GRM7-AS3 (GRM7 antisense RNA 3) - Rat Genome Database

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Gene: GRM7-AS3 (GRM7 antisense RNA 3) Homo sapiens
Analyze
Symbol: GRM7-AS3
Name: GRM7 antisense RNA 3
RGD ID: 5144601
HGNC Page HGNC:42444
Description:
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3836,632,358 - 6,805,449 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl36,631,008 - 6,805,479 (-)EnsemblGRCh38hg38GRCh38
GRCh3736,674,045 - 6,847,136 (-)NCBIGRCh37GRCh37hg19GRCh37
Celera36,610,869 - 6,784,676 (-)NCBICelera
Cytogenetic Map3p26.1NCBI
HuRef36,608,244 - 6,781,346 (-)NCBIHuRef
CHM1_136,624,766 - 6,797,809 (-)NCBICHM1_1
T2T-CHM13v2.036,622,736 - 6,796,027 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Genomics

Variants

.
Variants in GRM7-AS3
8 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NR_110123.1(GRM7-AS3):n.151-365G>T single nucleotide variant Lung cancer [RCV000093650] Chr3:6635562 [GRCh38]
Chr3:6677249 [GRCh37]
Chr3:3p26.1		 uncertain significance
NR_110123.1(GRM7-AS3):n.151-45467C>A single nucleotide variant Lung cancer [RCV000093654] Chr3:6680664 [GRCh38]
Chr3:6722351 [GRCh37]
Chr3:3p26.1		 uncertain significance
NR_110123.1(GRM7-AS3):n.62-2944G>C single nucleotide variant Lung cancer [RCV000093662] Chr3:6794085 [GRCh38]
Chr3:6835772 [GRCh37]
Chr3:3p26.1		 uncertain significance
NR_110123.1(GRM7-AS3):n.61+3992G>T single nucleotide variant Lung cancer [RCV000093664] Chr3:6801397 [GRCh38]
Chr3:6843084 [GRCh37]
Chr3:3p26.1		 uncertain significance
GRCh38/hg38 3p26.3-25.3(chr3:52266-9450310)x1 copy number loss See cases [RCV000137109] Chr3:52266..9450310 [GRCh38]
Chr3:93949..9491994 [GRCh37]
Chr3:68949..9466994 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-24.1(chr3:32241-30064208)x3 copy number gain See cases [RCV000138004] Chr3:32241..30064208 [GRCh38]
Chr3:73914..30105699 [GRCh37]
Chr3:48914..30080703 [NCBI36]
Chr3:3p26.3-24.1		 pathogenic
GRCh38/hg38 3p26.3-25.2(chr3:32241-12681483)x1 copy number loss See cases [RCV000138143] Chr3:32241..12681483 [GRCh38]
Chr3:73914..12722982 [GRCh37]
Chr3:48914..12697982 [NCBI36]
Chr3:3p26.3-25.2		 pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:32241-20334387)x3 copy number gain See cases [RCV000137941] Chr3:32241..20334387 [GRCh38]
Chr3:73914..20375879 [GRCh37]
Chr3:48914..20350883 [NCBI36]
Chr3:3p26.3-24.3		 pathogenic
GRCh38/hg38 3p26.3-26.1(chr3:32241-7056717)x1 copy number loss See cases [RCV000138287] Chr3:32241..7056717 [GRCh38]
Chr3:73914..7098404 [GRCh37]
Chr3:48914..7073404 [NCBI36]
Chr3:3p26.3-26.1		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-11379835)x1 copy number loss See cases [RCV000138376] Chr3:32241..11379835 [GRCh38]
Chr3:73914..11421309 [GRCh37]
Chr3:48914..11396309 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic|likely benign
GRCh38/hg38 3p26.3-25.3(chr3:32241-9469506)x1 copy number loss See cases [RCV000139253] Chr3:32241..9469506 [GRCh38]
Chr3:73914..9511190 [GRCh37]
Chr3:48914..9486190 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:52747-8370373)x1 copy number loss See cases [RCV000139164] Chr3:52747..8370373 [GRCh38]
Chr3:94430..8412059 [GRCh37]
Chr3:69430..8387059 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.1(chr3:32241-13613818)x3 copy number gain See cases [RCV000138946] Chr3:32241..13613818 [GRCh38]
Chr3:73914..13655318 [GRCh37]
Chr3:48914..13630319 [NCBI36]
Chr3:3p26.3-25.1		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-9574994)x1 copy number loss See cases [RCV000140239] Chr3:32241..9574994 [GRCh38]
Chr3:73914..9616678 [GRCh37]
Chr3:48914..9591678 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-8165256)x3 copy number gain See cases [RCV000141319] Chr3:32241..8165256 [GRCh38]
Chr3:73914..8206943 [GRCh37]
Chr3:48914..8181943 [NCBI36]
Chr3:3p26.3-25.3		 likely pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-9066287)x1 copy number loss See cases [RCV000140848] Chr3:32241..9066287 [GRCh38]
Chr3:73914..9107971 [GRCh37]
Chr3:48914..9082971 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-22.1(chr3:53308-41381521)x3 copy number gain See cases [RCV000141810] Chr3:53308..41381521 [GRCh38]
Chr3:94991..41423012 [GRCh37]
Chr3:69991..41398016 [NCBI36]
Chr3:3p26.3-22.1		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:20213-11221602)x1 copy number loss See cases [RCV000141731] Chr3:20213..11221602 [GRCh38]
Chr3:61891..11263288 [GRCh37]
Chr3:36891..11238288 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:20213-9362037)x1 copy number loss See cases [RCV000142284] Chr3:20213..9362037 [GRCh38]
Chr3:61891..9403721 [GRCh37]
Chr3:36891..9378721 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.1(chr3:6277545-6810651)x1 copy number loss See cases [RCV000142387] Chr3:6277545..6810651 [GRCh38]
Chr3:6319232..6852338 [GRCh37]
Chr3:6294232..6827338 [NCBI36]
Chr3:3p26.1		 benign
GRCh38/hg38 3p26.3-25.3(chr3:32241-10323124)x1 copy number loss See cases [RCV000143325] Chr3:32241..10323124 [GRCh38]
Chr3:73914..10364808 [GRCh37]
Chr3:48914..10339808 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:32241-10631310)x1 copy number loss See cases [RCV000143173] Chr3:32241..10631310 [GRCh38]
Chr3:73914..10672995 [GRCh37]
Chr3:48914..10647995 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:688897-11051142)x1 copy number loss See cases [RCV000143706] Chr3:688897..11051142 [GRCh38]
Chr3:730581..11092828 [GRCh37]
Chr3:705581..11067828 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:52266-11089569)x1 copy number loss See cases [RCV000051447] Chr3:52266..11089569 [GRCh38]
Chr3:93949..11131255 [GRCh37]
Chr3:68949..11106255 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:52266-8582037)x1 copy number loss See cases [RCV000051474] Chr3:52266..8582037 [GRCh38]
Chr3:93949..8623723 [GRCh37]
Chr3:68949..8598723 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-26.1(chr3:63843-6977502)x1 copy number loss See cases [RCV000051475] Chr3:63843..6977502 [GRCh38]
Chr3:105526..7019189 [GRCh37]
Chr3:80526..6994189 [NCBI36]
Chr3:3p26.3-26.1		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:63843-9507969)x1 copy number loss See cases [RCV000051476] Chr3:63843..9507969 [GRCh38]
Chr3:105526..9549653 [GRCh37]
Chr3:80526..9524653 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-25.3(chr3:63843-8258109)x1 copy number loss See cases [RCV000051478] Chr3:63843..8258109 [GRCh38]
Chr3:105526..8299796 [GRCh37]
Chr3:80526..8274796 [NCBI36]
Chr3:3p26.3-25.3		 pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:52066-20280127)x3 copy number gain See cases [RCV000051690] Chr3:52066..20280127 [GRCh38]
Chr3:93749..20321619 [GRCh37]
Chr3:68749..20296623 [NCBI36]
Chr3:3p26.3-24.3		 pathogenic
GRCh38/hg38 3p26.3-24.1(chr3:52266-29248782)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051718]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051718]|See cases [RCV000051718] Chr3:52266..29248782 [GRCh38]
Chr3:93949..29290273 [GRCh37]
Chr3:68949..29265277 [NCBI36]
Chr3:3p26.3-24.1		 pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:63843-19510600)x3 copy number gain See cases [RCV000051719] Chr3:63843..19510600 [GRCh38]
Chr3:105526..19552092 [GRCh37]
Chr3:80526..19527096 [NCBI36]
Chr3:3p26.3-24.3		 pathogenic
GRCh38/hg38 3p26.3-26.1(chr3:1984526-6852981)x1 copy number loss See cases [RCV000050822] Chr3:1984526..6852981 [GRCh38]
Chr3:2026210..6894668 [GRCh37]
Chr3:2001210..6869668 [NCBI36]
Chr3:3p26.3-26.1		 pathogenic
GRCh38/hg38 3p26.1(chr3:6476154-7285494)x3 copy number gain See cases [RCV000050613] Chr3:6476154..7285494 [GRCh38]
Chr3:6517841..7327181 [GRCh37]
Chr3:6492841..7302181 [NCBI36]
Chr3:3p26.1		 uncertain significance
GRCh38/hg38 3p26.3-22.2(chr3:52266-37148076)x3 copy number gain See cases [RCV000051097] Chr3:52266..37148076 [GRCh38]
Chr3:93949..37189567 [GRCh37]
Chr3:68949..37164571 [NCBI36]
Chr3:3p26.3-22.2		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:801
Count of miRNA genes:610
Interacting mature miRNAs:677
Transcripts:ENST00000412629, ENST00000417482, ENST00000424366, ENST00000445675, ENST00000449158, ENST00000452244, ENST00000454410, ENST00000455623, ENST00000458713
Prediction methods:Microtar, Miranda, Rnahybrid
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.

Markers in Region
D3S745  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh3736,741,306 - 6,741,901UniSTSGRCh37
Celera36,678,929 - 6,679,445UniSTS
HuRef36,675,290 - 6,676,122UniSTS


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 sensory system adipose tissue appendage entire extraembryonic component
High
Medium 21
Low 2 2 2 15 2 9 1 6 344 4 1
Below cutoff 208 122 221 50 183 25 232 84 1330 105 127 191 25 58 107

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000412629
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl36,631,555 - 6,805,479 (-)Ensembl
RefSeq Acc Id: ENST00000417482
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl36,731,172 - 6,805,438 (-)Ensembl
RefSeq Acc Id: ENST00000424366
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl36,739,538 - 6,805,427 (-)Ensembl
RefSeq Acc Id: ENST00000445675
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl36,631,900 - 6,664,906 (-)Ensembl
RefSeq Acc Id: ENST00000449158
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl36,721,315 - 6,791,105 (-)Ensembl
RefSeq Acc Id: ENST00000452244
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl36,740,367 - 6,742,687 (-)Ensembl
RefSeq Acc Id: ENST00000454410
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl36,788,934 - 6,805,409 (-)Ensembl
RefSeq Acc Id: ENST00000455623
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl36,631,689 - 6,644,894 (-)Ensembl
RefSeq Acc Id: ENST00000458713
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl36,632,536 - 6,664,943 (-)Ensembl
RefSeq Acc Id: ENST00000670757
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl36,631,008 - 6,791,124 (-)Ensembl
RefSeq Acc Id: NR_110123
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh3836,632,358 - 6,805,449 (-)NCBI
HuRef36,608,255 - 6,781,340 (-)NCBI
CHM1_136,624,777 - 6,797,803 (-)NCBI
T2T-CHM13v2.036,622,736 - 6,796,027 (-)NCBI
Sequence:
RefSeq Acc Id: NR_110125
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh3836,731,172 - 6,805,449 (-)NCBI
HuRef36,608,255 - 6,781,340 (-)NCBI
CHM1_136,723,532 - 6,797,803 (-)NCBI
T2T-CHM13v2.036,721,760 - 6,796,027 (-)NCBI
Sequence:
Promoters
RGD ID:15095561
Promoter ID:EPDNEWNC_H394
Type:initiation region
Name:GRM7-AS3_2
Description:GRM7 antisense RNA 3 [Source:HGNC Symbol;Acc:HGNC:42444]
SO ACC ID:SO:0000170
Source:EPDNEWNC (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh3836,664,934 - 6,664,994EPDNEWNC
RGD ID:15095560
Promoter ID:EPDNEWNC_H395
Type:initiation region
Name:GRM7-AS3_1
Description:GRM7 antisense RNA 3 [Source:HGNC Symbol;Acc:HGNC:42444]
SO ACC ID:SO:0000170
Source:EPDNEWNC (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh3836,805,451 - 6,805,511EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC GRM7-AS3 COSMIC
Ensembl Genes ENSG00000226258 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000417482 ENTREZGENE
GTEx ENSG00000226258 GTEx
HGNC ID HGNC:42444 ENTREZGENE
Human Proteome Map GRM7-AS3 Human Proteome Map
NCBI Gene GRM7-AS3 ENTREZGENE
RNAcentral URS000075A0C6 RNACentral
  URS000075D977 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-08-21 GRM7-AS3  GRM7 antisense RNA 3  GRM7-AS3  GRM7 antisense RNA 3 (non-protein coding)  Symbol and/or name change 5135510 APPROVED