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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8943,576,982 - 43,631,437 (-)NCBIGRCr8
mRatBN7.2936,081,033 - 36,135,309 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl936,081,484 - 36,135,228 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx944,577,961 - 44,632,176 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0949,709,148 - 49,763,363 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0947,991,063 - 48,045,276 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0938,297,253 - 38,351,312 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl938,297,322 - 38,351,024 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0937,980,049 - 38,033,453 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4932,598,694 - 32,656,071 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1932,563,161 - 32,633,061 (-)NCBI
Celera933,873,992 - 33,927,321 (-)NCBICelera
Cytogenetic Map9q21NCBI
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

Biological Process

Cellular Component
nucleus  (IBA,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 (-)NCBIGRCr8
mRatBN7.2936,081,033 - 36,135,309 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl936,081,484 - 36,135,228 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx944,577,961 - 44,632,176 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0949,709,148 - 49,763,363 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0947,991,063 - 48,045,276 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0938,297,253 - 38,351,312 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl938,297,322 - 38,351,024 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0937,980,049 - 38,033,453 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4932,598,694 - 32,656,071 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1932,563,161 - 32,633,061 (-)NCBI
Celera933,873,992 - 33,927,321 (-)NCBICelera
Cytogenetic Map9q21NCBI
BEND6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38656,955,107 - 57,027,346 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl656,955,107 - 57,027,346 (+)EnsemblGRCh38hg38GRCh38
GRCh37656,819,905 - 56,892,144 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36656,927,732 - 57,000,103 (+)NCBINCBI36Build 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 Ensembl
GRCm38133,852,052 - 33,907,933 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl133,852,052 - 33,907,816 (-)EnsemblGRCm38mm10GRCm38
MGSCv37133,908,897 - 33,964,466 (-)NCBIGRCm37MGSCv37mm9NCBIm37
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 (-)EnsemblChiLan1.0
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 (+)Ensemblpanpan1.1panPan2
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1224,084,247 - 24,143,298 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01224,693,267 - 24,752,305 (+)NCBIROS_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_1.0
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 (-)EnsemblSpeTri2.0SpeTri2.0 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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475318,778,611 - 18,848,599 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Bend6
383 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9510982642921101Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9510982650109826Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)9728325252283252Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)9895256053952560Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9895256053952560Rat
1600365Mcs20Mammary carcinoma susceptibility QTL 203mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)91353377042791750Rat
724543Cm20Cardiac mass QTL 203.9heart mass (VT:0007028)calculated heart weight (CMO:0000073)91696139840594091Rat
631680Cm11Cardiac mass QTL 113.10.00089heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)92043051965430519Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92207116986369743Rat
631643Bp120Blood pressure QTL 12030.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)92207120067071200Rat
1598823Memor16Memory QTL 161.9exploratory 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)92213332249968732Rat
7207805Bmd88Bone mineral density QTL 884femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)92375402458157242Rat
1300180Bw14Body weight QTL 143.776body mass (VT:0001259)body weight (CMO:0000012)92375402461381613Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)92375414483851531Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)92526804479271759Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)925661188100929786Rat
1641894Alcrsp12Alcohol response QTL 12response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)92746863972468639Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)93253550577535505Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)93253550577535505Rat

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
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 54 1 1
Low 3 43 31 15 19 15 7 7 20 32 40 10 7
Below cutoff 26 26 26 1 4 3 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000078157   ⟹   ENSRNOP00000074733
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl936,082,348 - 36,135,228 (-)Ensembl
Rnor_6.0 Ensembl938,297,322 - 38,345,949 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000088824   ⟹   ENSRNOP00000072521
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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 ENSRNOP00000072521.2
  ENSRNOP00000074733
  ENSRNOP00000074733.2
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000074733   ⟸   ENSRNOT00000078157
RefSeq 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)
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 ENTREZGENE
  ENSRNOT00000078157.2 UniProtKB/TrEMBL
  ENSRNOT00000088824.2 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