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) Rattus norvegicus
Analyze
Symbol: Mbd3l1
Name: methyl-CpG binding domain protein 3-like 1
RGD ID: 1308259
Description: Orthologous to human MBD3L1 (methyl-CpG binding domain protein 3 like 1); INTERACTS WITH atrazine; bisphenol A; arsane (ortholog).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC300389; methyl-CpG-binding domain protein 3-like 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
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
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_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0818,437,136 - 18,441,527 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0816,369,198 - 16,373,589 (+)NCBIRnor_WKY
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
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
arsane  (ISO)
arsenic atom  (ISO)
atrazine  (EXP,ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP)
chlorpyrifos  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Mbd3l1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0818,437,136 - 18,441,527 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0816,369,198 - 16,373,589 (+)NCBIRnor_WKY
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
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38198,832,377 - 8,843,319 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 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
(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
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
PanPan1.1199,100,704 - 9,104,367 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl199,103,715 - 9,104,296 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0198,407,146 - 8,411,314 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
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


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8124597739Rat
2317882Alcrsp24Alcohol response QTL 243.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)8125902202Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8209764047097640Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8209764047097640Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8209764047097640Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8209764047097640Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)8470581049705810Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)8470581049705810Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)8470581049705810Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8767057852670578Rat
1354595Despr4Despair related QTL 42.160.0036locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)8768895552688955Rat
1354627Despr14Despair related QTL 140.0056locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8768895552688955Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)8873663553736635Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)8873663553736635Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)8971222053356647Rat
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
1558646Swd5Spike wave discharge measurement QTL 53.450.00036brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)81490675159906751Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:108
Count of miRNA genes:93
Interacting mature miRNAs:103
Transcripts:ENSRNOT00000008341
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.


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 integumental system musculoskeletal system nervous system reproductive system respiratory system appendage
High
Medium 7
Low 1 1 7
Below cutoff 7 12 2 10 2 5 6 3 6 1 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000008341   ⟹   ENSRNOP00000008341
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl816,155,972 - 16,160,363 (+)Ensembl
Rnor_6.0 Ensembl818,430,302 - 18,434,695 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000104968   ⟹   ENSRNOP00000076816
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl816,155,812 - 16,160,404 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000105149   ⟹   ENSRNOP00000083801
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl816,156,617 - 16,160,404 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000113337   ⟹   ENSRNOP00000094324
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl816,153,472 - 16,160,404 (+)Ensembl
RefSeq Acc Id: NM_001106803   ⟹   NP_001100273
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2816,155,972 - 16,160,363 (+)NCBI
Rnor_6.0818,430,302 - 18,434,695 (+)NCBI
Rnor_5.0818,495,511 - 18,501,602 (+)NCBI
RGSC_v3.4816,543,608 - 16,547,999 (+)RGD
Celera817,574,644 - 17,578,982 (+)RGD
Sequence:
RefSeq Acc Id: XM_006242571   ⟹   XP_006242633
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2816,155,961 - 16,160,460 (+)NCBI
Rnor_6.0818,430,302 - 18,434,722 (+)NCBI
Rnor_5.0818,495,511 - 18,501,602 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006242576   ⟹   XP_006242638
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2816,155,962 - 16,160,463 (+)NCBI
Rnor_6.0818,430,308 - 18,434,722 (+)NCBI
Rnor_5.0818,495,511 - 18,501,602 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017595526   ⟹   XP_017451015
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2816,155,916 - 16,160,462 (+)NCBI
Rnor_6.0818,430,201 - 18,434,722 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017595527   ⟹   XP_017451016
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2816,150,539 - 16,160,463 (+)NCBI
Rnor_6.0818,428,438 - 18,434,722 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039080995   ⟹   XP_038936923
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2816,155,881 - 16,160,462 (+)NCBI
RefSeq Acc Id: XM_039080996   ⟹   XP_038936924
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2816,156,343 - 16,160,463 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001100273   ⟸   NM_001106803
- UniProtKB: D3ZQM6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242633   ⟸   XM_006242571
- Peptide Label: isoform X1
- UniProtKB: D3ZQM6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242638   ⟸   XM_006242576
- Peptide Label: isoform X1
- UniProtKB: D3ZQM6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017451016   ⟸   XM_017595527
- Peptide Label: isoform X1
- UniProtKB: D3ZQM6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017451015   ⟸   XM_017595526
- Peptide Label: isoform X1
- UniProtKB: D3ZQM6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000008341   ⟸   ENSRNOT00000008341
RefSeq Acc Id: XP_038936923   ⟸   XM_039080995
- Peptide Label: isoform X1
- UniProtKB: D3ZQM6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038936924   ⟸   XM_039080996
- Peptide Label: isoform X1
- UniProtKB: D3ZQM6 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000076816   ⟸   ENSRNOT00000104968
RefSeq Acc Id: ENSRNOP00000094324   ⟸   ENSRNOT00000113337
RefSeq Acc Id: ENSRNOP00000083801   ⟸   ENSRNOT00000105149
Protein Domains
MBD_C   MBDa

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZQM6-F1-model_v2 AlphaFold D3ZQM6 1-186 view protein structure

Transcriptome

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

Promoters
RGD ID:13695758
Promoter ID:EPDNEW_R6283
Type:initiation region
Name:Mbd3l1_1
Description:methyl-CpG binding domain protein 3-like 1
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_6.0818,430,277 - 18,430,337EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
8 18500926 18500927 C A snv IS-Tlk/Kyo (KyushuU), IS/Kyo (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308259 AgrOrtholog
BioCyc Gene G2FUF-31574 BioCyc
Ensembl Genes ENSRNOG00000006363 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000008341 ENTREZGENE
  ENSRNOP00000008341.2 UniProtKB/TrEMBL
  ENSRNOP00000076816 ENTREZGENE
  ENSRNOP00000076816.1 UniProtKB/TrEMBL
  ENSRNOP00000083801 ENTREZGENE
  ENSRNOP00000083801.1 UniProtKB/TrEMBL
  ENSRNOP00000094324 ENTREZGENE
  ENSRNOP00000094324.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008341 ENTREZGENE
  ENSRNOT00000008341.4 UniProtKB/TrEMBL
  ENSRNOT00000104968 ENTREZGENE
  ENSRNOT00000104968.1 UniProtKB/TrEMBL
  ENSRNOT00000105149 ENTREZGENE
  ENSRNOT00000105149.1 UniProtKB/TrEMBL
  ENSRNOT00000113337 ENTREZGENE
  ENSRNOT00000113337.1 UniProtKB/TrEMBL
InterPro MBD2/MBD3_p55-bd UniProtKB/TrEMBL
  MeCpG_bd_2/3_C_dom UniProtKB/TrEMBL
KEGG Report rno:300389 UniProtKB/TrEMBL
NCBI Gene 300389 ENTREZGENE
Pfam MBD_C UniProtKB/TrEMBL
  MBDa UniProtKB/TrEMBL
PhenoGen Mbd3l1 PhenoGen
UniProt D3ZQM6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Mbd3l1  methyl-CpG binding domain protein 3-like 1   Mbd3l1_predicted  methyl-CpG binding domain protein 3-like 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Mbd3l1_predicted  methyl-CpG binding domain protein 3-like 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED