Zbed3 (zinc finger, BED-type containing 3) - Rat Genome Database

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Gene: Zbed3 (zinc finger, BED-type containing 3) Rattus norvegicus
Analyze
Symbol: Zbed3
Name: zinc finger, BED-type containing 3
RGD ID: 1309665
Description: Predicted to be involved in several processes, including cytoskeleton organization; positive regulation of embryonic development; and response to insulin. Predicted to act upstream of or within positive regulation of canonical Wnt signaling pathway and protein stabilization. Predicted to be located in cytosol; extracellular space; and membrane. Orthologous to human ZBED3 (zinc finger BED-type containing 3); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3,4-methylenedioxymethamphetamine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC361881; MGC116104; zinc finger BED domain-containing protein 3; zinc finger, BED domain containing 3
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
GRCr8228,323,968 - 28,334,910 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl228,321,960 - 28,337,413 (+)EnsemblGRCr8
mRatBN7.2226,587,620 - 26,600,177 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl226,587,572 - 26,600,386 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx233,621,670 - 33,632,645 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0231,721,909 - 31,732,879 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0226,543,495 - 26,554,433 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0225,039,506 - 25,052,129 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl225,041,185 - 25,052,127 (+)Ensemblrn6Rnor6.0
Rnor_5.0244,197,989 - 44,210,611 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4225,692,721 - 25,703,663 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera222,655,097 - 22,666,039 (+)NCBICelera
RGSC_v3.1225,613,089 - 25,624,032 (+)NCBI
Cytogenetic Map2q12NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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
Additional References at PubMed
PMID:12477932   PMID:19141611   PMID:24270810  


Genomics

Comparative Map Data
Zbed3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8228,323,968 - 28,334,910 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl228,321,960 - 28,337,413 (+)EnsemblGRCr8
mRatBN7.2226,587,620 - 26,600,177 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl226,587,572 - 26,600,386 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx233,621,670 - 33,632,645 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0231,721,909 - 31,732,879 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0226,543,495 - 26,554,433 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0225,039,506 - 25,052,129 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl225,041,185 - 25,052,127 (+)Ensemblrn6Rnor6.0
Rnor_5.0244,197,989 - 44,210,611 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4225,692,721 - 25,703,663 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera222,655,097 - 22,666,039 (+)NCBICelera
RGSC_v3.1225,613,089 - 25,624,032 (+)NCBI
Cytogenetic Map2q12NCBI
ZBED3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38577,072,072 - 77,087,285 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl577,072,072 - 77,087,353 (-)Ensemblhg38GRCh38
GRCh37576,367,897 - 76,383,110 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36576,408,288 - 76,418,786 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34576,408,287 - 76,418,786NCBI
Celera572,266,829 - 72,277,326 (-)NCBICelera
Cytogenetic Map5q13.3NCBI
HuRef571,579,165 - 71,589,588 (-)NCBIHuRef
CHM1_1575,805,933 - 75,816,430 (-)NCBICHM1_1
T2T-CHM13v2.0577,553,725 - 77,568,916 (-)NCBIT2T-CHM13v2.0
Zbed3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391395,460,113 - 95,474,350 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1395,460,120 - 95,474,349 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381395,323,605 - 95,337,842 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1395,323,612 - 95,337,841 (+)Ensemblmm10GRCm38
MGSCv371396,095,192 - 96,107,796 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361396,425,936 - 96,438,540 (+)NCBIMGSCv36mm8
Celera1398,946,599 - 98,959,202 (+)NCBICelera
Cytogenetic Map13D1NCBI
cM Map1349.38NCBI
ZBED3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2438,210,911 - 38,225,966 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1536,364,538 - 36,379,593 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0538,214,260 - 38,229,373 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1538,740,437 - 38,750,367 (+)NCBIPanPan1.1PanPan1.1panPan2
ZBED3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha330,871,335 - 30,871,910 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0329,550,948 - 29,551,520 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.1329,487,671 - 29,488,243 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0329,468,575 - 29,469,146 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0329,837,639 - 29,838,211 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Zbed3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213185,722,467 - 185,734,770 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365495,127,358 - 5,133,984 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365495,124,079 - 5,136,873 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ZBED3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1285,945,357 - 85,958,452 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2287,565,326 - 87,574,064 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ZBED3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1471,320,447 - 71,331,662 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl471,321,665 - 71,322,360 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604920,155,697 - 20,169,999 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Zbed3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248691,586,477 - 1,602,312 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Zbed3
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v13200,992,324 - 201,003,791 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Zbed3
156 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:634
Count of miRNA genes:252
Interacting mature miRNAs:307
Transcripts:ENSRNOT00000040983
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10755430Coatc6Coat color QTL 60.02576coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)21332504158325041Rat
7387318Stl32Serum triglyceride level QTL 323.20.0003blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)22411781369117813Rat
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)220695736231474293Rat
738010Lnnr3Liver neoplastic nodule remodeling QTL 32.94liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)2142977529Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)227148328206613235Rat
9590080Insglur4Insulin/glucose ratio QTL 428.70.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)2615276751152767Rat
1579916Bp270Blood pressure QTL 2700.003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)21605188361051883Rat
731167Glom4Glomerulus QTL 42.40.0082kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)22203804467038044Rat
731166Mamtr2Mammary tumor resistance QTL 20.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2962358154623581Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)227148328206613235Rat
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)227148328145807373Rat
1331764Bp205Blood pressure QTL 2053.476arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)21436870759368707Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)227148328159440891Rat
1600379Mcs18Mammary carcinoma susceptibility QTL 182.6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2962358144538110Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)24265106205135428Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)227148328159440891Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)227148557159440760Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)227148328159440891Rat
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)27605533104774005Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)227148328159440891Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)227148328159440891Rat
1578664Bmd9Bone mineral QTL density 95femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)2573632550736325Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)227148557159440760Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)227148328159440891Rat
731184Mamtr4Mammary tumor resistance QTL 40.0003mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)21822713763227137Rat

Markers in Region
RH137329  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2226,599,901 - 26,600,081 (+)MAPPERmRatBN7.2
Rnor_6.0225,051,854 - 25,052,033NCBIRnor6.0
Rnor_5.0244,210,336 - 44,210,515UniSTSRnor5.0
RGSC_v3.4225,703,390 - 25,703,569UniSTSRGSC3.4
Celera222,665,766 - 22,665,945UniSTS
RH 3.4 Map213.3UniSTS
Cytogenetic Map2q12UniSTS


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 67 162 91 90 59 92 59 6 356 192 11 141 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000040983   ⟹   ENSRNOP00000044761
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl228,323,729 - 28,334,954 (+)Ensembl
mRatBN7.2 Ensembl226,590,567 - 26,600,246 (+)Ensembl
Rnor_6.0 Ensembl225,041,185 - 25,052,127 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000101430   ⟹   ENSRNOP00000097794
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl228,323,198 - 28,337,413 (+)Ensembl
mRatBN7.2 Ensembl226,588,601 - 26,600,386 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000120277   ⟹   ENSRNOP00000092532
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl228,324,326 - 28,336,250 (+)Ensembl
mRatBN7.2 Ensembl226,587,572 - 26,600,386 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000135063   ⟹   ENSRNOP00000103133
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl228,321,960 - 28,337,413 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000137736   ⟹   ENSRNOP00000099610
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl228,327,509 - 28,337,413 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000146858   ⟹   ENSRNOP00000103737
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl228,324,207 - 28,336,250 (+)Ensembl
RefSeq Acc Id: NM_001025729   ⟹   NP_001020900
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8228,323,968 - 28,334,910 (+)NCBI
mRatBN7.2226,589,233 - 26,600,175 (+)NCBI
Rnor_6.0225,041,185 - 25,052,127 (+)NCBI
Rnor_5.0244,197,989 - 44,210,611 (+)NCBI
RGSC_v3.4225,692,721 - 25,703,663 (+)RGD
Celera222,655,097 - 22,666,039 (+)RGD
Sequence:
RefSeq Acc Id: NP_001020900   ⟸   NM_001025729
- UniProtKB: Q4V7E3 (UniProtKB/TrEMBL),   A6I4Y7 (UniProtKB/TrEMBL),   A6I4Y6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000044761   ⟸   ENSRNOT00000040983
Ensembl Acc Id: ENSRNOP00000097794   ⟸   ENSRNOT00000101430
Ensembl Acc Id: ENSRNOP00000092532   ⟸   ENSRNOT00000120277
Ensembl Acc Id: ENSRNOP00000099610   ⟸   ENSRNOT00000137736
Ensembl Acc Id: ENSRNOP00000103737   ⟸   ENSRNOT00000146858
Ensembl Acc Id: ENSRNOP00000103133   ⟸   ENSRNOT00000135063

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q4V7E3-F1-model_v2 AlphaFold Q4V7E3 1-235 view protein structure

Transcriptome

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

Promoters
RGD ID:13691075
Promoter ID:EPDNEW_R1600
Type:multiple initiation site
Name:Zbed3_1
Description:zinc finger, BED-type containing 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_6.0225,041,173 - 25,041,233EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309665 AgrOrtholog
BioCyc Gene G2FUF-54814 BioCyc
Ensembl Genes ENSRNOG00000028941 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000040983.5 UniProtKB/TrEMBL
  ENSRNOT00000101430 ENTREZGENE
  ENSRNOT00000101430.2 UniProtKB/TrEMBL
  ENSRNOT00000120277.2 UniProtKB/TrEMBL
  ENSRNOT00000135063.1 UniProtKB/TrEMBL
  ENSRNOT00000137736.1 UniProtKB/TrEMBL
  ENSRNOT00000146858.1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7442124 IMAGE-MGC_LOAD
InterPro ZBED2/3 UniProtKB/TrEMBL
  Znf_C2H2_sf UniProtKB/TrEMBL
KEGG Report rno:361881 UniProtKB/TrEMBL
MGC_CLONE MGC:116104 IMAGE-MGC_LOAD
NCBI Gene 361881 ENTREZGENE
PANTHER PTHR35827 UniProtKB/TrEMBL
  PTHR35827:SF2 UniProtKB/TrEMBL
PhenoGen Zbed3 PhenoGen
RatGTEx ENSRNOG00000028941 RatGTEx
SMART ZnF_BED UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/TrEMBL
UniProt A6I4Y6 ENTREZGENE, UniProtKB/TrEMBL
  A6I4Y7 ENTREZGENE
  Q4V7E3 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary A6I4Y7 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-12-15 Zbed3  zinc finger, BED-type containing 3  Zbed3  zinc finger, BED domain containing 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Zbed3  zinc finger, BED domain containing 3  Zbed3_predicted  zinc finger, BED domain containing 3 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Zbed3_predicted  zinc finger, BED domain containing 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED