Bend6 (BEN domain containing 6) - Rat Genome Database

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Gene: Bend6 (BEN domain containing 6) Rattus norvegicus
Analyze
Symbol: Bend6
Name: BEN domain containing 6
RGD ID: 1310392
Description: Predicted to enable chromatin binding activity and transcription corepressor activity. Predicted to be involved in negative regulation of Notch signaling pathway and positive regulation of neuron differentiation. Predicted to be active in nucleus. Orthologous to human BEND6 (BEN domain containing 6); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: BEN domain-containing protein 6; LOC363212; RGD1310392; similar to RIKEN cDNA B230209C24 gene
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8943,576,982 - 43,631,437 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl943,576,982 - 43,631,194 (-)EnsemblGRCr8
mRatBN7.2936,081,033 - 36,135,309 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl936,081,484 - 36,135,228 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx944,577,961 - 44,632,176 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0949,709,148 - 49,763,363 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0947,991,063 - 48,045,276 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0938,297,253 - 38,351,312 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl938,297,322 - 38,351,024 (+)Ensemblrn6Rnor6.0
Rnor_5.0937,980,049 - 38,033,453 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4932,598,694 - 32,656,071 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera933,873,992 - 33,927,321 (-)NCBICelera
RGSC_v3.1932,563,161 - 32,633,061 (-)NCBI
Cytogenetic Map9q21NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IBA,IEA,ISO)

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. 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
Additional References at PubMed
PMID:23571214   PMID:25561495  


Genomics

Comparative Map Data
Bend6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8943,576,982 - 43,631,437 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl943,576,982 - 43,631,194 (-)EnsemblGRCr8
mRatBN7.2936,081,033 - 36,135,309 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl936,081,484 - 36,135,228 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx944,577,961 - 44,632,176 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0949,709,148 - 49,763,363 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0947,991,063 - 48,045,276 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0938,297,253 - 38,351,312 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl938,297,322 - 38,351,024 (+)Ensemblrn6Rnor6.0
Rnor_5.0937,980,049 - 38,033,453 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4932,598,694 - 32,656,071 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera933,873,992 - 33,927,321 (-)NCBICelera
RGSC_v3.1932,563,161 - 32,633,061 (-)NCBI
Cytogenetic Map9q21NCBI
BEND6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38656,955,107 - 57,027,346 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl656,954,924 - 57,027,832 (+)Ensemblhg38GRCh38
GRCh37656,819,905 - 56,892,144 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36656,927,732 - 57,000,103 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34656,928,048 - 57,000,099NCBI
Celera658,482,926 - 58,555,295 (+)NCBICelera
Cytogenetic Map6p12.1NCBI
HuRef656,653,688 - 56,725,834 (+)NCBIHuRef
CHM1_1656,820,114 - 56,892,458 (+)NCBICHM1_1
T2T-CHM13v2.0656,794,154 - 56,866,397 (+)NCBIT2T-CHM13v2.0
Bend6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39133,891,133 - 33,946,925 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl133,891,133 - 33,946,897 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38133,852,052 - 33,907,933 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl133,852,052 - 33,907,816 (-)Ensemblmm10GRCm38
MGSCv37133,908,897 - 33,964,466 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36133,796,598 - 33,852,167 (-)NCBIMGSCv36mm8
Celera133,626,568 - 33,682,229 (-)NCBICelera
Cytogenetic Map1BNCBI
cM Map112.85NCBI
Bend6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555023,124,202 - 3,143,278 (-)Ensembl
ChiLan1.0NW_0049555023,123,024 - 3,152,121 (-)NCBIChiLan1.0ChiLan1.0
BEND6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2571,452,447 - 71,498,338 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1667,307,286 - 67,379,764 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0656,513,496 - 56,586,227 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1658,144,948 - 58,216,965 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl658,144,948 - 58,216,965 (+)EnsemblpanPan2panpan1.1
BEND6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11224,195,068 - 24,254,098 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1224,195,899 - 24,253,229 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1224,084,247 - 24,143,298 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01224,693,267 - 24,752,305 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1224,693,165 - 24,752,298 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11224,190,941 - 24,249,996 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01224,291,978 - 24,351,309 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01224,423,435 - 24,482,648 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Bend6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494659,616,217 - 59,681,950 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364764,279,491 - 4,317,431 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049364764,278,306 - 4,344,085 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BEND6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl728,769,902 - 28,811,933 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1728,769,888 - 28,811,923 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2733,231,064 - 33,273,079 (-)NCBISscrofa10.2Sscrofa10.2susScr3
BEND6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11714,576,290 - 14,651,878 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1714,576,080 - 14,651,671 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605820,682,525 - 20,758,355 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Bend6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475318,795,568 - 18,823,842 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462475318,778,611 - 18,848,599 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Bend6
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v14110,107,321 - 110,137,250 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Bend6
326 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:29
Count of miRNA genes:25
Interacting mature miRNAs:29
Transcripts:ENSRNOT00000060419
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)9671488884474983Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9534647950346479Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)94002992585029925Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9875049253750492Rat
1300180Bw14Body weight QTL 143.776body mass (VT:0001259)body weight (CMO:0000012)93125043268875676Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)92956766474567664Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92956766483835942Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)94172029586720295Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)949664545496645Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9621499551214995Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9875049253750492Rat
7207805Bmd88Bone mineral density QTL 884femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)93125043265651574Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9534647950416711Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)949664545496645Rat
1600365Mcs20Mammary carcinoma susceptibility QTL 203mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)92103143049025574Rat
1581517Bp284Blood pressure QTL 284arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)93922018684220186Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)949664545496645Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)94002992585029925Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9621499551214995Rat
1598823Memor16Memory QTL 161.9exploratory behavior trait (VT:0010471)difference between duration of physical contact or close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)93145606157460683Rat
1641894Alcrsp12Alcohol response QTL 12response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)93496059079960590Rat

Markers in Region
RH131831  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0938,033,589 - 38,033,777UniSTSRnor5.0
Celera933,873,668 - 33,873,856UniSTS
RH 3.4 Map9353.7UniSTS
Cytogenetic Map9q21UniSTS
UniSTS:546686  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2936,087,861 - 36,089,483 (-)MAPPERmRatBN7.2
Rnor_6.0938,343,007 - 38,344,628NCBIRnor6.0
Rnor_5.0938,025,668 - 38,027,289UniSTSRnor5.0
Celera933,880,061 - 33,881,682UniSTS
Cytogenetic Map9q21UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 59 59 6 316 159 11 144 74 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000078157   ⟹   ENSRNOP00000074733
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl943,578,206 - 43,631,194 (-)Ensembl
mRatBN7.2 Ensembl936,082,348 - 36,135,228 (-)Ensembl
Rnor_6.0 Ensembl938,297,322 - 38,345,949 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000088824   ⟹   ENSRNOP00000072521
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl943,576,982 - 43,631,194 (-)Ensembl
mRatBN7.2 Ensembl936,081,484 - 36,135,228 (-)Ensembl
Rnor_6.0 Ensembl938,297,371 - 38,351,024 (+)Ensembl
RefSeq Acc Id: NM_001393774   ⟹   NP_001380703
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8943,576,982 - 43,631,194 (-)NCBI
mRatBN7.2936,081,033 - 36,135,248 (-)NCBI
RefSeq Acc Id: XM_063267364   ⟹   XP_063123434
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8943,576,982 - 43,631,437 (-)NCBI
RefSeq Acc Id: XR_010054613
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8943,576,982 - 43,631,254 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001380703 (Get FASTA)   NCBI Sequence Viewer  
  XP_063123434 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL99314 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000072521
  ENSRNOP00000072521.3
  ENSRNOP00000074733.3
Ensembl Acc Id: ENSRNOP00000074733   ⟸   ENSRNOT00000078157
Ensembl Acc Id: ENSRNOP00000072521   ⟸   ENSRNOT00000088824
RefSeq Acc Id: NP_001380703   ⟸   NM_001393774
- UniProtKB: A0A0G2K8T8 (UniProtKB/TrEMBL),   A6IN97 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063123434   ⟸   XM_063267364
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K8T8 (UniProtKB/TrEMBL),   A6IN97 (UniProtKB/TrEMBL)
Protein Domains
BEN

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K369-F1-model_v2 AlphaFold A0A0G2K369 1-277 view protein structure

Transcriptome

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

Promoters
RGD ID:13696594
Promoter ID:EPDNEW_R7115
Type:initiation region
Name:Bend6_1
Description:BEN domain containing 6
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_6.0938,297,257 - 38,297,317EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310392 AgrOrtholog
BioCyc Gene G2FUF-27871 BioCyc
Ensembl Genes ENSRNOG00000052376 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000078157.3 UniProtKB/TrEMBL
  ENSRNOT00000088824 ENTREZGENE
  ENSRNOT00000088824.3 UniProtKB/TrEMBL
Gene3D-CATH BEN domain UniProtKB/TrEMBL
InterPro BEN_domain UniProtKB/TrEMBL
  BEND6 UniProtKB/TrEMBL
NCBI Gene 363212 ENTREZGENE
PANTHER BEN DOMAIN-CONTAINING PROTEIN 6 UniProtKB/TrEMBL
  PTHR35346 UniProtKB/TrEMBL
Pfam BEN UniProtKB/TrEMBL
PhenoGen Bend6 PhenoGen
PROSITE BEN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000052376 RatGTEx
SMART BEN UniProtKB/TrEMBL
UniProt A0A0G2K369_RAT UniProtKB/TrEMBL
  A0A0G2K8T8 ENTREZGENE, UniProtKB/TrEMBL
  A6IN97 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-06-12 Bend6  BEN domain containing 6  RGD1310392  similar to RIKEN cDNA B230209C24 gene   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1310392  similar to RIKEN cDNA B230209C24 gene   RGD1310392_predicted  similar to RIKEN cDNA B230209C24 gene (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1310392_predicted  similar to RIKEN cDNA B230209C24 gene (predicted)  LOC363212_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC363212_predicted  similar to RIKEN cDNA B230209C24 gene (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL