LINC02860 (long intergenic non-protein coding RNA 2860) - Rat Genome Database

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Advanced Search (OLGA)
Gene: LINC02860 (long intergenic non-protein coding RNA 2860) Homo sapiens
Analyze
Symbol: LINC02860
Name: long intergenic non-protein coding RNA 2860
RGD ID: 3030166
HGNC Page HGNC:22364
Description: ASSOCIATED WITH Pleomorphic xanthoastrocytoma; pleomorphic xanthoastrocytoma; INTERACTS WITH benzo[a]pyrene; bisphenol A; cyclosporin A
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: C7orf71; chromosome 7 open reading frame 71; hypothetical protein LOC285941; putative uncharacterized protein C7orf71; uncharacterized protein LOC285941
RGD Orthologs
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38726,637,871 - 26,647,272 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl726,637,865 - 26,647,305 (+)EnsemblGRCh38hg38GRCh38
GRCh37726,677,490 - 26,686,891 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36726,644,015 - 26,653,493 (+)NCBINCBI36Build 36hg18NCBI36
Celera726,666,461 - 26,675,896 (+)NCBICelera
Cytogenetic Map7p15.2NCBI
HuRef726,558,639 - 26,567,887 (+)NCBIHuRef
CHM1_1726,677,210 - 26,686,642 (+)NCBICHM1_1
T2T-CHM13v2.0726,773,589 - 26,782,993 (+)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2726,728,678 - 26,738,112 (+)NCBI
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
Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References
Additional References at PubMed
PMID:12107410   PMID:12477932   PMID:12690205   PMID:14702039   PMID:24684796  


Genomics

Comparative Map Data
LINC02860
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38726,637,871 - 26,647,272 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl726,637,865 - 26,647,305 (+)EnsemblGRCh38hg38GRCh38
GRCh37726,677,490 - 26,686,891 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36726,644,015 - 26,653,493 (+)NCBINCBI36Build 36hg18NCBI36
Celera726,666,461 - 26,675,896 (+)NCBICelera
Cytogenetic Map7p15.2NCBI
HuRef726,558,639 - 26,567,887 (+)NCBIHuRef
CHM1_1726,677,210 - 26,686,642 (+)NCBICHM1_1
T2T-CHM13v2.0726,773,589 - 26,782,993 (+)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2726,728,678 - 26,738,112 (+)NCBI
LINC02860
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11845,811,294 - 45,812,778 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
LINC02860
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12131,718,559 - 31,726,462 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604273,007,805 - 73,014,990 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in LINC02860
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 7p22.3-14.1(chr7:54185-41875885)x3 copy number gain See cases [RCV000051159] Chr7:54185..41875885 [GRCh38]
Chr7:54185..41915483 [GRCh37]
Chr7:149268..41882008 [NCBI36]
Chr7:7p22.3-14.1		 pathogenic
GRCh38/hg38 7p15.2-14.3(chr7:25511691-30421133)x1 copy number loss See cases [RCV000052310] Chr7:25511691..30421133 [GRCh38]
Chr7:25551310..30460749 [GRCh37]
Chr7:25517835..30427274 [NCBI36]
Chr7:7p15.2-14.3		 pathogenic
GRCh38/hg38 7p22.3-q36.3(chr7:53985-159282531)x1 copy number loss See cases [RCV000052250] Chr7:53985..159282531 [GRCh38]
Chr7:53985..159075220 [GRCh37]
Chr7:149068..158767981 [NCBI36]
Chr7:7p22.3-q36.3		 pathogenic
GRCh38/hg38 7p22.3-14.2(chr7:54185-37089712)x3 copy number gain See cases [RCV000053530] Chr7:54185..37089712 [GRCh38]
Chr7:54185..37129317 [GRCh37]
Chr7:149268..37095842 [NCBI36]
Chr7:7p22.3-14.2		 pathogenic
GRCh38/hg38 7p21.1-15.2(chr7:20210912-27849400)x1 copy number loss See cases [RCV000134333] Chr7:20210912..27849400 [GRCh38]
Chr7:20250535..27889019 [GRCh37]
Chr7:20217060..27855544 [NCBI36]
Chr7:7p21.1-15.2		 pathogenic
GRCh38/hg38 7p22.3-q36.3(chr7:54185-159282390)x1 copy number loss See cases [RCV000135401] Chr7:54185..159282390 [GRCh38]
Chr7:54185..159075079 [GRCh37]
Chr7:149268..158767840 [NCBI36]
Chr7:7p22.3-q36.3		 pathogenic
GRCh38/hg38 7p22.3-15.2(chr7:54185-26827634)x3 copy number gain See cases [RCV000136557] Chr7:54185..26827634 [GRCh38]
Chr7:54185..26867253 [GRCh37]
Chr7:149268..26833778 [NCBI36]
Chr7:7p22.3-15.2		 pathogenic
GRCh38/hg38 7p21.1-14.3(chr7:20561456-32005143)x1 copy number loss See cases [RCV000136775] Chr7:20561456..32005143 [GRCh38]
Chr7:20601079..32044755 [GRCh37]
Chr7:20567604..32011280 [NCBI36]
Chr7:7p21.1-14.3		 pathogenic
GRCh38/hg38 7p22.1-15.2(chr7:5682209-27230311)x3 copy number gain See cases [RCV000136649] Chr7:5682209..27230311 [GRCh38]
Chr7:5721840..27269930 [GRCh37]
Chr7:5688366..27236455 [NCBI36]
Chr7:7p22.1-15.2		 pathogenic
GRCh38/hg38 7p15.2(chr7:25903388-27022498)x1 copy number loss See cases [RCV000140657] Chr7:25903388..27022498 [GRCh38]
Chr7:25943008..27062117 [GRCh37]
Chr7:25909533..27028642 [NCBI36]
Chr7:7p15.2		 likely pathogenic
GRCh38/hg38 7p22.3-15.2(chr7:1698124-27207295)x3 copy number gain See cases [RCV000143060] Chr7:1698124..27207295 [GRCh38]
Chr7:1737760..27246914 [GRCh37]
Chr7:1704286..27213439 [NCBI36]
Chr7:7p22.3-15.2		 pathogenic
GRCh38/hg38 7p22.3-15.2(chr7:43360-27196404)x3 copy number gain See cases [RCV000143586] Chr7:43360..27196404 [GRCh38]
Chr7:43360..27236023 [GRCh37]
Chr7:138443..27202548 [NCBI36]
Chr7:7p22.3-15.2		 pathogenic
GRCh37/hg19 7p15.3-14.3(chr7:22935369-32621975)x1 copy number loss See cases [RCV000240125] Chr7:22935369..32621975 [GRCh37]
Chr7:7p15.3-14.3		 pathogenic
TMEM106B-BRAF fusion deletion Pleomorphic xanthoastrocytoma [RCV000454357] Chr7:12258147..140494267 [GRCh37]
Chr7:7p21.3-q34		 pathogenic
GRCh37/hg19 7p21.3-14.2(chr7:11562624-36395416)x3 copy number gain See cases [RCV000446478] Chr7:11562624..36395416 [GRCh37]
Chr7:7p21.3-14.2		 pathogenic
GRCh37/hg19 7p22.3-q36.3(chr7:43360-159119707)x1 copy number loss See cases [RCV000446044] Chr7:43360..159119707 [GRCh37]
Chr7:7p22.3-q36.3		 pathogenic
GRCh37/hg19 7p15.3-15.2(chr7:25448425-27578387)x3 copy number gain See cases [RCV000447735] Chr7:25448425..27578387 [GRCh37]
Chr7:7p15.3-15.2		 likely pathogenic
GRCh37/hg19 7p21.3-12.1(chr7:11048840-52863626)x3 copy number gain See cases [RCV000512091] Chr7:11048840..52863626 [GRCh37]
Chr7:7p21.3-12.1		 pathogenic
GRCh37/hg19 7p22.3-q36.3(chr7:43361-159119707) copy number gain See cases [RCV000510686] Chr7:43361..159119707 [GRCh37]
Chr7:7p22.3-q36.3		 pathogenic
GRCh37/hg19 7p22.3-14.3(chr7:704573-29257946)x3 copy number gain See cases [RCV000510275] Chr7:704573..29257946 [GRCh37]
Chr7:7p22.3-14.3		 pathogenic
GRCh37/hg19 7p15.3-14.3(chr7:24344104-28879357)x1 copy number loss See cases [RCV000510695] Chr7:24344104..28879357 [GRCh37]
Chr7:7p15.3-14.3		 pathogenic
GRCh37/hg19 7p22.3-q36.3(chr7:43361-159119707)x3 copy number gain See cases [RCV000511549] Chr7:43361..159119707 [GRCh37]
Chr7:7p22.3-q36.3		 pathogenic
NC_000007.13:g.(20954043_21001537)_(114528369_114556605)inv inversion Childhood apraxia of speech [RCV000234948] Chr7:21001537..114528369 [GRCh37]
Chr7:7p15.3-q31.1		 pathogenic
GRCh37/hg19 7p22.3-q36.3(chr7:44935-159126310)x3 copy number gain not provided [RCV000746280] Chr7:44935..159126310 [GRCh37]
Chr7:7p22.3-q36.3		 pathogenic
GRCh37/hg19 7p22.3-q36.3(chr7:10704-159122532)x3 copy number gain not provided [RCV000746278] Chr7:10704..159122532 [GRCh37]
Chr7:7p22.3-q36.3		 pathogenic
GRCh37/hg19 7p22.3-q36.3(chr7:10365-159119707)x3 copy number gain not provided [RCV000848126] Chr7:10365..159119707 [GRCh37]
Chr7:7p22.3-q36.3		 pathogenic
GRCh37/hg19 7p15.3-14.3(chr7:23877135-33139446)x1 copy number loss not provided [RCV001005924] Chr7:23877135..33139446 [GRCh37]
Chr7:7p15.3-14.3		 pathogenic
NC_000007.13:g.23236782_30690453del7453672 deletion Silver Russell Syndrome-related disorder [RCV000785664] Chr7:23236782..30690453 [GRCh37]
Chr7:7p15.3-14.3		 pathogenic
GRCh37/hg19 7p21.3-14.2(chr7:10745750-35305167) copy number gain not specified [RCV002053668] Chr7:10745750..35305167 [GRCh37]
Chr7:7p21.3-14.2		 likely pathogenic
GRCh37/hg19 7p15.2(chr7:26270121-27193008) copy number gain not specified [RCV002053676] Chr7:26270121..27193008 [GRCh37]
Chr7:7p15.2		 uncertain significance
Single allele complex Ring chromosome 7 [RCV002280646] Chr7:43360..159119707 [GRCh37]
Chr7:7p22.3-q36.3		 pathogenic
GRCh37/hg19 7p22.3-q36.3(chr7:56604613-96692931)x1 copy number loss See cases [RCV002287832] Chr7:56604613..96692931 [GRCh37]
Chr7:7p22.3-q36.3		 uncertain significance
GRCh37/hg19 7p15.3-14.3(chr7:25451740-33864069) copy number loss Cyclical vomiting syndrome [RCV002280775] Chr7:25451740..33864069 [GRCh37]
Chr7:7p15.3-14.3		 pathogenic
GRCh37/hg19 7p15.2-15.1(chr7:26418391-28323299)x3 copy number gain not provided [RCV002474593] Chr7:26418391..28323299 [GRCh37]
Chr7:7p15.2-15.1		 uncertain significance
GRCh37/hg19 7p21.1-14.3(chr7:17736012-30663423)x1 copy number loss not specified [RCV003986712] Chr7:17736012..30663423 [GRCh37]
Chr7:7p21.1-14.3		 pathogenic
GRCh37/hg19 7p21.3-15.2(chr7:13107394-27514163)x1 copy number loss not specified [RCV003986690] Chr7:13107394..27514163 [GRCh37]
Chr7:7p21.3-15.2		 pathogenic
NR_161201.1(LINC02860):n.1210C>T single nucleotide variant not specified [RCV004415329] Chr7:26646524 [GRCh38]
Chr7:26686143 [GRCh37]
Chr7:7p15.2		 uncertain significance
NC_000007.13:g.(?_26232136)_(28172587_?)del deletion not provided [RCV004583626] Chr7:26232136..28172587 [GRCh37]
Chr7:7p15.2-15.1		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:250
Count of miRNA genes:228
Interacting mature miRNAs:237
Transcripts:ENST00000409974
Prediction methods: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
2289453BW297_HBody weight QTL 297 (human)3.83Body weightbody mass index72334946449349464Human

Markers in Region
STS-N29318  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37726,686,682 - 26,686,874UniSTSGRCh37
Build 36726,653,207 - 26,653,399RGDNCBI36
Celera726,675,654 - 26,675,846RGD
Cytogenetic Map7p15.2UniSTS
HuRef726,567,645 - 26,567,837UniSTS
CRA_TCAGchr7v2726,737,870 - 26,738,062UniSTS
GeneMap99-GB4 RH Map7113.81UniSTS
NCBI RH Map7415.5UniSTS


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
864 1786 1349 847 2434 901 1265 3 231 1164 152 1388 3475 3680 9 1650 453 1089 949 82

Sequence


Ensembl Acc Id: ENST00000409974
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl726,637,871 - 26,647,270 (+)Ensembl
Ensembl Acc Id: ENST00000614528
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl726,638,457 - 26,647,305 (+)Ensembl
Ensembl Acc Id: ENST00000719426
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl726,637,865 - 26,646,916 (+)Ensembl
Ensembl Acc Id: ENST00000719427
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl726,638,358 - 26,647,274 (+)Ensembl
Ensembl Acc Id: ENST00000719428
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl726,638,356 - 26,647,272 (+)Ensembl
Ensembl Acc Id: ENST00000719429
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl726,638,365 - 26,647,272 (+)Ensembl
Ensembl Acc Id: ENST00000719430
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl726,638,356 - 26,639,371 (+)Ensembl
Ensembl Acc Id: ENST00000719431
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl726,638,358 - 26,639,371 (+)Ensembl
RefSeq Acc Id: NR_161201
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38726,637,871 - 26,647,272 (+)NCBI
T2T-CHM13v2.0726,773,589 - 26,782,993 (+)NCBI
Sequence:
RefSeq Acc Id: NR_161202
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38726,637,871 - 26,647,272 (+)NCBI
T2T-CHM13v2.0726,773,589 - 26,782,993 (+)NCBI
Sequence:
Protein Sequences
GenBank Protein EAL24232 (Get FASTA)   NCBI Sequence Viewer  

Promoters
RGD ID:6805345
Promoter ID:HG_KWN:56651
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:K562
Transcripts:NM_001145531
Position:
Human AssemblyChrPosition (strand)Source
Build 36726,644,146 - 26,644,646 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
COSMIC LINC02860 COSMIC
Ensembl Genes ENSG00000222004 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000409974 ENTREZGENE
GTEx ENSG00000222004 GTEx
HGNC ID HGNC:22364 ENTREZGENE
Human Proteome Map LINC02860 Human Proteome Map
NCBI Gene 285941 ENTREZGENE
RNAcentral URS0000E60AC8 RNACentral
  URS0000E60B38 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-07-09 LINC02860  long intergenic non-protein coding RNA 2860  C7orf71  chromosome 7 open reading frame 71  Symbol and/or name change 5135510 APPROVED