Cul4b (cullin 4B) - Rat Genome Database

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Gene: Cul4b (cullin 4B) Rattus norvegicus
Analyze
Symbol: Cul4b
Name: cullin 4B
RGD ID: 1564494
Description: Predicted to enable ubiquitin protein ligase binding activity. Predicted to contribute to damaged DNA binding activity. Involved in neuron projection development. Predicted to be located in cytosol and nucleoplasm. Predicted to be part of Cul4A-RING E3 ubiquitin ligase complex and Cul4B-RING E3 ubiquitin ligase complex. Human ortholog(s) of this gene implicated in syndromic X-linked intellectual disability Cabezas type. Orthologous to human CUL4B (cullin 4B); PARTICIPATES IN nucleotide excision repair pathway; ubiquitin/proteasome degradation pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; 2-methoxyethanol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: cullin-4B; LOC302502; RGD1564494; similar to cullin 4B
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X122,154,332 - 122,192,299 (-)NCBIGRCr8
mRatBN7.2X117,287,481 - 117,326,688 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX117,287,484 - 117,326,688 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX119,387,179 - 119,425,184 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X122,956,187 - 122,994,194 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X120,501,572 - 120,539,675 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X124,831,391 - 124,870,329 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX124,832,628 - 124,870,329 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X124,915,933 - 124,954,871 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X6,800,506 - 6,838,023 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX116,505,114 - 116,543,077 (-)NCBICelera
Cytogenetic MapXq35NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. X-linked mental retardation gene CUL4B targets ubiquitylation of H3K4 methyltransferase component WDR5 and regulates neuronal gene expression. Nakagawa T and Xiong Y, Mol Cell. 2011 Aug 5;43(3):381-91. doi: 10.1016/j.molcel.2011.05.033.
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:16949367   PMID:18602923   PMID:18794347   PMID:19056867   PMID:19056892   PMID:21628527   PMID:22334663   PMID:25970626   PMID:26021757   PMID:26711351   PMID:28437394   PMID:29626254  
PMID:34779995   PMID:38254314  


Genomics

Comparative Map Data
Cul4b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X122,154,332 - 122,192,299 (-)NCBIGRCr8
mRatBN7.2X117,287,481 - 117,326,688 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX117,287,484 - 117,326,688 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX119,387,179 - 119,425,184 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X122,956,187 - 122,994,194 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X120,501,572 - 120,539,675 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X124,831,391 - 124,870,329 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX124,832,628 - 124,870,329 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X124,915,933 - 124,954,871 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X6,800,506 - 6,838,023 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX116,505,114 - 116,543,077 (-)NCBICelera
Cytogenetic MapXq35NCBI
CUL4B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X120,523,858 - 120,575,532 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX120,505,920 - 120,604,074 (-)EnsemblGRCh38hg38GRCh38
GRCh37X119,657,713 - 119,709,387 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X119,542,472 - 119,593,712 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X119,442,379 - 119,491,531NCBI
CeleraX120,122,944 - 120,174,184 (-)NCBICelera
Cytogenetic MapXq24NCBI
HuRefX109,109,003 - 109,160,669 (-)NCBIHuRef
CHM1_1X119,570,086 - 119,621,321 (-)NCBICHM1_1
T2T-CHM13v2.0X118,899,322 - 118,951,000 (-)NCBIT2T-CHM13v2.0
Cul4b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X37,620,493 - 37,665,073 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX37,622,151 - 37,665,073 (-)EnsemblGRCm39 Ensembl
GRCm38X38,531,616 - 38,576,196 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX38,533,274 - 38,576,196 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X35,884,793 - 35,929,373 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X34,777,901 - 34,820,823 (-)NCBIMGSCv36mm8
CeleraX26,177,720 - 26,222,300 (-)NCBICelera
Cytogenetic MapXA3.3NCBI
cM MapX22.81NCBI
Cul4b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555721,308,491 - 1,365,147 (+)NCBIChiLan1.0ChiLan1.0
CUL4B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X120,074,814 - 120,110,349 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X120,078,753 - 120,113,952 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X109,798,279 - 109,870,469 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X119,985,109 - 120,034,715 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX119,985,116 - 120,034,702 (-)Ensemblpanpan1.1panPan2
CUL4B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X92,489,981 - 92,538,199 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX92,491,114 - 92,537,672 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX78,521,518 - 78,569,760 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X94,236,531 - 94,284,539 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX94,236,532 - 94,283,990 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X91,685,541 - 91,733,782 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X93,448,317 - 93,496,329 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X93,223,172 - 93,271,175 (-)NCBIUU_Cfam_GSD_1.0
Cul4b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X91,451,497 - 91,509,969 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364799,479,133 - 9,534,262 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364799,490,717 - 9,535,998 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CUL4B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX98,668,953 - 98,730,565 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X98,668,945 - 98,730,582 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X112,668,459 - 112,716,028 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CUL4B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Vero_WHO_p1.0NW_02366606533,233,605 - 33,271,128 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cul4b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624931431,835 - 568,609 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cul4b
120 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:525
Count of miRNA genes:265
Interacting mature miRNAs:332
Transcripts:ENSRNOT00000065023
Prediction methods:Microtar, Miranda, Pita
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat
724551Glom1Glomerulus QTL 12.80.0004kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)X75294106120294106Rat
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X93956491138956491Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX100567703150256146Rat
1598809Memor15Memory QTL 154.4exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X103312877148312877Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X103312877148312877Rat
738029Stresp2Stress response QTL 23.40.0004stress-related behavior trait (VT:0010451)defensive burying - approachX112934952138400867Rat
5685004Bss104Bone structure and strength QTL 1043.9tibia area (VT:1000281)tibia area measurement (CMO:0001382)X113805422126975220Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X113937816152453651Rat

Markers in Region
RH141795  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X117,289,193 - 117,289,388 (+)MAPPERmRatBN7.2
Rnor_6.0X124,833,104 - 124,833,298NCBIRnor6.0
Rnor_5.0X124,917,646 - 124,917,840UniSTSRnor5.0
RGSC_v3.4X6,837,353 - 6,837,547UniSTSRGSC3.4
CeleraX116,505,590 - 116,505,784UniSTS
RH 3.4 Map11397.2UniSTS
Cytogenetic MapXq11UniSTS
G16011  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X117,316,169 - 117,316,318 (+)MAPPERmRatBN7.2
Rnor_6.0X124,860,079 - 124,860,227NCBIRnor6.0
Rnor_5.0X124,944,621 - 124,944,769UniSTSRnor5.0
RGSC_v3.4X6,810,423 - 6,810,571UniSTSRGSC3.4
CeleraX116,532,569 - 116,532,717UniSTS
Cytogenetic MapXq11UniSTS


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 3 29 54 38 19 38 2 2 74 35 41 11 2
Low 14 3 3 3 6 9 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000065023   ⟹   ENSRNOP00000060639
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX117,288,718 - 117,326,688 (-)Ensembl
Rnor_6.0 EnsemblX124,832,628 - 124,870,329 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000099962   ⟹   ENSRNOP00000097090
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX117,287,484 - 117,316,759 (-)Ensembl
RefSeq Acc Id: NM_001106951   ⟹   NP_001100421
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X122,154,332 - 122,192,299 (-)NCBI
mRatBN7.2X117,288,718 - 117,326,688 (-)NCBI
Rnor_6.0X124,832,628 - 124,870,329 (-)NCBI
Rnor_5.0X124,915,933 - 124,954,871 (-)NCBI
RGSC_v3.4X6,800,506 - 6,838,023 (+)RGD
CeleraX116,505,114 - 116,543,077 (-)RGD
Sequence:
RefSeq Acc Id: XM_006257489   ⟹   XP_006257551
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X122,154,734 - 122,186,845 (-)NCBI
mRatBN7.2X117,287,481 - 117,317,194 (-)NCBI
Rnor_6.0X124,831,391 - 124,860,965 (-)NCBI
Rnor_5.0X124,915,933 - 124,954,871 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099624   ⟹   XP_038955552
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X122,154,734 - 122,182,374 (-)NCBI
mRatBN7.2X117,287,481 - 117,316,758 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001100421 (Get FASTA)   NCBI Sequence Viewer  
  XP_006257551 (Get FASTA)   NCBI Sequence Viewer  
  XP_038955552 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM10867 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000060639
  ENSRNOP00000060639.1
  ENSRNOP00000097090
  ENSRNOP00000097090.1
Reference Protein Sequences
RefSeq Acc Id: NP_001100421   ⟸   NM_001106951
- UniProtKB: D3ZK73 (UniProtKB/TrEMBL),   A6JMK5 (UniProtKB/TrEMBL),   A0A8I6B5A8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257551   ⟸   XM_006257489
- Peptide Label: isoform X1
- UniProtKB: A0A8I6B5A8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000060639   ⟸   ENSRNOT00000065023
RefSeq Acc Id: XP_038955552   ⟸   XM_039099624
- Peptide Label: isoform X2
- UniProtKB: A0A8I6B5A8 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000097090   ⟸   ENSRNOT00000099962
Protein Domains
Cullin family profile

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZK73-F1-model_v2 AlphaFold D3ZK73 1-971 view protein structure

Transcriptome

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

Promoters
RGD ID:13701998
Promoter ID:EPDNEW_R12522
Type:single initiation site
Name:Cul4b_1
Description:cullin 4B
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_6.0X124,870,345 - 124,870,405EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564494 AgrOrtholog
BioCyc Gene G2FUF-1257 BioCyc
Ensembl Genes ENSRNOG00000002585 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000065023 ENTREZGENE
  ENSRNOT00000065023.3 UniProtKB/TrEMBL
  ENSRNOT00000099962.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
  Cullin Repeats UniProtKB/TrEMBL
InterPro Cullin UniProtKB/TrEMBL
  Cullin_CS UniProtKB/TrEMBL
  Cullin_homology UniProtKB/TrEMBL
  Cullin_homology_sf UniProtKB/TrEMBL
  Cullin_N UniProtKB/TrEMBL
  Cullin_neddylation_domain UniProtKB/TrEMBL
  Cullin_repeat-like_dom UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/TrEMBL
KEGG Report rno:302502 UniProtKB/TrEMBL
NCBI Gene 302502 ENTREZGENE
PANTHER PTHR11932 UniProtKB/TrEMBL
  PTHR11932:SF66 UniProtKB/TrEMBL
Pfam Cullin UniProtKB/TrEMBL
  Cullin_Nedd8 UniProtKB/TrEMBL
PharmGKB CUL4B RGD
PhenoGen Cul4b PhenoGen
PROSITE CULLIN_1 UniProtKB/TrEMBL
  CULLIN_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000002585 RatGTEx
SMART CULLIN UniProtKB/TrEMBL
  Cullin_Nedd8 UniProtKB/TrEMBL
Superfamily-SCOP Cullin_homology UniProtKB/TrEMBL
  Cullin_repeat-like UniProtKB/TrEMBL
  SSF46785 UniProtKB/TrEMBL
UniProt A0A8I6B5A8 ENTREZGENE, UniProtKB/TrEMBL
  A6JMK5 ENTREZGENE, UniProtKB/TrEMBL
  D3ZK73 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Cul4b  cullin 4B   Cul4b_predicted  cullin 4B (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Cul4b_predicted  cullin 4B (predicted)  RGD1564494_predicted  similar to cullin 4B (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1564494_predicted  similar to cullin 4B (predicted)  LOC302502  similar to cullin 4B  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC302502  similar to cullin 4B      Symbol and Name status set to provisional 70820 PROVISIONAL