Bean1 (brain expressed, associated with NEDD4, 1) - Rat Genome Database

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Gene: Bean1 (brain expressed, associated with NEDD4, 1) Rattus norvegicus
Analyze
Symbol: Bean1
Name: brain expressed, associated with NEDD4, 1
RGD ID: 1562003
Description: Predicted to be located in membrane. Human ortholog(s) of this gene implicated in spinocerebellar ataxia type 31. Orthologous to human BEAN1 (brain expressed associated with NEDD4 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; C60 fullerene; copper atom.
Type: protein-coding
RefSeq Status: INFERRED
Previously known as: Bean; brain expressed, associated with Nedd4; LOC361358; RGD1562003; similar to Nedd4-binding brain specific protein BEAN
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
GRCr819745,993 - 792,853 (-)NCBIGRCr8
mRatBN7.219739,551 - 786,395 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl19739,551 - 787,537 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx19736,950 - 789,868 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0191,503,751 - 1,556,673 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.019778,969 - 831,875 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.019947,862 - 993,467 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl19949,607 - 983,556 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.019948,774 - 983,510 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.419698,197 - 744,853 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera19734,752 - 780,042 (-)NCBICelera
Cytogenetic Map19p14NCBI
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

Cellular Component
membrane  (IEA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Bean1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr819745,993 - 792,853 (-)NCBIGRCr8
mRatBN7.219739,551 - 786,395 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl19739,551 - 787,537 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx19736,950 - 789,868 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0191,503,751 - 1,556,673 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.019778,969 - 831,875 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.019947,862 - 993,467 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl19949,607 - 983,556 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.019948,774 - 983,510 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.419698,197 - 744,853 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera19734,752 - 780,042 (-)NCBICelera
Cytogenetic Map19p14NCBI
BEAN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381666,427,295 - 66,495,288 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1666,427,295 - 66,493,529 (+)EnsemblGRCh38hg38GRCh38
GRCh371666,461,198 - 66,529,191 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361665,018,120 - 65,074,249 (+)NCBINCBI36Build 36hg18NCBI36
Celera1650,966,717 - 51,023,308 (+)NCBICelera
Cytogenetic Map16q21NCBI
HuRef1652,336,981 - 52,403,356 (+)NCBIHuRef
CHM1_11667,868,459 - 67,934,640 (+)NCBICHM1_1
T2T-CHM13v2.01672,221,512 - 72,289,583 (+)NCBIT2T-CHM13v2.0
Bean1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398104,897,110 - 104,945,730 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8104,897,074 - 104,945,754 (+)EnsemblGRCm39 Ensembl
GRCm388104,170,379 - 104,219,098 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8104,170,442 - 104,219,122 (+)EnsemblGRCm38mm10GRCm38
MGSCv378106,694,413 - 106,742,998 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368107,057,027 - 107,108,251 (+)NCBIMGSCv36mm8
Celera8108,374,057 - 108,450,555 (+)NCBICelera
Cytogenetic Map8D3NCBI
cM Map853.04NCBI
Bean1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543323,017,335 - 23,061,467 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543323,017,335 - 23,059,054 (+)NCBIChiLan1.0ChiLan1.0
BEAN1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21875,929,750 - 76,007,144 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11681,841,858 - 81,895,598 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01646,745,246 - 46,813,376 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11665,857,543 - 65,902,996 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1665,857,543 - 65,913,340 (+)Ensemblpanpan1.1panPan2
BEAN1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1582,772,693 - 82,803,066 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl582,772,685 - 82,798,667 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha582,760,976 - 82,795,925 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0583,209,313 - 83,244,274 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl583,209,310 - 83,239,674 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1583,032,308 - 83,067,248 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0582,725,642 - 82,760,725 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0583,357,825 - 83,392,945 (-)NCBIUU_Cfam_GSD_1.0
Bean1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934942,750,977 - 42,787,830 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647516,791,640 - 16,838,137 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647516,801,307 - 16,838,127 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BEAN1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl627,176,024 - 27,215,367 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1627,176,023 - 27,217,749 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
BEAN1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1552,121,684 - 52,182,820 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604723,732,410 - 23,794,171 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Bean1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474619,969,508 - 20,015,660 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474619,970,532 - 20,015,592 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Bean1
326 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:102
Count of miRNA genes:62
Interacting mature miRNAs:65
Transcripts:ENSRNOT00000017774, ENSRNOT00000064781
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7411590Foco7Food consumption QTL 76.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)19124688055Rat
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127355345Rat
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19128982497Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19128982497Rat
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19131963836Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19136824771Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19136824771Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19136824771Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19136824771Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat

Markers in Region
RH130313  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.219739,726 - 739,939 (+)MAPPERmRatBN7.2
Rnor_6.019948,038 - 948,250NCBIRnor6.0
Rnor_5.019948,950 - 949,162UniSTSRnor5.0
RGSC_v3.419698,373 - 698,585UniSTSRGSC3.4
Celera19734,928 - 735,140UniSTS
RH 3.4 Map190.0UniSTS
Cytogenetic Map19p14UniSTS
RH129036  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.219739,604 - 739,817 (+)MAPPERmRatBN7.2
Rnor_6.019947,916 - 948,128NCBIRnor6.0
Rnor_5.019948,828 - 949,040UniSTSRnor5.0
RGSC_v3.419698,251 - 698,463UniSTSRGSC3.4
Celera19734,806 - 735,018UniSTS
RH 3.4 Map190.0UniSTS
Cytogenetic Map19p14UniSTS


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 23 6 9 10
Low 1 43 35 20 15 20 8 11 51 20 32 1 8
Below cutoff 2 21 21 4 21 9

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000017774   ⟹   ENSRNOP00000017774
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl19949,607 - 955,626 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000064781   ⟹   ENSRNOP00000062938
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl19949,607 - 983,556 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000095190   ⟹   ENSRNOP00000085069
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl19739,551 - 787,537 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000101901   ⟹   ENSRNOP00000082959
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl19739,571 - 787,537 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000112028   ⟹   ENSRNOP00000083124
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl19739,551 - 787,537 (-)Ensembl
RefSeq Acc Id: NM_001400978   ⟹   NP_001387907
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr819745,993 - 792,853 (-)NCBI
mRatBN7.219739,564 - 786,395 (-)NCBI
RefSeq Acc Id: XM_008772259   ⟹   XP_008770481
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr819745,993 - 792,156 (-)NCBI
mRatBN7.219739,551 - 785,693 (-)NCBI
Rnor_6.019947,862 - 993,467 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039098227   ⟹   XP_038954155
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr819745,993 - 792,156 (-)NCBI
mRatBN7.219739,551 - 785,693 (-)NCBI
RefSeq Acc Id: XM_039098228   ⟹   XP_038954156
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr819745,993 - 781,652 (-)NCBI
mRatBN7.219739,551 - 775,242 (-)NCBI
RefSeq Acc Id: XM_039098229   ⟹   XP_038954157
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr819745,993 - 782,182 (-)NCBI
mRatBN7.219739,551 - 777,243 (-)NCBI
RefSeq Acc Id: XM_039098230   ⟹   XP_038954158
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr819745,993 - 792,585 (-)NCBI
mRatBN7.219743,361 - 786,122 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_008770481   ⟸   XM_008772259
- Peptide Label: isoform X1
- UniProtKB: A0A8I6GBJ0 (UniProtKB/TrEMBL),   A0A8I5ZYA5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000017774   ⟸   ENSRNOT00000017774
RefSeq Acc Id: ENSRNOP00000062938   ⟸   ENSRNOT00000064781
RefSeq Acc Id: XP_038954155   ⟸   XM_039098227
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZYA5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038954157   ⟸   XM_039098229
- Peptide Label: isoform X3
- UniProtKB: A6JXX1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038954156   ⟸   XM_039098228
- Peptide Label: isoform X3
- UniProtKB: A6JXX1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038954158   ⟸   XM_039098230
- Peptide Label: isoform X1
- UniProtKB: A0A8I6GBJ0 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000085069   ⟸   ENSRNOT00000095190
RefSeq Acc Id: ENSRNOP00000083124   ⟸   ENSRNOT00000112028
RefSeq Acc Id: ENSRNOP00000082959   ⟸   ENSRNOT00000101901
RefSeq Acc Id: NP_001387907   ⟸   NM_001400978

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZFF6-F1-model_v2 AlphaFold D3ZFF6 1-324 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562003 AgrOrtholog
BioCyc Gene G2FUF-6633 BioCyc
Ensembl Genes ENSRNOG00000013301 Ensembl
  ENSRNOG00000066314 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000095190.1 UniProtKB/TrEMBL
  ENSRNOT00000101901.1 UniProtKB/TrEMBL
  ENSRNOT00000112028.1 UniProtKB/TrEMBL
InterPro BEAN1 UniProtKB/TrEMBL
KEGG Report rno:361358 UniProtKB/TrEMBL
NCBI Gene 361358 ENTREZGENE
PANTHER PROTEIN BEAN1 UniProtKB/TrEMBL
  PTHR36464 UniProtKB/TrEMBL
PhenoGen Bean1 PhenoGen
RatGTEx ENSRNOG00000013301 RatGTEx
  ENSRNOG00000066314 RatGTEx
UniProt A0A8I5ZYA5 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZYP9_RAT UniProtKB/TrEMBL
  A0A8I6GBJ0 ENTREZGENE, UniProtKB/TrEMBL
  A6JXX1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-02 Bean1  brain expressed, associated with NEDD4, 1  Bean1  brain expressed, associated with NEDD4, 1  Data merged from RGD:149736398 737654 PROVISIONAL
2021-08-09 Bean1  brain expressed, associated with NEDD4, 1      Symbol and Name status set to provisional 45752 PROVISIONAL
2008-02-29 Bean  brain expressed, associated with Nedd4  RGD1562003_predicted  similar to Nedd4-binding brain specific protein BEAN (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1562003_predicted  similar to Nedd4-binding brain specific protein BEAN (predicted)  LOC361358  similar to Nedd4-binding brain specific protein BEAN  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC361358  similar to Nedd4-binding brain specific protein BEAN      Symbol and Name status set to provisional 70820 PROVISIONAL