LINC00852 (long intergenic non-protein coding RNA 852) - Rat Genome Database

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Advanced Search (OLGA)
Gene: LINC00852 (long intergenic non-protein coding RNA 852) Homo sapiens
Analyze
Symbol: LINC00852
Name: long intergenic non-protein coding RNA 852
RGD ID: 1606766
HGNC Page HGNC:29904
Description: ASSOCIATED WITH Disease Progression; Experimental Neoplasms; Stomach Neoplasms; INTERACTS WITH 17beta-estradiol; 2-hydroxypropanoic acid; cisplatin
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: C3orf42; GHRL-AS2; GHRLOS2; NAG73
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38310,284,419 - 10,285,746 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl310,284,419 - 10,285,746 (+)EnsemblGRCh38hg38GRCh38
GRCh37310,326,103 - 10,327,430 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36310,301,151 - 10,302,430 (+)NCBINCBI36Build 36hg18NCBI36
Celera310,261,911 - 10,263,238 (+)NCBICelera
Cytogenetic Map3p25.3NCBI
HuRef310,261,513 - 10,262,840 (+)NCBIHuRef
CHM1_1310,276,240 - 10,277,567 (+)NCBICHM1_1
T2T-CHM13v2.0310,277,718 - 10,279,045 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
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
Additional References at PubMed
PMID:12477932   PMID:25820252   PMID:32673448   PMID:33128330   PMID:34496800   PMID:35088190   PMID:36471281  


Genomics

Variants

.
Variants in LINC00852
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_001134944.1(GHRL):c.310G>A (p.Asp104Asn) single nucleotide variant Malignant melanoma [RCV000065747] Chr3:10285883 [GRCh38]
Chr3:10327567 [GRCh37]
Chr3:10302567 [NCBI36]
Chr3:3p25.3		 not provided
GRCh38/hg38 3p26.1-25.3(chr3:8038727-11240931)x4 copy number gain See cases [RCV000135641] Chr3:8038727..11240931 [GRCh38]
Chr3:8080414..11282617 [GRCh37]
Chr3:8055414..11257617 [NCBI36]
Chr3:3p26.1-25.3		 likely pathogenic
GRCh38/hg38 3p25.3-25.2(chr3:9394874-11690612)x1 copy number loss See cases [RCV000137433] Chr3:9394874..11690612 [GRCh38]
Chr3:9436558..11732086 [GRCh37]
Chr3:9411558..11707086 [NCBI36]
Chr3:3p25.3-25.2		 pathogenic
GRCh38/hg38 3p26.1-25.2(chr3:7975734-12636917)x3 copy number gain See cases [RCV000137309] Chr3:7975734..12636917 [GRCh38]
Chr3:8017421..12678416 [GRCh37]
Chr3:7992421..12653416 [NCBI36]
Chr3:3p26.1-25.2		 likely 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 3p26.3-24.1(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 3p26.3-24.3(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 3p25.3(chr3:9875909-10572677)x1 copy number loss See cases [RCV000137755] Chr3:9875909..10572677 [GRCh38]
Chr3:9917593..10614361 [GRCh37]
Chr3:9892593..10589361 [NCBI36]
Chr3:3p25.3		 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 3p26.3-25.1(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 3p26.3-22.1(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 3p25.3(chr3:10220962-11165449)x1 copy number loss See cases [RCV000143098] Chr3:10220962..11165449 [GRCh38]
Chr3:10262646..11207135 [GRCh37]
Chr3:10237646..11182135 [NCBI36]
Chr3:3p25.3		 uncertain significance
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 3p26.1-25.1(chr3:7356110-14360442)x3 copy number gain See cases [RCV000143766] Chr3:7356110..14360442 [GRCh38]
Chr3:7397797..14401942 [GRCh37]
Chr3:7372797..14376946 [NCBI36]
Chr3:3p26.1-25.1		 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 3p25.3-25.2(chr3:8581778-12015238)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051480]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051480]|See cases [RCV000051480] Chr3:8581778..12015238 [GRCh38]
Chr3:8623464..12056738 [GRCh37]
Chr3:8598464..12031738 [NCBI36]
Chr3:3p25.3-25.2		 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 3p25.3-25.2(chr3:10019780-12251358)x1 copy number loss See cases [RCV000051506] Chr3:10019780..12251358 [GRCh38]
Chr3:10061464..12292857 [GRCh37]
Chr3:10036464..12267857 [NCBI36]
Chr3:3p25.3-25.2		 pathogenic
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 (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:337
Count of miRNA genes:186
Interacting mature miRNAs:188
Transcripts:ENST00000475197, ENST00000538717
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.


QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
597520015GWAS1616089_Hghrelin measurement QTL GWAS1616089 (human)1e-15blood ghrelin amount (VT:0010695)31028448510284486Human
2316345GLUCO224_HGlucose level QTL 224 (human)1.270.008Glucose level3121543441Human

Markers in Region
SHGC-34896  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37310,327,280 - 10,327,429UniSTSGRCh37
Build 36310,302,280 - 10,302,429RGDNCBI36
Celera310,263,088 - 10,263,237RGD
Cytogenetic Map3p26-p25UniSTS
Cytogenetic Map3p25.3UniSTS
HuRef310,262,690 - 10,262,839UniSTS
GeneMap99-GB4 RH Map349.54UniSTS
Whitehead-RH Map356.8UniSTS
NCBI RH Map3132.9UniSTS
GeneMap99-G3 RH Map38645.0UniSTS
G72349  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37310,327,244 - 10,327,673UniSTSGRCh37
Build 36310,302,244 - 10,302,673RGDNCBI36
Celera310,263,052 - 10,263,481RGD
Cytogenetic Map3p26-p25UniSTS
Cytogenetic Map3p25.3UniSTS
HuRef310,262,654 - 10,263,083UniSTS


Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
entire extraembryonic component
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
1204 2432 2784 2245 4938 1722 2340 4 621 1944 463 2267 7267 6447 52 3705 844 1730 1609 170

Sequence


Ensembl Acc Id: ENST00000475197
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl310,284,419 - 10,285,746 (+)Ensembl
Ensembl Acc Id: ENST00000538717
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl310,284,419 - 10,285,745 (+)Ensembl
RefSeq Acc Id: NR_026829
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38310,284,419 - 10,285,746 (+)NCBI
GRCh37310,326,103 - 10,327,430 (+)RGD
Celera310,261,911 - 10,263,238 (+)RGD
HuRef310,261,513 - 10,262,840 (+)ENTREZGENE
CHM1_1310,276,240 - 10,277,567 (+)NCBI
T2T-CHM13v2.0310,277,718 - 10,279,045 (+)NCBI
Sequence:
Protein Sequences
GenBank Protein AAK15459 (Get FASTA)   NCBI Sequence Viewer  
  EAW64073 (Get FASTA)   NCBI Sequence Viewer  

Promoters
RGD ID:6801119
Promoter ID:HG_KWN:43706
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   HeLa_S3,   K562,   Lymphoblastoid,   NB4
Transcripts:NR_004431,   NR_024144,   NR_024145,   NR_024146,   OTTHUMT00000339647
Position:
Human AssemblyChrPosition (strand)Source
Build 36310,300,976 - 10,301,882 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
COSMIC LINC00852 COSMIC
Ensembl Genes ENSG00000231177 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000475197 ENTREZGENE
GTEx ENSG00000231177 GTEx
HGNC ID HGNC:29904 ENTREZGENE
Human Proteome Map LINC00852 Human Proteome Map
NCBI Gene 84657 ENTREZGENE
PharmGKB PA142672377 PharmGKB
RNAcentral URS00002474BE RNACentral
  URS0000759B4D RNACentral
  URS00008B8F82 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-02-20 LINC00852  long intergenic non-protein coding RNA 852  GHRLOS2  ghrelin opposite strand/antisense RNA 2 (tail to tail)  Symbol and/or name change 5135510 APPROVED
2012-10-23 GHRLOS2  ghrelin opposite strand/antisense RNA 2 (tail to tail)    ghrelin opposite strand RNA 2 (non-protein coding)  Symbol and/or name change 5135510 APPROVED
2011-07-27 GHRLOS2  ghrelin opposite strand RNA 2 (non-protein coding)  C3orf42  chromosome 3 open reading frame 42  Symbol and/or name change 5135510 APPROVED