Dcaf12l2 (DDB1 and CUL4 associated factor 12-like 2) - Rat Genome Database

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Gene: Dcaf12l2 (DDB1 and CUL4 associated factor 12-like 2) Rattus norvegicus
Analyze
Symbol: Dcaf12l2
Name: DDB1 and CUL4 associated factor 12-like 2
RGD ID: 1560768
Description: Predicted to be part of Cul4-RING E3 ubiquitin ligase complex. Orthologous to human DCAF12L2 (DDB1 and CUL4 associated factor 12 like 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; copper atom.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: DDB1- and CUL4-associated factor 12-like protein 2; LOC298159; RGD1560768; similar to RIKEN cDNA A130007F10 gene; WD repeat domain 40C; Wdr40c
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X128,167,040 - 128,169,829 (-)NCBIGRCr8
mRatBN7.2X123,293,761 - 123,296,550 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX123,294,744 - 123,296,156 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0X130,823,651 - 130,825,369 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX130,823,866 - 130,825,305 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X130,906,292 - 130,907,919 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X598,952 - 602,981 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX122,356,923 - 122,358,641 (-)NCBICelera
Cytogenetic MapXq35NCBI
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

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Dcaf12l2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X128,167,040 - 128,169,829 (-)NCBIGRCr8
mRatBN7.2X123,293,761 - 123,296,550 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX123,294,744 - 123,296,156 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0X130,823,651 - 130,825,369 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX130,823,866 - 130,825,305 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X130,906,292 - 130,907,919 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X598,952 - 602,981 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX122,356,923 - 122,358,641 (-)NCBICelera
Cytogenetic MapXq35NCBI
DCAF12L2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X126,163,499 - 126,166,289 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX126,163,499 - 126,166,289 (-)EnsemblGRCh38hg38GRCh38
GRCh37X125,297,482 - 125,300,272 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X125,126,195 - 125,127,615 (-)NCBINCBI36Build 36hg18NCBI36
CeleraX125,683,150 - 125,685,748 (-)NCBICelera
Cytogenetic MapXq25NCBI
HuRefX114,677,469 - 114,680,067 (-)NCBIHuRef
CHM1_1X125,208,368 - 125,210,966 (-)NCBICHM1_1
T2T-CHM13v2.0X124,476,206 - 124,478,996 (-)NCBIT2T-CHM13v2.0
Dcaf12l2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X43,454,334 - 43,457,214 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX43,454,335 - 43,457,219 (-)EnsemblGRCm39 Ensembl
GRCm38X44,365,457 - 44,368,337 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX44,365,458 - 44,368,342 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X41,718,634 - 41,721,514 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X40,610,085 - 40,612,969 (-)NCBIMGSCv36mm8
CeleraX31,900,316 - 31,903,196 (-)NCBICelera
Cytogenetic MapXA4NCBI
cM MapX23.85NCBI
Dcaf12l2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554738,744,885 - 8,746,279 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554738,744,863 - 8,746,589 (+)NCBIChiLan1.0ChiLan1.0
DCAF12L2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X125,637,005 - 125,639,898 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X125,640,617 - 125,643,504 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X115,346,153 - 115,349,054 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X125,525,080 - 125,527,429 (-)NCBIpanpan1.1PanPan1.1panPan2
LOC609540
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_TashaX83,835,516 - 83,837,103 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X99,542,727 - 99,544,556 (-)NCBIROS_Cfam_1.0
UNSW_CanFamBas_1.0X98,794,007 - 98,795,577 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X98,521,261 - 98,522,828 (-)NCBIUU_Cfam_GSD_1.0
LOC100521308
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX103,325,989 - 103,327,383 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X103,322,468 - 103,327,458 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X118,320,653 - 118,323,147 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103247388
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Vero_WHO_p1.0NW_02366606538,870,103 - 38,872,678 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Dcaf12l2
3 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:24
Count of miRNA genes:23
Interacting mature miRNAs:24
Transcripts:ENSRNOT00000047171
Prediction methods:Miranda, Pita, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
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
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


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

circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system nervous system renal system reproductive system respiratory system
High
Medium
Low 4 50 2 14
Below cutoff 18 11 8 1 8 24 14 14 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000047171   ⟹   ENSRNOP00000046551
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX123,294,744 - 123,296,156 (-)Ensembl
Rnor_6.0 EnsemblX130,823,866 - 130,825,305 (-)Ensembl
RefSeq Acc Id: NM_001408841   ⟹   NP_001395770
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X128,167,040 - 128,169,829 (-)NCBI
mRatBN7.2X123,293,761 - 123,296,550 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001395770 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM10894 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000046551
  ENSRNOP00000046551.4
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000046551   ⟸   ENSRNOT00000047171
RefSeq Acc Id: NP_001395770   ⟸   NM_001408841
- UniProtKB: D3ZKN9 (UniProtKB/TrEMBL),   A6JMN2 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZKN9-F1-model_v2 AlphaFold D3ZKN9 1-480 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:1560768 AgrOrtholog
BioCyc Gene G2FUF-1213 BioCyc
Ensembl Genes ENSRNOG00000031533 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000047171 ENTREZGENE
  ENSRNOT00000047171.4 UniProtKB/TrEMBL
Gene3D-CATH 2.130.10.10 UniProtKB/TrEMBL
InterPro WD40/YVTN_repeat-like_dom UniProtKB/TrEMBL
  WD40_repeat UniProtKB/TrEMBL
  WD40_repeat_dom_sf UniProtKB/TrEMBL
KEGG Report rno:298159 UniProtKB/TrEMBL
NCBI Gene 298159 ENTREZGENE
PANTHER DDB1- AND CUL4-ASSOCIATED FACTOR 12-LIKE PROTEIN 2 UniProtKB/TrEMBL
  DDB1- AND CUL4-ASSOCIATED FACTOR 12-RELATED UniProtKB/TrEMBL
Pfam WD40 UniProtKB/TrEMBL
PhenoGen Dcaf12l2 PhenoGen
PROSITE WD_REPEATS_2 UniProtKB/TrEMBL
  WD_REPEATS_REGION UniProtKB/TrEMBL
RatGTEx ENSRNOG00000031533 RatGTEx
SMART WD40 UniProtKB/TrEMBL
Superfamily-SCOP WD40_like UniProtKB/TrEMBL
UniProt A6JMN2 ENTREZGENE, UniProtKB/TrEMBL
  D3ZKN9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-05-05 Dcaf12l2  DDB1 and CUL4 associated factor 12-like 2  Wdr40c  WD repeat domain 40C  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-28 Wdr40c  WD repeat domain 40C  RGD1560768_predicted  similar to RIKEN cDNA A130007F10 gene (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1560768_predicted  similar to RIKEN cDNA A130007F10 gene (predicted)  LOC298159  similar to RIKEN cDNA A130007F10 gene  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC298159  similar to RIKEN cDNA A130007F10 gene      Symbol and Name status set to provisional 70820 PROVISIONAL