136,700 - 61,155,127 (+)Ensembl
RefSeq Acc Id: NM_001107467   ⟹   NP_001100937
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8169,864,628 - 69,876,881 (+)NCBI
mRatBN7.2161,191,746 - 61,203,999 (+)NCBI
Rnor_6.0161,314,070 - 61,326,284 (+)NCBI
Rnor_5.0163,764,847 - 63,803,750 (+)NCBI
RGSC_v3.4159,370,984 - 59,383,096 (+)RGD
Celera157,305,324 - 57,317,883 (+)RGD
Sequence:
RefSeq Acc Id: XM_039110828   ⟹   XP_038966756
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8169,864,213 - 69,876,870 (+)NCBI
mRatBN7.2161,190,806 - 61,205,841 (+)NCBI
RefSeq Acc Id: XM_039110833   ⟹   XP_038966761
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8169,864,463 - 69,876,870 (+)NCBI
mRatBN7.2161,191,679 - 61,205,841 (+)NCBI
RefSeq Acc Id: XM_063288591   ⟹   XP_063144661
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8169,864,615 - 69,876,870 (+)NCBI
RefSeq Acc Id: XM_063288594   ⟹   XP_063144664
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8169,864,555 - 69,876,870 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001100937   ⟸   NM_001107467
- UniProtKB: B5DEZ5 (UniProtKB/TrEMBL),   A0A0G2K3R3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000072743   ⟸   ENSRNOT00000077642
RefSeq Acc Id: XP_038966756   ⟸   XM_039110828
- Peptide Label: isoform X1
- UniProtKB: B5DEZ5 (UniProtKB/TrEMBL),   A0A0G2K3R3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038966761   ⟸   XM_039110833
- Peptide Label: isoform X1
- UniProtKB: B5DEZ5 (UniProtKB/TrEMBL),   A0A0G2K3R3 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000072773   ⟸   ENSRNOT00000082730
RefSeq Acc Id: XP_063144664   ⟸   XM_063288594
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063144661   ⟸   XM_063288591
- Peptide Label: isoform X1
Protein Domains
C2H2-type   KRAB

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B5DEZ5-F1-model_v2 AlphaFold B5DEZ5 1-586 view protein structure

Transcriptome

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

Promoters
RGD ID:13689653
Promoter ID:EPDNEW_R177
Type:single initiation site
Name:Zfp54_1
Description:zinc finger protein 54
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_6.0161,314,038 - 61,314,098EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307738 AgrOrtholog
BioCyc Gene G2FUF-61174 BioCyc
Ensembl Genes ENSRNOG00000051578 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000077642 ENTREZGENE
  ENSRNOT00000077642.2 UniProtKB/TrEMBL
  ENSRNOT00000082730.2 UniProtKB/TrEMBL
Gene3D-CATH 6.10.140.140 UniProtKB/TrEMBL
  Classic Zinc Finger UniProtKB/TrEMBL
InterPro KRAB_dom_sf UniProtKB/TrEMBL
  Krueppel-associated_box UniProtKB/TrEMBL
  Znf_C2H2/integrase_DNA-bd UniProtKB/TrEMBL
  Znf_C2H2_sf UniProtKB/TrEMBL
KEGG Report rno:308232 UniProtKB/TrEMBL
NCBI Gene 308232 ENTREZGENE
PANTHER FI01424P-RELATED UniProtKB/TrEMBL
  ZINC FINGER AND SCAN DOMAIN-CONTAINING UniProtKB/TrEMBL
  ZINC FINGER PROTEIN UniProtKB/TrEMBL
  ZINC FINGER PROTEIN 853 UniProtKB/TrEMBL
Pfam KRAB UniProtKB/TrEMBL
  zf-C2H2 UniProtKB/TrEMBL
  zf-C2H2_4 UniProtKB/TrEMBL
  zf-C2H2_6 UniProtKB/TrEMBL
PhenoGen Zfp54 PhenoGen
PROSITE KRAB UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_1 UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000051578 RatGTEx
SMART KRAB UniProtKB/TrEMBL
  ZnF_C2H2 UniProtKB/TrEMBL
Superfamily-SCOP Krueppel-associated_box UniProtKB/TrEMBL
  SSF57667 UniProtKB/TrEMBL
UniProt A0A0G2K3R3 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2K3T8_RAT UniProtKB/TrEMBL
  B5DEZ5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-11-27 Zfp54  zinc finger protein 54  Zfp51  zinc finger protein 51  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-03 Zfp51  zinc finger protein 51  Zfp54_predicted  zinc finger protein 54 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Zfp54_predicted  zinc finger protein 54 (predicted)      Symbol and Name status set to approved 70820 APPROVED