Bcl11b (BAF chromatin remodeling complex subunit BCL11B) - Rat Genome Database

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Gene: Bcl11b (BAF chromatin remodeling complex subunit BCL11B) Rattus norvegicus
Analyze
Symbol: Bcl11b
Name: BAF chromatin remodeling complex subunit BCL11B
RGD ID: 1311128
Description: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in hematopoietic stem cell migration; lymphoid lineage cell migration into thymus; and positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including animal organ development; cell morphogenesis involved in differentiation; and regulation of keratinocyte proliferation. Predicted to be located in neuron projection. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in immunodeficiency 49. Orthologous to human BCL11B (BAF chromatin remodeling complex subunit BCL11B); INTERACTS WITH 1,2-dimethylhydrazine; 17alpha-ethynylestradiol; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: B-cell CLL/lymphoma 11B; B-cell CLL/lymphoma 11B (zinc finger protein); B-cell leukemia/lymphoma 11B; B-cell lymphoma/leukemia 11B; BCL11B, BAF complex component; COUP-TF-interacting protein 2 long form; Ctip2; LOC314423
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.26126,834,531 - 126,927,720 (-)NCBI
Rnor_6.0 Ensembl6131,834,097 - 131,926,272 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.06131,834,097 - 131,927,251 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06141,004,477 - 141,097,643 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46132,292,671 - 132,384,572 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16132,296,789 - 132,389,378 (-)NCBI
Celera6124,393,881 - 124,486,186 (-)NCBICelera
Cytogenetic Map6q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
neuron projection  (ISO)
nucleus  (IBA,ISO)

References

Additional References at PubMed
PMID:12477932   PMID:12565905   PMID:12717433   PMID:15664173   PMID:16670294   PMID:16809611   PMID:17998389   PMID:18199763   PMID:18215621   PMID:18255031   PMID:18595722   PMID:19092943  
PMID:19251658   PMID:21752992   PMID:22082260   PMID:23144223   PMID:24705758   PMID:25100583   PMID:26096706   PMID:27577752   PMID:27959403   PMID:27959755  


Genomics

Comparative Map Data
Bcl11b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.26126,834,531 - 126,927,720 (-)NCBI
Rnor_6.0 Ensembl6131,834,097 - 131,926,272 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.06131,834,097 - 131,927,251 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06141,004,477 - 141,097,643 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46132,292,671 - 132,384,572 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16132,296,789 - 132,389,378 (-)NCBI
Celera6124,393,881 - 124,486,186 (-)NCBICelera
Cytogenetic Map6q32NCBI
BCL11B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1499,169,287 - 99,272,197 (-)EnsemblGRCh38hg38GRCh38
GRCh381499,169,287 - 99,272,197 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371499,635,624 - 99,738,534 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361498,705,377 - 98,807,575 (-)NCBINCBI36hg18NCBI36
Build 341498,705,376 - 98,807,575NCBI
Celera1479,691,368 - 79,793,512 (-)NCBI
Cytogenetic Map14q32.2NCBI
HuRef1479,819,226 - 79,921,464 (-)NCBIHuRef
CHM1_11499,573,389 - 99,675,578 (-)NCBICHM1_1
Bcl11b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3912107,876,662 - 107,970,404 (-)NCBIGRCm39mm39
GRCm39 Ensembl12107,876,662 - 107,969,861 (-)Ensembl
GRCm3812107,910,403 - 108,004,145 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl12107,910,403 - 108,003,602 (-)EnsemblGRCm38mm10GRCm38
MGSCv3712109,148,613 - 109,241,624 (-)NCBIGRCm37mm9NCBIm37
MGSCv3612108,363,030 - 108,451,028 (-)NCBImm8
Celera12109,151,974 - 109,245,238 (-)NCBICelera
Cytogenetic Map12F1NCBI
cM Map1259.1NCBI
Bcl11b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543820,564,449 - 20,637,103 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543820,562,345 - 20,637,662 (-)NCBIChiLan1.0ChiLan1.0
BCL11B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11499,122,231 - 99,205,962 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v01479,795,262 - 79,898,472 (-)NCBIMhudiblu_PPA_v0panPan3
BCL11B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1867,622,592 - 67,713,922 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl867,622,708 - 67,714,404 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha867,145,953 - 67,237,226 (-)NCBI
ROS_Cfam_1.0867,909,299 - 68,000,574 (-)NCBI
UMICH_Zoey_3.1867,570,743 - 67,661,895 (-)NCBI
UNSW_CanFamBas_1.0867,636,646 - 67,728,187 (-)NCBI
UU_Cfam_GSD_1.0868,033,837 - 68,125,174 (-)NCBI
Bcl11b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244086406,972,307 - 7,063,288 (+)NCBI
SpeTri2.0NW_0049366043,023,781 - 3,110,104 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BCL11B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl7120,205,008 - 120,295,815 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.17120,205,008 - 120,295,737 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.27127,759,537 - 127,855,267 (-)NCBISscrofa10.2Sscrofa10.2susScr3
BCL11B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12477,122,591 - 77,222,562 (-)NCBI
ChlSab1.1 Ensembl2477,122,689 - 77,221,454 (-)Ensembl
Vero_WHO_p1.0NW_02366605364,224,342 - 64,347,710 (-)NCBI
Bcl11b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247344,560,362 - 4,649,219 (+)NCBI

Position Markers
Bcl11b  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26126,837,358 - 126,837,583 (+)MAPPER
Rnor_6.06131,836,925 - 131,837,149NCBIRnor6.0
Rnor_5.06141,007,305 - 141,007,529UniSTSRnor5.0
RGSC_v3.46132,294,397 - 132,294,621UniSTSRGSC3.4
Celera6124,396,709 - 124,396,933UniSTS
Cytogenetic Map6q32UniSTS
stSG632080  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26126,835,779 - 126,837,168 (+)MAPPER
Rnor_6.06131,835,346 - 131,836,734NCBIRnor6.0
Rnor_5.06141,005,726 - 141,007,114UniSTSRnor5.0
RGSC_v3.46132,292,818 - 132,294,206UniSTSRGSC3.4
Celera6124,395,130 - 124,396,518UniSTS
Cytogenetic Map6q32UniSTS
stSG632129  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26126,888,831 - 126,889,797 (+)MAPPER
Rnor_6.06131,888,435 - 131,889,400NCBIRnor6.0
Rnor_5.06141,058,815 - 141,059,780UniSTSRnor5.0
RGSC_v3.46132,345,869 - 132,346,834UniSTSRGSC3.4
Celera6124,448,318 - 124,449,283UniSTS
Cytogenetic Map6q32UniSTS
ECD17061  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26126,838,523 - 126,838,935 (+)MAPPER
Rnor_6.06131,838,090 - 131,838,501NCBIRnor6.0
Rnor_5.06141,008,470 - 141,008,881UniSTSRnor5.0
RGSC_v3.46132,295,562 - 132,295,973UniSTSRGSC3.4
Celera6124,397,874 - 124,398,285UniSTS
Cytogenetic Map6q32UniSTS
REN47704  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26126,836,818 - 126,837,102 (+)MAPPER
Rnor_6.06131,836,385 - 131,836,668NCBIRnor6.0
Rnor_5.06141,006,765 - 141,007,048UniSTSRnor5.0
RGSC_v3.46132,293,857 - 132,294,140UniSTSRGSC3.4
Celera6124,396,169 - 124,396,452UniSTS
Cytogenetic Map6q32UniSTS
REN47709  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26126,838,402 - 126,838,659 (+)MAPPER
Rnor_6.06131,837,969 - 131,838,225NCBIRnor6.0
Rnor_5.06141,008,349 - 141,008,605UniSTSRnor5.0
RGSC_v3.46132,295,441 - 132,295,697UniSTSRGSC3.4
Celera6124,397,753 - 124,398,009UniSTS
Cytogenetic Map6q32UniSTS
REN47699  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26126,835,712 - 126,835,946 (+)MAPPER
Rnor_6.06131,835,279 - 131,835,512NCBIRnor6.0
Rnor_5.06141,005,659 - 141,005,892UniSTSRnor5.0
RGSC_v3.46132,292,751 - 132,292,984UniSTSRGSC3.4
Celera6124,395,063 - 124,395,296UniSTS
Cytogenetic Map6q32UniSTS
REN47882  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26126,875,656 - 126,875,897 (+)MAPPER
Rnor_6.06131,875,262 - 131,875,502NCBIRnor6.0
Rnor_5.06141,045,642 - 141,045,882UniSTSRnor5.0
RGSC_v3.46132,332,696 - 132,332,936UniSTSRGSC3.4
Celera6124,435,125 - 124,435,365UniSTS
Cytogenetic Map6q32UniSTS
REN47927  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26126,883,083 - 126,883,373 (+)MAPPER
Rnor_6.06131,882,687 - 131,882,976NCBIRnor6.0
Rnor_5.06141,053,067 - 141,053,356UniSTSRnor5.0
RGSC_v3.46132,340,121 - 132,340,410UniSTSRGSC3.4
Celera6124,442,550 - 124,442,839UniSTS
Cytogenetic Map6q32UniSTS
REN47976  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26126,893,425 - 126,893,712 (+)MAPPER
Rnor_6.06131,893,029 - 131,893,315NCBIRnor6.0
Rnor_5.06141,063,409 - 141,063,695UniSTSRnor5.0
RGSC_v3.46132,350,463 - 132,350,749UniSTSRGSC3.4
Celera6124,452,989 - 124,453,275UniSTS
Cytogenetic Map6q32UniSTS
Bcl11b  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26126,837,375 - 126,837,775 (+)MAPPER
Rnor_6.06131,836,942 - 131,837,341NCBIRnor6.0
Rnor_5.06141,007,322 - 141,007,721UniSTSRnor5.0
Celera6124,396,726 - 124,397,125UniSTS
Cytogenetic Map6q32UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)688996335139410483Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)675623277136143011Rat
1331725Bp212Blood pressure QTL 2123.52475arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)697949772133849286Rat
1298087Iddm18Insulin dependent diabetes mellitus QTL 180.0001urine glucose amount (VT:0001758)percentage of study population developing diabetes mellitus during a period of time (CMO:0001114)6121224054135658578Rat
737976Pia24Pristane induced arthritis QTL 24joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)6117355600147991367Rat
1331797Bp213Blood pressure QTL 2133.291arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)6108154445133849286Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)675623277136426962Rat
1581550Pur8Proteinuria QTL 8total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)675623393136142742Rat
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
738034Anxrr5Anxiety related response QTL 55.9exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)688507712133507712Rat
1641917Colcr5Colorectal carcinoma resistance QTL 53.180.0009intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)6127286494144745573Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)675623393136142742Rat
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6104381930138066274Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6104363890147991367Rat
1300076Glom8Glomerulus QTL 870.000000009kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)691703409136703409Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
2312560Pur20Proteinuria QTL 202.10.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)6130561943144745573Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (CMO:0000132)692879510137879510Rat
2293085Iddm29Insulin dependent diabetes mellitus QTL 297.66blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)6127286494147249902Rat
61329Eae9Experimental allergic encephalomyelitis QTL 93.7body mass (VT:0001259)change in body weight (CMO:0002045)6127286494147991367Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)699273921144792678Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)6101207574147991367Rat
10054138Gmadr3Adrenal mass QTL 33.680.00045adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)689631358134631358Rat
10054123Srcrt6Stress Responsive Cort QTL 62.50.0043blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)689631358134631358Rat
4145118Mcs26Mammary carcinoma susceptibility QTL 260.0001mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6111134524138065254Rat
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)699273921144273921Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:392
Count of miRNA genes:218
Interacting mature miRNAs:256
Transcripts:ENSRNOT00000007602
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

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 1 8 11 60
Low 2 42 14 6 8 6 8 32 39 11
Below cutoff 1 18 18 18 8 8 6 3 2 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000007602   ⟹   ENSRNOP00000007602
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl6131,836,674 - 131,914,028 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000084057   ⟹   ENSRNOP00000068641
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl6131,834,097 - 131,926,272 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000088421   ⟹   ENSRNOP00000069404
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl6131,834,097 - 131,926,272 (-)Ensembl
RefSeq Acc Id: NM_001277287   ⟹   NP_001264216
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26126,834,531 - 126,926,674 (-)NCBI
Rnor_6.06131,834,097 - 131,926,272 (-)NCBI
Rnor_5.06141,004,477 - 141,097,643 (-)NCBI
Celera6124,393,881 - 124,486,186 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001277288   ⟹   NP_001264217
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26126,834,531 - 126,926,674 (-)NCBI
Rnor_6.06131,834,097 - 131,926,272 (-)NCBI
Rnor_5.06141,004,477 - 141,097,643 (-)NCBI
Celera6124,393,881 - 124,486,186 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006240540   ⟹   XP_006240602
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26126,834,536 - 126,927,714 (-)NCBI
Rnor_6.06131,836,621 - 131,927,251 (-)NCBI
Rnor_5.06141,004,477 - 141,097,643 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039112399   ⟹   XP_038968327
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26126,834,536 - 126,927,719 (-)NCBI
RefSeq Acc Id: XM_039112400   ⟹   XP_038968328
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26126,834,536 - 126,927,720 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001264217   ⟸   NM_001277288
- Peptide Label: isoform 2
- UniProtKB: H9N1L3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001264216   ⟸   NM_001277287
- Peptide Label: isoform 1
- UniProtKB: H9N1L4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006240602   ⟸   XM_006240540
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000007602   ⟸   ENSRNOT00000007602
RefSeq Acc Id: ENSRNOP00000068641   ⟸   ENSRNOT00000084057
RefSeq Acc Id: ENSRNOP00000069404   ⟸   ENSRNOT00000088421
RefSeq Acc Id: XP_038968328   ⟸   XM_039112400
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038968327   ⟸   XM_039112399
- Peptide Label: isoform X1
Protein Domains
C2H2-type

Transcriptome

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

Promoters
RGD ID:13694816
Promoter ID:EPDNEW_R5341
Type:single initiation site
Name:Bcl11b_1
Description:B-cell CLL/lymphoma 11B
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_6.06131,926,366 - 131,926,426EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311128 AgrOrtholog
Ensembl Genes ENSRNOG00000005776 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000007602 UniProtKB/TrEMBL
  ENSRNOP00000068641 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000069404 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000007602 UniProtKB/TrEMBL
  ENSRNOT00000084057 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000088421 ENTREZGENE, UniProtKB/TrEMBL
InterPro Znf_C2H2/integrase_DNA-bd UniProtKB/TrEMBL
  Znf_C2H2_sf UniProtKB/TrEMBL
KEGG Report rno:314423 UniProtKB/TrEMBL
NCBI Gene 314423 ENTREZGENE
Pfam zf-C2H2 UniProtKB/TrEMBL
PhenoGen Bcl11b PhenoGen
PROSITE ZINC_FINGER_C2H2_1 UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/TrEMBL
SMART ZnF_C2H2 UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/TrEMBL
UniProt D4A0W4_RAT UniProtKB/TrEMBL
  H9N1L3 ENTREZGENE, UniProtKB/TrEMBL
  H9N1L4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-04-02 Bcl11b  BAF chromatin remodeling complex subunit BCL11B  Bcl11b  BCL11B, BAF complex component  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2018-11-09 Bcl11b  BCL11B, BAF complex component  Bcl11b  B-cell CLL/lymphoma 11B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-01-13 Bcl11b  B-cell CLL/lymphoma 11B  Bcl11b  B-cell CLL/lymphoma 11B (zinc finger protein)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Bcl11b  B-cell CLL/lymphoma 11B (zinc finger protein)  Bcl11b  B-cell leukemia/lymphoma 11B   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Bcl11b  B-cell leukemia/lymphoma 11B   Bcl11b_predicted  B-cell leukemia/lymphoma 11B (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Bcl11b_predicted  B-cell leukemia/lymphoma 11B (predicted)      Symbol and Name status set to approved 70820 APPROVED