ZBED3 (zinc finger BED-type containing 3) - Rat Genome Database

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Pathways
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Gene: ZBED3 (zinc finger BED-type containing 3) Chlorocebus sabaeus
Analyze
Symbol: ZBED3
Name: zinc finger BED-type containing 3
RGD ID: 18450215
Description: ENCODES a protein that exhibits DNA binding (inferred); metal ion binding (inferred); INVOLVED IN negative regulation of protein phosphorylation (ortholog); positive regulation of canonical Wnt signaling pathway (ortholog); protein stabilization (ortholog); ASSOCIATED WITH genetic disease (ortholog); Hermansky-Pudlak syndrome 2 (ortholog); Neurodevelopmental Disorders (ortholog); FOUND IN cytoplasm (inferred); cytosol (inferred); extracellular space (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: zinc finger BED domain-containing protein 3
RGD Orthologs
Human
Mouse
Rat
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: ChlSab1.1 - Green Monkey 1.1 Assembly
Position:
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 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604920,155,697 - 20,169,999 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:30032202  


Genomics

Comparative Map Data
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 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604920,155,697 - 20,169,999 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
ZBED3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38577,072,072 - 77,087,285 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl577,072,072 - 77,087,285 (-)EnsemblGRCh38hg38GRCh38
GRCh37576,367,897 - 76,383,110 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36576,408,288 - 76,418,786 (-)NCBINCBI36Build 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 Ensembl
GRCm381395,323,605 - 95,337,842 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1395,323,612 - 95,337,841 (+)EnsemblGRCm38mm10GRCm38
MGSCv371396,095,192 - 96,107,796 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361396,425,936 - 96,438,540 (+)NCBIMGSCv36mm8
Celera1398,946,599 - 98,959,202 (+)NCBICelera
Cytogenetic Map13D1NCBI
cM Map1349.38NCBI
Zbed3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8228,323,968 - 28,334,910 (+)NCBIGRCr8
mRatBN7.2226,587,620 - 26,600,177 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl226,587,572 - 26,600,386 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx233,621,670 - 33,632,645 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0231,721,909 - 31,732,879 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0226,543,495 - 26,554,433 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0225,039,506 - 25,052,129 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl225,041,185 - 25,052,127 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0244,197,989 - 44,210,611 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4225,692,721 - 25,703,663 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1225,613,089 - 25,624,032 (+)NCBI
Celera222,655,097 - 22,666,039 (+)NCBICelera
Cytogenetic Map2q12NCBI
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_Tasha
ROS_Cfam_1.0329,550,948 - 29,551,520 (+)NCBIROS_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_1.0
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 (-)EnsemblSpeTri2.0SpeTri2.0 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
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248691,586,477 - 1,602,312 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


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

endocrine system hemolymphoid system nervous system
High
Medium 3 2
Low 33 12 58
Below cutoff 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSCSAT00000019507   ⟹   ENSCSAP00000018925
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1 Ensembl471,321,665 - 71,322,360 (-)Ensembl
RefSeq Acc Id: XM_007976013   ⟹   XP_007974204
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1471,320,447 - 71,331,662 (-)NCBI
Vero_WHO_p1.0NW_02366604920,156,645 - 20,169,999 (-)NCBI
Sequence:
RefSeq Acc Id: XM_037982124   ⟹   XP_037838052
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366604920,155,697 - 20,164,133 (-)NCBI
RefSeq Acc Id: XM_037982125   ⟹   XP_037838053
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366604920,156,645 - 20,169,563 (-)NCBI
Protein Sequences
Protein RefSeqs XP_007974204 (Get FASTA)   NCBI Sequence Viewer  
  XP_037838052 (Get FASTA)   NCBI Sequence Viewer  
  XP_037838053 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCSAP00000018925.1
Reference Protein Sequences
RefSeq Acc Id: XP_007974204   ⟸   XM_007976013
- UniProtKB: A0A0D9SDI6 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCSAP00000018925   ⟸   ENSCSAT00000019507
RefSeq Acc Id: XP_037838052   ⟸   XM_037982124
- UniProtKB: A0A0D9SDI6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_037838053   ⟸   XM_037982125
- UniProtKB: A0A0D9SDI6 (UniProtKB/TrEMBL)


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCSAG00000019417 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCSAT00000019507.1 UniProtKB/TrEMBL
InterPro ZBED2/3 UniProtKB/TrEMBL
  Znf_BED UniProtKB/TrEMBL
  Znf_C2H2_sf UniProtKB/TrEMBL
KEGG Report csab:103223439 UniProtKB/TrEMBL
NCBI Gene ZBED3 ENTREZGENE
PANTHER PTHR35827 UniProtKB/TrEMBL
  PTHR35827:SF2 UniProtKB/TrEMBL
Pfam zf-BED UniProtKB/TrEMBL
PROSITE ZF_BED UniProtKB/TrEMBL
SMART ZnF_BED UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/TrEMBL
UniProt A0A0D9SDI6 ENTREZGENE, UniProtKB/TrEMBL