Borcs5 (BLOC-1 related complex subunit 5) - Rat Genome Database

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Gene: Borcs5 (BLOC-1 related complex subunit 5) Rattus norvegicus
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Symbol: Borcs5
Name: BLOC-1 related complex subunit 5
RGD ID: 1307624
Description: Predicted to be involved in lysosome localization; organelle transport along microtubule; and positive regulation of anterograde synaptic vesicle transport. Predicted to be located in intracellular membrane-bounded organelle and plasma membrane. Predicted to be part of BORC complex and plus-end kinesin complex. Predicted to be active in cytoplasmic side of lysosomal membrane and synaptic vesicle membrane. Human ortholog(s) of this gene implicated in colorectal adenocarcinoma. Orthologous to human BORCS5 (BLOC-1 related complex subunit 5); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; paracetamol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: BLOC-1-related complex subunit 5; LOC362452; Loh12cr1; loss of heterozygosity, 12, chromosomal region 1; loss of heterozygosity, 12, chromosomal region 1 homolog; loss of heterozygosity, 12, chromosomal region 1 homolog (human)
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
GRCr84169,190,025 - 169,272,335 (+)NCBIGRCr8
mRatBN7.24167,458,640 - 167,543,556 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4167,473,177 - 167,540,993 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4173,766,789 - 173,834,399 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04169,549,869 - 169,617,480 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04168,175,487 - 168,241,125 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04168,396,034 - 168,466,968 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4168,396,775 - 168,464,352 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04232,664,705 - 232,748,296 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44171,545,892 - 171,614,610 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14171,790,759 - 171,858,467 (+)NCBI
Celera4156,072,931 - 156,138,582 (+)NCBICelera
Cytogenetic Map4q43NCBI
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

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. Impact of Genetic Variation in MicroRNA-binding Site on Susceptibility to Colorectal Cancer. Kang BW, etal., Anticancer Res. 2016 Jul;36(7):3353-61.
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:25898167  


Genomics

Comparative Map Data
Borcs5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84169,190,025 - 169,272,335 (+)NCBIGRCr8
mRatBN7.24167,458,640 - 167,543,556 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4167,473,177 - 167,540,993 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4173,766,789 - 173,834,399 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04169,549,869 - 169,617,480 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04168,175,487 - 168,241,125 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04168,396,034 - 168,466,968 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4168,396,775 - 168,464,352 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04232,664,705 - 232,748,296 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44171,545,892 - 171,614,610 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14171,790,759 - 171,858,467 (+)NCBI
Celera4156,072,931 - 156,138,582 (+)NCBICelera
Cytogenetic Map4q43NCBI
BORCS5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381212,357,078 - 12,471,233 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1212,357,078 - 12,471,233 (+)EnsemblGRCh38hg38GRCh38
GRCh371212,510,012 - 12,624,167 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361212,401,322 - 12,511,105 (+)NCBINCBI36Build 36hg18NCBI36
Build 341212,401,321 - 12,511,105NCBI
Celera1217,653,635 - 17,763,988 (+)NCBICelera
Cytogenetic Map12p13.2NCBI
HuRef1212,275,116 - 12,385,078 (+)NCBIHuRef
CHM1_11212,475,001 - 12,584,853 (+)NCBICHM1_1
T2T-CHM13v2.01212,226,205 - 12,340,409 (+)NCBIT2T-CHM13v2.0
Borcs5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396134,616,475 - 134,688,147 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6134,616,473 - 134,688,150 (+)EnsemblGRCm39 Ensembl
GRCm386134,639,512 - 134,711,184 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6134,639,510 - 134,711,187 (+)EnsemblGRCm38mm10GRCm38
MGSCv376134,589,530 - 134,661,202 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv366134,606,674 - 134,676,863 (+)NCBIMGSCv36mm8
Celera6137,587,872 - 137,663,447 (+)NCBICelera
Cytogenetic Map6G1NCBI
cM Map665.77NCBI
Borcs5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554139,309,861 - 9,399,378 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554139,309,766 - 9,399,378 (+)NCBIChiLan1.0ChiLan1.0
BORCS5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21017,823,289 - 17,950,691 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11217,820,048 - 17,950,110 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01212,380,071 - 12,488,735 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11212,749,085 - 12,857,043 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1212,749,104 - 12,857,043 (+)Ensemblpanpan1.1panPan2
BORCS5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12733,839,345 - 33,949,056 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2733,837,318 - 33,934,896 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2712,496,789 - 12,606,369 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02734,146,425 - 34,256,421 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2734,144,391 - 34,242,102 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12734,039,090 - 34,148,751 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02733,988,879 - 34,098,859 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02712,228,438 - 12,340,603 (+)NCBIUU_Cfam_GSD_1.0
Borcs5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494595,078,900 - 95,178,702 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365874,806,113 - 4,906,411 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365874,806,537 - 4,906,301 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BORCS5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl559,970,260 - 60,072,942 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1559,969,806 - 60,072,976 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
BORCS5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11112,259,080 - 12,363,576 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1112,259,495 - 12,364,740 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606922,956,199 - 23,063,114 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Borcs5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475225,382,796 - 25,504,989 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475225,418,206 - 25,504,658 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Borcs5
248 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1127
Count of miRNA genes:336
Interacting mature miRNAs:454
Transcripts:ENSRNOT00000008645
Prediction methods:Microtar, Miranda, 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
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4110275411168266883Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123143783168143783Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4124303370169303370Rat
6478778Anxrr51Anxiety related response QTL 510.25384locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4124778595169778595Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4125590636170590636Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4146565735175236377Rat
1582237Kidm34Kidney mass QTL 3440.0001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)4148090542168069246Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4155561574182687754Rat
1300109Rf13Renal function QTL 133.91renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)4157710145182687754Rat

Markers in Region
BE099340  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24167,517,550 - 167,517,704 (+)MAPPERmRatBN7.2
Rnor_6.04168,440,916 - 168,441,069NCBIRnor6.0
Rnor_5.04232,722,379 - 232,722,532UniSTSRnor5.0
RGSC_v3.44171,590,756 - 171,590,909UniSTSRGSC3.4
Celera4156,115,151 - 156,115,304UniSTS
RH 3.4 Map4951.2UniSTS
Cytogenetic Map4q43UniSTS


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 2 3 60 3 14 3
Low 1 43 57 41 16 41 8 11 14 32 27 8 8
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000008645   ⟹   ENSRNOP00000008645
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4167,473,177 - 167,540,993 (+)Ensembl
Rnor_6.0 Ensembl4168,396,775 - 168,464,352 (+)Ensembl
RefSeq Acc Id: NM_001108650   ⟹   NP_001102120
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84169,204,718 - 169,272,331 (+)NCBI
mRatBN7.24167,473,373 - 167,540,993 (+)NCBI
Rnor_6.04168,396,775 - 168,464,354 (+)NCBI
Rnor_5.04232,664,705 - 232,748,296 (+)NCBI
RGSC_v3.44171,545,892 - 171,614,610 (+)RGD
Celera4156,072,931 - 156,138,582 (+)RGD
Sequence:
RefSeq Acc Id: XM_006237528   ⟹   XP_006237590
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84169,203,044 - 169,264,430 (+)NCBI
mRatBN7.24167,472,057 - 167,539,544 (+)NCBI
Rnor_6.04168,396,034 - 168,458,444 (+)NCBI
Rnor_5.04232,664,705 - 232,748,296 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039107905   ⟹   XP_038963833
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84169,190,025 - 169,272,335 (+)NCBI
mRatBN7.24167,458,677 - 167,543,556 (+)NCBI
RefSeq Acc Id: XM_039107907   ⟹   XP_038963835
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84169,190,025 - 169,272,335 (+)NCBI
mRatBN7.24167,458,677 - 167,543,556 (+)NCBI
RefSeq Acc Id: NP_001102120   ⟸   NM_001108650
- UniProtKB: B1H257 (UniProtKB/TrEMBL),   F7EXS9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237590   ⟸   XM_006237528
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000008645   ⟸   ENSRNOT00000008645
RefSeq Acc Id: XP_038963833   ⟸   XM_039107905
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038963835   ⟸   XM_039107907
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B1H257-F1-model_v2 AlphaFold B1H257 1-195 view protein structure

Transcriptome

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

Promoters
RGD ID:13693451
Promoter ID:EPDNEW_R3976
Type:multiple initiation site
Name:Borcs5_1
Description:BLOC-1 related complex subunit 5
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_6.04168,396,678 - 168,396,738EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307624 AgrOrtholog
BioCyc Gene G2FUF-42651 BioCyc
Ensembl Genes ENSRNOG00000006505 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008645 ENTREZGENE
  ENSRNOT00000008645.8 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7365768 IMAGE-MGC_LOAD
InterPro Tumour_supressor_LOH1CR12 UniProtKB/TrEMBL
KEGG Report rno:362452 UniProtKB/TrEMBL
MGC_CLONE MGC:188238 IMAGE-MGC_LOAD
NCBI Gene 362452 ENTREZGENE
PANTHER BLOC-1-RELATED COMPLEX SUBUNIT 5 UniProtKB/TrEMBL
  PTHR31634 UniProtKB/TrEMBL
Pfam LOH1CR12 UniProtKB/TrEMBL
PhenoGen Borcs5 PhenoGen
RatGTEx ENSRNOG00000006505 RatGTEx
UniProt B1H257 ENTREZGENE, UniProtKB/TrEMBL
  F7EXS9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-08-13 Borcs5  BLOC-1 related complex subunit 5  Loh12cr1  loss of heterozygosity, 12, chromosomal region 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-01-17 Loh12cr1  loss of heterozygosity, 12, chromosomal region 1  Loh12cr1  loss of heterozygosity, 12, chromosomal region 1 homolog (human)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Loh12cr1  loss of heterozygosity, 12, chromosomal region 1 homolog (human)   Loh12cr1_predicted  loss of heterozygosity, 12, chromosomal region 1 homolog (human) (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Loh12cr1_predicted  loss of heterozygosity, 12, chromosomal region 1 homolog (human) (predicted)    loss of heterozygosity, 12, chromosomal region 1 homolog (predicted)  Name updated 1299863 APPROVED
2005-01-12 Loh12cr1_predicted  loss of heterozygosity, 12, chromosomal region 1 homolog (predicted)      Symbol and Name status set to approved 70820 APPROVED