Dgcr6 (DiGeorge syndrome critical region gene 6) - Rat Genome Database

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Gene: Dgcr6 (DiGeorge syndrome critical region gene 6) Rattus norvegicus
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Symbol: Dgcr6
Name: DiGeorge syndrome critical region gene 6
RGD ID: 1309390
Description: Orthologous to several human genes including DGCR6 (DiGeorge syndrome critical region gene 6); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-sulfonyldiphenol; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC303794
RGD Orthologs
Human
Mouse
Bonobo
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81196,432,024 - 96,442,766 (-)NCBIGRCr8
mRatBN7.21182,927,725 - 82,932,823 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1182,927,725 - 82,932,823 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1191,656,101 - 91,661,137 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01184,317,219 - 84,322,255 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01183,370,836 - 83,375,872 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01187,076,205 - 87,081,306 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1187,076,381 - 87,081,950 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01190,168,058 - 90,173,154 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41184,922,649 - 84,927,694 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11184,963,245 - 84,968,334 (-)NCBI
Celera1181,703,405 - 81,708,450 (-)NCBICelera
Cytogenetic Map11q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
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:12477932  


Genomics

Comparative Map Data
Dgcr6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81196,432,024 - 96,442,766 (-)NCBIGRCr8
mRatBN7.21182,927,725 - 82,932,823 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1182,927,725 - 82,932,823 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1191,656,101 - 91,661,137 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01184,317,219 - 84,322,255 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01183,370,836 - 83,375,872 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01187,076,205 - 87,081,306 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1187,076,381 - 87,081,950 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01190,168,058 - 90,173,154 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41184,922,649 - 84,927,694 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11184,963,245 - 84,968,334 (-)NCBI
Celera1181,703,405 - 81,708,450 (-)NCBICelera
Cytogenetic Map11q23NCBI
DGCR6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382218,906,223 - 18,912,088 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2218,906,028 - 18,914,238 (+)EnsemblGRCh38hg38GRCh38
GRCh372218,893,833 - 18,899,601 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362217,273,779 - 17,279,601 (+)NCBINCBI36Build 36hg18NCBI36
Build 342217,268,345 - 17,274,146NCBI
Celera222,745,929 - 2,751,791 (+)NCBICelera
Cytogenetic Map22q11.21NCBI
HuRef222,515,964 - 2,521,863 (+)NCBIHuRef
CHM1_12218,893,495 - 18,899,360 (+)NCBICHM1_1
T2T-CHM13v2.02219,281,581 - 19,287,480 (+)NCBIT2T-CHM13v2.0
Dgcr6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391617,870,736 - 17,889,497 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1617,870,724 - 17,889,496 (+)EnsemblGRCm39 Ensembl
GRCm381618,052,860 - 18,071,633 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1618,052,860 - 18,071,632 (+)EnsemblGRCm38mm10GRCm38
MGSCv371618,052,953 - 18,071,435 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361617,966,423 - 17,984,905 (+)NCBIMGSCv36mm8
Celera1618,625,430 - 18,643,927 (+)NCBICelera
Cytogenetic Map16A3NCBI
cM Map1611.19NCBI
DGCR6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22328,531,539 - 28,538,834 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12231,080,221 - 31,086,535 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0221,647,018 - 1,653,326 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12217,348,556 - 17,350,597 (+)NCBIpanpan1.1PanPan1.1panPan2

Variants

.
Variants in Dgcr6
19 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:69
Count of miRNA genes:56
Interacting mature miRNAs:62
Transcripts:ENSRNOT00000002574
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
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
634339Niddm50Non-insulin dependent diabetes mellitus QTL 503.32blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)116642214886241447Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116642214886241447Rat
2302043Pia27Pristane induced arthritis QTL 2718.60.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)118256654583440803Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)115513672982993457Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115635142486241447Rat
10450831Scl80Serum cholesterol level QTL 804.70.01blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)117695713183051965Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116034659086241447Rat

Markers in Region
Dgcr6  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21182,927,925 - 82,929,587 (+)MAPPERmRatBN7.2
Rnor_6.01187,076,406 - 87,078,067NCBIRnor6.0
Rnor_5.01190,168,259 - 90,169,920UniSTSRnor5.0
RGSC_v3.41184,922,850 - 84,924,511UniSTSRGSC3.4
Celera1181,703,606 - 81,705,267UniSTS
Cytogenetic Map11q23UniSTS


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 3 35 21 21 21 3 74 27 37 3
Low 8 36 20 19 20 8 8 8 4 8 8
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000002574   ⟹   ENSRNOP00000002574
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1182,927,728 - 82,932,823 (-)Ensembl
Rnor_6.0 Ensembl1187,076,381 - 87,081,950 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000102550   ⟹   ENSRNOP00000096660
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1182,927,725 - 82,932,757 (-)Ensembl
RefSeq Acc Id: NM_001107080   ⟹   NP_001100550
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81196,432,024 - 96,437,069 (-)NCBI
mRatBN7.21182,927,725 - 82,932,770 (-)NCBI
Rnor_6.01187,076,205 - 87,081,250 (-)NCBI
Rnor_5.01190,168,058 - 90,173,154 (-)NCBI
RGSC_v3.41184,922,649 - 84,927,694 (-)RGD
Celera1181,703,405 - 81,708,450 (-)RGD
Sequence:
RefSeq Acc Id: XM_006248609   ⟹   XP_006248671
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81196,432,024 - 96,442,766 (-)NCBI
mRatBN7.21182,927,725 - 82,932,823 (-)NCBI
Rnor_6.01187,076,205 - 87,081,306 (-)NCBI
Rnor_5.01190,168,058 - 90,173,154 (-)NCBI
Sequence:
RefSeq Acc Id: XM_063270459   ⟹   XP_063126529
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81196,432,024 - 96,437,129 (-)NCBI
RefSeq Acc Id: XM_063270460   ⟹   XP_063126530
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81196,433,247 - 96,437,129 (-)NCBI
RefSeq Acc Id: XM_063270461   ⟹   XP_063126531
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81196,433,936 - 96,437,122 (-)NCBI
RefSeq Acc Id: NP_001100550   ⟸   NM_001107080
- UniProtKB: B0BNH6 (UniProtKB/TrEMBL),   A6JSJ1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006248671   ⟸   XM_006248609
- Peptide Label: isoform X1
- UniProtKB: F7FP83 (UniProtKB/TrEMBL),   A0A8I6AQQ6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000002574   ⟸   ENSRNOT00000002574
RefSeq Acc Id: ENSRNOP00000096660   ⟸   ENSRNOT00000102550
RefSeq Acc Id: XP_063126529   ⟸   XM_063270459
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063126530   ⟸   XM_063270460
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063126531   ⟸   XM_063270461
- Peptide Label: isoform X4

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B0BNH6-F1-model_v2 AlphaFold B0BNH6 1-198 view protein structure

Transcriptome

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

Promoters
RGD ID:13698311
Promoter ID:EPDNEW_R8836
Type:multiple initiation site
Name:Dgcr6_1
Description:DiGeorge syndrome critical region gene 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_6.01187,081,278 - 87,081,338EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309390 AgrOrtholog
BioCyc Gene G2FUF-20633 BioCyc
Ensembl Genes ENSRNOG00000001880 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002574.7 UniProtKB/TrEMBL
  ENSRNOT00000102550.1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7378165 IMAGE-MGC_LOAD
InterPro DGCR6 UniProtKB/TrEMBL
KEGG Report rno:303794 UniProtKB/TrEMBL
MGC_CLONE MGC:188273 IMAGE-MGC_LOAD
NCBI Gene 303794 ENTREZGENE
PANTHER DGCR6 UniProtKB/TrEMBL
  PROTEIN DGCR6 UniProtKB/TrEMBL
Pfam DGCR6 UniProtKB/TrEMBL
PhenoGen Dgcr6 PhenoGen
RatGTEx ENSRNOG00000001880 RatGTEx
UniProt A0A8I6AQQ6 ENTREZGENE, UniProtKB/TrEMBL
  A6JSJ1 ENTREZGENE, UniProtKB/TrEMBL
  B0BNH6 ENTREZGENE, UniProtKB/TrEMBL
  F7FP83 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Dgcr6  DiGeorge syndrome critical region gene 6   Dgcr6_predicted  DiGeorge syndrome critical region gene 6 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Dgcr6_predicted  DiGeorge syndrome critical region gene 6 (predicted)      Symbol and Name status set to approved 70820 APPROVED