Mbd3l1 (methyl-CpG binding domain protein 3-like 1) - Rat Genome Database

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Gene: Mbd3l1 (methyl-CpG binding domain protein 3-like 1) Mus musculus
Analyze
Symbol: Mbd3l1
Name: methyl-CpG binding domain protein 3-like 1
RGD ID: 1317931
MGI Page MGI
Description: Predicted to enable methyl-CpG binding activity. Predicted to be involved in DNA methylation-dependent heterochromatin formation and negative regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. Orthologous to human MBD3L1 (methyl-CpG binding domain protein 3 like 1).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 1700070G05Rik; 1700095H13Rik; Mbd3; MBD3-like protein 1; Mbd3l; methyl-CpG-binding domain protein 3-like 1
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39918,389,655 - 18,396,594 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl918,389,655 - 18,396,594 (+)EnsemblGRCm39 Ensembl
GRCm38918,478,359 - 18,485,298 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl918,478,359 - 18,485,298 (+)EnsemblGRCm38mm10GRCm38
MGSCv37918,282,839 - 18,289,736 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36918,228,797 - 18,235,694 (+)NCBIMGSCv36mm8
Celera915,761,938 - 15,768,835 (+)NCBICelera
Cytogenetic Map9A2NCBI
cM Map97.06NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleus  (IBA,ISO)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. MGDs mouse GO annotations MGD data from the GO Consortium
2. MGD IEA MGD IEA
3. Mouse MP Annotation Import Pipeline RGD automated import pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:12504854   PMID:15456747   PMID:15489334   PMID:16141072   PMID:16141073   PMID:18942147  
PMID:20059953   PMID:21873635  


Genomics

Comparative Map Data
Mbd3l1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39918,389,655 - 18,396,594 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl918,389,655 - 18,396,594 (+)EnsemblGRCm39 Ensembl
GRCm38918,478,359 - 18,485,298 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl918,478,359 - 18,485,298 (+)EnsemblGRCm38mm10GRCm38
MGSCv37918,282,839 - 18,289,736 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36918,228,797 - 18,235,694 (+)NCBIMGSCv36mm8
Celera915,761,938 - 15,768,835 (+)NCBICelera
Cytogenetic Map9A2NCBI
cM Map97.06NCBI
MBD3L1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38198,832,377 - 8,843,319 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl198,832,377 - 8,843,340 (+)EnsemblGRCh38hg38GRCh38
GRCh37198,943,053 - 8,953,995 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36198,814,332 - 8,814,995 (+)NCBINCBI36Build 36hg18NCBI36
Build 34198,814,331 - 8,814,995NCBI
Celera198,836,084 - 8,836,831 (+)NCBICelera
Cytogenetic Map19p13.2NCBI
HuRef198,530,702 - 8,531,449 (+)NCBIHuRef
CHM1_1198,952,763 - 8,953,510 (+)NCBICHM1_1
T2T-CHM13v2.0198,943,334 - 8,954,286 (+)NCBIT2T-CHM13v2.0
Mbd3l1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8824,426,865 - 24,436,687 (+)NCBIGRCr8
mRatBN7.2816,150,539 - 16,160,463 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl816,153,472 - 16,160,404 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx820,139,329 - 20,143,720 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0818,437,136 - 18,441,527 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0816,369,198 - 16,373,589 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0818,428,438 - 18,434,722 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl818,430,302 - 18,434,695 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0818,495,511 - 18,501,602 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4816,543,608 - 16,547,999 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1816,547,290 - 16,547,851 (+)NCBI
Celera817,574,644 - 17,578,982 (+)NCBICelera
Cytogenetic Map8q13NCBI
Mbd3l1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_004955563584,541 - 588,597 (-)NCBIChiLan1.0ChiLan1.0
MBD3L1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22013,787,111 - 13,794,163 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11912,771,949 - 12,777,650 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0198,407,146 - 8,411,314 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1199,100,704 - 9,104,367 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl199,103,715 - 9,104,296 (+)Ensemblpanpan1.1panPan2
MBD3L1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12051,876,729 - 51,880,970 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2051,876,827 - 51,877,408 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2051,746,015 - 51,750,468 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02052,405,413 - 52,410,703 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2052,406,558 - 52,407,139 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12051,609,971 - 51,615,260 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02052,054,283 - 52,058,735 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02052,283,680 - 52,288,708 (-)NCBIUU_Cfam_GSD_1.0
Mbd3l1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118212,330,307 - 212,332,717 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049365885,503,722 - 5,504,297 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MBD3L1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.168,100,552 - 8,104,201 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl68,103,561 - 8,104,142 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607412,084,227 - 12,094,726 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Mbd3l1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248281,496,714 - 1,505,864 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Mbd3l1
187 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:90
Count of miRNA genes:88
Interacting mature miRNAs:90
Transcripts:ENSMUST00000069218
Prediction methods: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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4142326Tgq19_mtriglyceride QTL 19 (mouse)Not determined121060750Mouse
1300899Chol6_mcholesterol 6 (mouse)Not determined9129902913Mouse
13434920Dcollq1_mdifferential colonization level QTL 1 (mouse)9130341840Mouse
35673312Ari7_mantibody response to influenza 7, day 45, IgG3 (mouse)9780000122211296Mouse
1300849Sles4_msystemic lupus erythmatosus suppressor 4 (mouse)Not determined9910756237306370Mouse
13504833Bglu19_mblood glucose level 19 (mouse)9991076843910768Mouse
1300532Tbs2_mtuberculosis severity 2 (mouse)Not determined91236997046370114Mouse
10043917Obq37_mobesity QTL 37 (mouse)Not determined91339117547391175Mouse
1357637Si5lq2_mserum IGFBP-5 level QTL 2 (mouse)Not determined91541175149411890Mouse
4141591Cq4_mcholesterol QTL 4 (mouse)Not determined91541175149411890Mouse
1301421Lgth4_mbody length 4 (mouse)Not determined91541175149411890Mouse
4141447Cfmq2_mcystic fibrosis modifier QTL 2 (mouse)Not determined91541175149411890Mouse
12790993Adq1_maortic diameter QTL 1 (mouse)91574962749749627Mouse
11354951Pdcc3_mplasmacytoid dentritic cell compartment 3 (mouse)91574962749749627Mouse
12790997Adq2_maortic diameter QTL 2 (mouse)91574962749749627Mouse
12880415V125Dq7_mvitamin D active form serum level QTL 7 (mouse)91601129650011296Mouse
12880416V125Dq8_mvitamin D active form serum level QTL 8 (mouse)91601129650011296Mouse
13504834Hdlq109_mHDL QTL 109 (mouse)91670964150709641Mouse
1357465Vtbt6_mvertebral trabecular bone trait 6 (mouse)Not determined91697884050978943Mouse

Markers in Region
D9Mit187  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38918,478,102 - 18,478,232UniSTSGRCm38
MGSCv37918,282,546 - 18,282,676UniSTSGRCm37
Celera915,761,647 - 15,761,775UniSTS
Cytogenetic Map9A3UniSTS
cM Map96.0UniSTS
Whitehead Genetic94.4UniSTS
D9Mit187.1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38918,478,307 - 18,478,436UniSTSGRCm38
MGSCv37918,282,751 - 18,282,880UniSTSGRCm37
Celera915,761,850 - 15,761,979UniSTS
Cytogenetic Map9A3UniSTS
cM Map96.0UniSTS
cM Map9 UniSTS
Whitehead Genetic94.4UniSTS


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000069218   ⟹   ENSMUSP00000063957
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl918,389,675 - 18,396,594 (+)Ensembl
GRCm38.p6 Ensembl918,478,379 - 18,485,298 (+)Ensembl
RefSeq Acc Id: ENSMUST00000213625   ⟹   ENSMUSP00000149619
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl918,389,655 - 18,396,588 (+)Ensembl
GRCm38.p6 Ensembl918,478,359 - 18,485,292 (+)Ensembl
RefSeq Acc Id: ENSMUST00000215255   ⟹   ENSMUSP00000149425
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl918,389,699 - 18,396,535 (+)Ensembl
GRCm38.p6 Ensembl918,478,403 - 18,485,239 (+)Ensembl
RefSeq Acc Id: NM_001357418   ⟹   NP_001344347
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39918,389,655 - 18,396,594 (+)NCBI
GRCm38918,478,359 - 18,485,298 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001357419   ⟹   NP_001344348
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39918,389,655 - 18,396,594 (+)NCBI
GRCm38918,478,359 - 18,485,298 (+)NCBI
Sequence:
RefSeq Acc Id: NM_028557   ⟹   NP_082833
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39918,389,655 - 18,396,594 (+)NCBI
GRCm38918,478,359 - 18,485,298 (+)NCBI
MGSCv37918,282,839 - 18,289,736 (+)RGD
Celera915,761,938 - 15,768,835 (+)RGD
cM Map9 ENTREZGENE
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_082833   ⟸   NM_028557
- UniProtKB: Q6P8W5 (UniProtKB/Swiss-Prot),   Q9D2S3 (UniProtKB/Swiss-Prot),   Q9D9H3 (UniProtKB/Swiss-Prot),   Q0P5Y0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001344348   ⟸   NM_001357419
- UniProtKB: Q9D9H3 (UniProtKB/Swiss-Prot),   Q6P8W5 (UniProtKB/Swiss-Prot),   Q9D2S3 (UniProtKB/Swiss-Prot),   Q0P5Y0 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001344347   ⟸   NM_001357418
- UniProtKB: Q9D9H3 (UniProtKB/Swiss-Prot),   Q6P8W5 (UniProtKB/Swiss-Prot),   Q9D2S3 (UniProtKB/Swiss-Prot),   Q0P5Y0 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSMUSP00000149619   ⟸   ENSMUST00000213625
RefSeq Acc Id: ENSMUSP00000063957   ⟸   ENSMUST00000069218
RefSeq Acc Id: ENSMUSP00000149425   ⟸   ENSMUST00000215255
Protein Domains
Methyl-CpG binding protein 2/3 C-terminal   Methyl-CpG-binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9D9H3-F1-model_v2 AlphaFold Q9D9H3 1-186 view protein structure

Promoters
RGD ID:8668864
Promoter ID:EPDNEW_M12463
Type:initiation region
Name:Mbd3l1_1
Description:Mus musculus methyl-CpG binding domain protein 3-like 1 , transcriptvariant 1, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38918,478,372 - 18,478,432EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1920753 AgrOrtholog
Ensembl Genes ENSMUSG00000038691 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000069218 ENTREZGENE
  ENSMUST00000069218.5 UniProtKB/Swiss-Prot
  ENSMUST00000213625 ENTREZGENE
  ENSMUST00000213625.2 UniProtKB/Swiss-Prot
  ENSMUST00000215255 ENTREZGENE
  ENSMUST00000215255.2 UniProtKB/Swiss-Prot
InterPro MBD2/MBD3_p55-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MeCpG-bd_2/3_C_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:73503 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:1920753 ENTREZGENE
NCBI Gene 73503 ENTREZGENE
Pfam MBD_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MBDa UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Mbd3l1 PhenoGen
UniProt MB3L1_MOUSE UniProtKB/Swiss-Prot
  Q0P5Y0 ENTREZGENE, UniProtKB/TrEMBL
  Q6P8W5 ENTREZGENE
  Q9D2S3 ENTREZGENE
  Q9D9H3 ENTREZGENE
UniProt Secondary Q6P8W5 UniProtKB/Swiss-Prot
  Q9D2S3 UniProtKB/Swiss-Prot