Zfp654 (zinc finger protein 654) - Rat Genome Database

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Gene: Zfp654 (zinc finger protein 654) Rattus norvegicus
Analyze
Symbol: Zfp654
Name: zinc finger protein 654
RGD ID: 1308321
Description: Predicted to enable DNA binding activity and DNA-binding transcription factor activity, RNA polymerase II-specific. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. Orthologous to human ZNF654 (zinc finger protein 654); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; amitrole.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: AABR07033023.1; hypothetical LOC288354; LOC288354; LOC679644; RGD1308321; similar to Zinc finger protein Rlf (Rearranged L-myc fusion gene protein) (Zn-15 related protein); Znf654
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81115,947,425 - 16,011,957 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1115,949,373 - 16,011,969 (-)EnsemblGRCr8
mRatBN7.2112,500,892 - 2,565,552 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl112,503,508 - 2,565,637 (-)EnsemblmRatBN7.2
Rnor_6.0111,831,378 - 1,895,814 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl111,835,185 - 1,836,897 (-)NCBIrn6Rnor6.0
Rnor_5.0111,811,954 - 1,876,664 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4112,120,729 - 2,123,544 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera112,482,441 - 2,547,648 (-)NCBICelera
RGSC_v3.1112,120,489 - 2,182,377 (-)NCBI
Cytogenetic Map11p12NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleus  (IBA,IEA)

Molecular Function

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

Genomics

Comparative Map Data
Zfp654
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81115,947,425 - 16,011,957 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1115,949,373 - 16,011,969 (-)EnsemblGRCr8
mRatBN7.2112,500,892 - 2,565,552 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl112,503,508 - 2,565,637 (-)EnsemblmRatBN7.2
Rnor_6.0111,831,378 - 1,895,814 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl111,835,185 - 1,836,897 (-)NCBIrn6Rnor6.0
Rnor_5.0111,811,954 - 1,876,664 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4112,120,729 - 2,123,544 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera112,482,441 - 2,547,648 (-)NCBICelera
RGSC_v3.1112,120,489 - 2,182,377 (-)NCBI
Cytogenetic Map11p12NCBI
ZNF654
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38388,059,255 - 88,144,660 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl388,058,723 - 88,144,662 (+)Ensemblhg38GRCh38
GRCh37388,108,405 - 88,193,810 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36388,270,952 - 88,276,504 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34388,271,164 - 88,273,912NCBI
Celera388,942,131 - 88,947,592 (+)NCBICelera
Cytogenetic Map3p11.1NCBI
HuRef388,201,768 - 88,207,323 (+)NCBIHuRef
CHM1_1388,141,379 - 88,146,934 (+)NCBICHM1_1
T2T-CHM13v2.0388,135,096 - 88,220,495 (+)NCBIT2T-CHM13v2.0
Zfp654
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391664,600,710 - 64,672,300 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1664,600,710 - 64,672,015 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381664,780,347 - 64,851,937 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1664,780,347 - 64,851,652 (-)Ensemblmm10GRCm38
MGSCv371664,780,173 - 64,786,147 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361664,722,549 - 64,728,523 (-)NCBIMGSCv36mm8
Celera1665,074,987 - 65,080,961 (-)NCBICelera
Cytogenetic Map16C1.3NCBI
cM Map1637.1NCBI
ZNF654
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2288,216,425 - 88,302,008 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1388,221,235 - 88,306,796 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0388,197,558 - 88,283,050 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1390,309,186 - 90,395,198 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl390,309,186 - 90,395,198 (+)EnsemblpanPan2panpan1.1
ZNF654
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.131114,287 - 207,313 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl31117,435 - 247,237 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha31157,349 - 250,290 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.03197,631 - 190,614 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3198,938 - 230,942 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13177,668 - 170,327 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.031124,661 - 217,597 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.031429,341 - 522,297 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Znf654
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049711,604,587 - 1,683,015 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366101,604,575 - 1,683,021 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366101,604,591 - 1,683,009 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ZNF654
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13167,807,263 - 167,895,736 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.113167,807,705 - 167,895,783 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
ZNF654
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12288,782,957 - 88,864,512 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2288,782,940 - 88,799,268 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604177,850,024 - 77,932,500 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Znf654
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247894,449,045 - 4,525,664 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247894,448,957 - 4,528,641 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Znf654
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v17109,588,116 - 109,653,049 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Zfp654
336 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:99
Count of miRNA genes:79
Interacting mature miRNAs:87
Transcripts:ENSRNOT00000050533
Prediction methods:Microtar, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598842Glom10Glomerulus QTL 103.4kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)11381815448818154Rat
1600394Edcs1Endometrial carcinoma susceptibility QTL12.90.04uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)111282315257823152Rat
634339Niddm50Non-insulin dependent diabetes mellitus QTL 503.32blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)111080612555806125Rat

Markers in Region
UniSTS:486248  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2112,504,998 - 2,506,374 (+)MAPPERmRatBN7.2
Rnor_6.0111,835,478 - 1,836,853NCBIRnor6.0
Rnor_5.0111,816,054 - 1,817,429UniSTSRnor5.0
RGSC_v3.4112,122,125 - 2,123,500UniSTSRGSC3.4
Celera112,486,541 - 2,487,916UniSTS
Cytogenetic Map11p12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
hemolymphoid system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
sensory system
visual system
7 1 18 52 67 138 95 11 51 36 32 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000050533   ⟹   ENSRNOP00000039110
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1115,949,373 - 16,011,969 (-)Ensembl
mRatBN7.2 Ensembl112,503,508 - 2,565,637 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000118668   ⟹   ENSRNOP00000081202
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1115,949,373 - 16,011,898 (-)Ensembl
mRatBN7.2 Ensembl112,503,508 - 2,565,637 (-)Ensembl
RefSeq Acc Id: XM_039088760   ⟹   XP_038944688
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81115,947,425 - 15,968,191 (-)NCBI
mRatBN7.2112,500,892 - 2,519,086 (-)NCBI
RefSeq Acc Id: XM_063270836   ⟹   XP_063126906
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81115,947,425 - 15,990,833 (-)NCBI
RefSeq Acc Id: XM_237855   ⟹   XP_237855
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81115,947,425 - 16,011,957 (-)NCBI
mRatBN7.2112,500,899 - 2,565,552 (-)NCBI
Rnor_6.0111,831,378 - 1,895,814 (-)NCBI
Rnor_5.0111,811,954 - 1,876,664 (-)NCBI
RGSC_v3.4112,120,729 - 2,123,544 (-)RGD
Sequence:
RefSeq Acc Id: XP_237855   ⟸   XM_237855
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_038944688   ⟸   XM_039088760
- Peptide Label: isoform X2
- UniProtKB: A6K4W1 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000081202   ⟸   ENSRNOT00000118668
Ensembl Acc Id: ENSRNOP00000039110   ⟸   ENSRNOT00000050533
RefSeq Acc Id: XP_063126906   ⟸   XM_063270836
- Peptide Label: isoform X2
Protein Domains
C2H2-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZMK5-F1-model_v2 AlphaFold D3ZMK5 1-571 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:1308321 AgrOrtholog
BioCyc Gene G2FUF-22321 BioCyc
Ensembl Genes ENSRNOG00000029956 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000050533 ENTREZGENE
  ENSRNOT00000050533.5 UniProtKB/TrEMBL
  ENSRNOT00000118668.2 UniProtKB/TrEMBL
Gene3D-CATH Classic Zinc Finger UniProtKB/TrEMBL
InterPro GH-ZnFinger_Regulators UniProtKB/TrEMBL
  Znf_C2H2_sf UniProtKB/TrEMBL
  Znf_C2H2_type UniProtKB/TrEMBL
NCBI Gene 288354 ENTREZGENE
PANTHER ZINC FINGER PROTEIN 654 UniProtKB/TrEMBL
  ZINC FINGER PROTEIN RLF UniProtKB/TrEMBL
Pfam TPR_Rlf UniProtKB/TrEMBL
  zf-C2H2 UniProtKB/TrEMBL
  zf-C2H2_ZN292 UniProtKB/TrEMBL
PhenoGen Zfp654 PhenoGen
PROSITE ZINC_FINGER_C2H2_1 UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000029956 RatGTEx
SMART ZnF_C2H2 UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/TrEMBL
UniProt A0A8I5ZUK3_RAT UniProtKB/TrEMBL
  A6K4W1 ENTREZGENE, UniProtKB/TrEMBL
  D3ZMK5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-02 Zfp654  zinc finger protein 654  AABR07033023.1    Data merged from RGD:15003784 737654 PROVISIONAL
2021-09-02 AABR07033023.1    Zfp654  zinc finger protein 654  Symbol and/or name change 19259462 PROVISIONAL
2021-08-09 Zfp654  zinc finger protein 654  AABR07033023.1    Symbol and/or name change 19259462 PROVISIONAL
2019-11-08 AABR07033023.1        Symbol and Name status set to provisional 45752 PROVISIONAL
2015-07-29 Zfp654  zinc finger protein 654  LOC679644  similar to Zinc finger protein Rlf (Rearranged L-myc fusion gene protein) (Zn-15 related protein)  Data merged from RGD:1585945 737654 PROVISIONAL
2011-07-19 Zfp654  zinc finger protein 654  Znf654  zinc finger protein 654  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Znf654  zinc finger protein 654  Zfp654  zinc finger protein 654  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-26 Zfp654  zinc finger protein 654  RGD1308321_predicted  hypothetical LOC288354 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC679644  similar to Zinc finger protein Rlf (Rearranged L-myc fusion gene protein) (Zn-15 related protein)      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-01-20 RGD1308321_predicted  hypothetical LOC288354 (predicted)  LOC288354_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC288354_predicted  hypothetical LOC288354 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL