Zfp54 (zinc finger protein 54) - Rat Genome Database

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Gene: Zfp54 (zinc finger protein 54) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Zfp54 (Ensembl: Zfp677)
Name: zinc finger protein 54 (Ensembl:zinc finger protein 677)
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. Orthologous to several human genes including ZNF28 (zinc finger protein 28); ZNF320 (zinc finger protein 320); and ZNF415 (zinc finger protein 415); INTERACTS WITH 2,4-dinitrotoluene; valproic acid.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC308232; Zfp51; zinc finger protein 51
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8169,864,213 - 69,876,881 (+)NCBIGRCr8GRCr8GRCr8
mRatBN7.2161,190,806 - 61,205,841 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl161,136,700 - 61,203,995 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx165,954,674 - 65,966,956 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0174,637,365 - 74,649,643 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0167,864,713 - 67,876,995 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0161,286,077 - 61,338,888 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl161,314,070 - 61,326,280 (+)Ensemblrn6Rnor6.0
Rnor_5.0163,764,847 - 63,803,750 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4159,370,984 - 59,383,096 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera157,305,324 - 57,317,883 (+)NCBICelera
RGSC_v3.1159,373,930 - 59,385,075 (+)NCBI
Cytogenetic Map1q12NCBI
JBrowse:




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

Biological Process

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
136 total Variants

QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331732Srn4Serum renin concentration QTL 44.467renin activity (VT:0005581)plasma renin activity level (CMO:0000116)14345783787558729Rat
1357397Bw41Body weight QTL 414.190.0001body mass (VT:0001259)body weight (CMO:0000012)12940927974409279Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)151940904101229020Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)139728272132889942Rat
4889929Bss87Bone structure and strength QTL 876.7tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)14630261591302615Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151941022208479811Rat
1331792Rf29Renal function QTL 294.589urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)14345783787558729Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)14630261591302615Rat
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)14350995288509952Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)151940904168768703Rat
1354643Foco2Food consumption QTL 27.170.0001eating behavior trait (VT:0001431)food intake rate (CMO:0000427)14212296887122968Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)14630261591302615Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)14630261591302615Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)166404680111404680Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134184556172281316Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)14630261591302615Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)166009857160501508Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134565911208798288Rat
1331778Rf28Renal function QTL 284.66urine potassium amount (VT:0010539)urine potassium excretion rate (CMO:0000761)14345783787558729Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)14630261591302615Rat
1302788Scl19Serum cholesterol QTL 194.60.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)166400974132889942Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)151511344153680016Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)13070837587558729Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16540563796805205Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13456572679565726Rat
4889962Bss94Bone structure and strength QTL 943.8tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)15190920691302615Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)158769992103769992Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)14630261591302615Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)166077886111077886Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)14630261591302615Rat
9589820Insglur3Insulin/glucose ratio QTL 310.750.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)14350995288509952Rat
152025249Scl82Serum cholesterol level QTL 824.77blood cholesterol amount (VT:0000180)152891222109116986Rat
1354599Bw29Body weight QTL 293.460.001body mass (VT:0001259)body weight (CMO:0000012)14212296887122968Rat
4889919Bss86Bone structure and strength QTL 864.1tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)14630261591302615Rat
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)14350995288509952Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 89 59 6 352 189 11 144 80 92 31 17 17

Sequence


Ensembl 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
Ensembl 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
RefSeq Acc Id: NP_001100937   ⟸   NM_001107467
- UniProtKB: B5DEZ5 (UniProtKB/TrEMBL),   A0A0G2K3R3 (UniProtKB/TrEMBL)
- Sequence:
Ensembl 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)
Ensembl Acc Id: ENSRNOP00000072773   ⟸   ENSRNOT00000082730
RefSeq Acc Id: XP_063144664   ⟸   XM_063288594
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K3R3 (UniProtKB/TrEMBL),   B5DEZ5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063144661   ⟸   XM_063288591
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K3R3 (UniProtKB/TrEMBL),   B5DEZ5 (UniProtKB/TrEMBL)
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
  ENSRNOG00000071332 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000121017.2 UniProtKB/TrEMBL
  ENSRNOT00000121018.2 UniProtKB/TrEMBL
  ENSRNOT00000121019 ENTREZGENE
  ENSRNOT00000121019.2 UniProtKB/TrEMBL
  ENSRNOT00000121022.2 UniProtKB/TrEMBL
Gene3D-CATH 6.10.140.140 UniProtKB/TrEMBL
  Classic Zinc Finger UniProtKB/TrEMBL
InterPro C2H2-ZF_domain-containing UniProtKB/TrEMBL
  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 REDUCED EXPRESSION 2-RELATED UniProtKB/TrEMBL
  ZINC FINGER PROTEIN 200 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
  ENSRNOG00000071332 RatGTEx
SMART KRAB UniProtKB/TrEMBL
  ZnF_C2H2 UniProtKB/TrEMBL
Superfamily-SCOP Krueppel-associated_box UniProtKB/TrEMBL
  SSF57667 UniProtKB/TrEMBL
UniProt A0A0G2K3R3 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0L3K9_RAT UniProtKB/TrEMBL
  A0ABK0L486_RAT UniProtKB/TrEMBL
  A0ABK0LAJ4_RAT UniProtKB/TrEMBL
  A0ABK0LD83_RAT UniProtKB/TrEMBL
  B5DEZ5 ENTREZGENE


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