LINC01865 (long intergenic non-protein coding RNA 1865) - Rat Genome Database

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Gene: LINC01865 (long intergenic non-protein coding RNA 1865) Homo sapiens
Analyze
Symbol: LINC01865
Name: long intergenic non-protein coding RNA 1865
RGD ID: 11569548
HGNC Page HGNC:52684
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
GRCh382316,284 - 337,054 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2317,823 - 422,312 (+)EnsemblGRCh38hg38GRCh38
GRCh372316,284 - 337,054 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map2p25.3NCBI
CHM1_12313,018 - 335,226 (+)NCBICHM1_1
T2T-CHM13v2.02315,119 - 335,870 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Genomics

Variants

.
Variants in LINC01865
2 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2p25.3-23.2(chr2:30341-28419664)x3 copy number gain See cases [RCV000135398] Chr2:30341..28419664 [GRCh38]
Chr2:30341..28642531 [GRCh37]
Chr2:20341..28496035 [NCBI36]
Chr2:2p25.3-23.2		 pathogenic
GRCh38/hg38 2p25.3(chr2:12770-2748672)x1 copy number loss See cases [RCV000141849] Chr2:12770..2748672 [GRCh38]
Chr2:12770..2752444 [GRCh37]
Chr2:2770..2731451 [NCBI36]
Chr2:2p25.3		 pathogenic
GRCh38/hg38 2p25.3-23.3(chr2:12770-25039694)x3 copy number gain See cases [RCV000141877] Chr2:12770..25039694 [GRCh38]
Chr2:12770..25262563 [GRCh37]
Chr2:2770..25116067 [NCBI36]
Chr2:2p25.3-23.3		 pathogenic
GRCh38/hg38 2p25.3(chr2:30341-3449132)x1 copy number loss See cases [RCV000135536] Chr2:30341..3449132 [GRCh38]
Chr2:30341..3452903 [GRCh37]
Chr2:20341..3431910 [NCBI36]
Chr2:2p25.3		 pathogenic
GRCh38/hg38 2p25.3(chr2:30341-1969402)x1 copy number loss See cases [RCV000135569] Chr2:30341..1969402 [GRCh38]
Chr2:30341..1973174 [GRCh37]
Chr2:20341..1952181 [NCBI36]
Chr2:2p25.3		 pathogenic
GRCh38/hg38 2p25.3(chr2:131730-2713517)x1 copy number loss See cases [RCV000142884] Chr2:131730..2713517 [GRCh38]
Chr2:131730..2717289 [GRCh37]
Chr2:121730..2696296 [NCBI36]
Chr2:2p25.3		 pathogenic
GRCh38/hg38 2p25.3(chr2:30341-429942)x1 copy number loss See cases [RCV000052097] Chr2:30341..429942 [GRCh38]
Chr2:30341..429942 [GRCh37]
Chr2:20341..419942 [NCBI36]
Chr2:2p25.3		 uncertain significance
GRCh38/hg38 2p25.3(chr2:30341-943088)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052098]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052098]|See cases [RCV000052098] Chr2:30341..943088 [GRCh38]
Chr2:30341..938774 [GRCh37]
Chr2:20341..928774 [NCBI36]
Chr2:2p25.3		 uncertain significance
GRCh38/hg38 2p25.3-25.2(chr2:30341-4642399)x3 copy number gain See cases [RCV000142735] Chr2:30341..4642399 [GRCh38]
Chr2:30341..4689989 [GRCh37]
Chr2:20341..4667864 [NCBI36]
Chr2:2p25.3-25.2		 pathogenic
GRCh38/hg38 2p25.3(chr2:39193-1542734)x1 copy number loss See cases [RCV000136750] Chr2:39193..1542734 [GRCh38]
Chr2:39193..1546506 [GRCh37]
Chr2:29193..1525513 [NCBI36]
Chr2:2p25.3		 pathogenic
GRCh38/hg38 2p25.3(chr2:330817-943088)x3 copy number gain See cases [RCV000136975] Chr2:330817..943088 [GRCh38]
Chr2:330817..938774 [GRCh37]
Chr2:320817..928774 [NCBI36]
Chr2:2p25.3		 benign
GRCh38/hg38 2p25.3-21(chr2:236816-45983232)x3 copy number gain See cases [RCV000143682] Chr2:236816..45983232 [GRCh38]
Chr2:236816..46210371 [GRCh37]
Chr2:226816..46063875 [NCBI36]
Chr2:2p25.3-21		 pathogenic
GRCh38/hg38 2p25.3(chr2:12770-4318861)x3 copy number gain See cases [RCV000143781] Chr2:12770..4318861 [GRCh38]
Chr2:12770..4366451 [GRCh37]
Chr2:2770..4344326 [NCBI36]
Chr2:2p25.3		 uncertain significance
GRCh38/hg38 2p25.3-23.3(chr2:17019-26318846)x3 copy number gain See cases [RCV000137344] Chr2:17019..26318846 [GRCh38]
Chr2:17019..26541714 [GRCh37]
Chr2:7019..26395218 [NCBI36]
Chr2:2p25.3-23.3		 pathogenic
GRCh38/hg38 2p25.3(chr2:30341-507042)x3 copy number gain See cases [RCV000148198] Chr2:30341..507042 [GRCh38]
Chr2:30341..507042 [GRCh37]
Chr2:20341..497042 [NCBI36]
Chr2:2p25.3		 pathogenic
GRCh38/hg38 2p25.3-24.3(chr2:30141-14494040)x3 copy number gain See cases [RCV000052928] Chr2:30141..14494040 [GRCh38]
Chr2:30141..14634164 [GRCh37]
Chr2:20141..14551615 [NCBI36]
Chr2:2p25.3-24.3		 pathogenic
GRCh38/hg38 2p25.3-23.1(chr2:30141-31766749)x3 copy number gain See cases [RCV000052929] Chr2:30141..31766749 [GRCh38]
Chr2:30141..31991818 [GRCh37]
Chr2:20141..31845322 [NCBI36]
Chr2:2p25.3-23.1		 pathogenic
GRCh38/hg38 2p25.3(chr2:30341-507042)x3 copy number gain See cases [RCV000052930] Chr2:30341..507042 [GRCh38]
Chr2:30341..507042 [GRCh37]
Chr2:20341..497042 [NCBI36]
Chr2:2p25.3		 pathogenic|uncertain significance|conflicting data from submitters
GRCh38/hg38 2p25.3-24.3(chr2:30342-14866951)x3 copy number gain See cases [RCV000052931] Chr2:30342..14866951 [GRCh38]
Chr2:30342..15007075 [GRCh37]
Chr2:20342..14924526 [NCBI36]
Chr2:2p25.3-24.3		 pathogenic
GRCh38/hg38 2p25.3-25.1(chr2:50661-9652907)x3 copy number gain See cases [RCV000052932] Chr2:50661..9652907 [GRCh38]
Chr2:50661..9793036 [GRCh37]
Chr2:40661..9710487 [NCBI36]
Chr2:2p25.3-25.1		 pathogenic
GRCh38/hg38 2p25.3-16.1(chr2:66097-55570637)x3 copy number gain See cases [RCV000052933] Chr2:66097..55570637 [GRCh38]
Chr2:66097..55797773 [GRCh37]
Chr2:56097..55651277 [NCBI36]
Chr2:2p25.3-16.1		 pathogenic
GRCh38/hg38 2p25.3(chr2:17019-1029157)x1 copy number loss See cases [RCV000137786] Chr2:17019..1029157 [GRCh38]
Chr2:17019..1024843 [GRCh37]
Chr2:7019..1014843 [NCBI36]
Chr2:2p25.3		 uncertain significance
GRCh38/hg38 2p25.3(chr2:17019-1645317)x1 copy number loss See cases [RCV000137954] Chr2:17019..1645317 [GRCh38]
Chr2:17019..1649089 [GRCh37]
Chr2:7019..1628096 [NCBI36]
Chr2:2p25.3		 likely pathogenic
GRCh38/hg38 2p25.3(chr2:17019-774946)x1 copy number loss See cases [RCV000137982] Chr2:17019..774946 [GRCh38]
Chr2:17019..774946 [GRCh37]
Chr2:7019..764946 [NCBI36]
Chr2:2p25.3		 uncertain significance
GRCh38/hg38 2p25.3(chr2:24400-817581)x3 copy number gain See cases [RCV000139175] Chr2:24400..817581 [GRCh38]
Chr2:24400..813454 [GRCh37]
Chr2:14400..803454 [NCBI36]
Chr2:2p25.3		 pathogenic
GRCh38/hg38 2p25.3(chr2:50661-3293835)x1 copy number loss See cases [RCV000053977] Chr2:50661..3293835 [GRCh38]
Chr2:50661..3297606 [GRCh37]
Chr2:40661..3276613 [NCBI36]
Chr2:2p25.3		 pathogenic
GRCh38/hg38 2p25.3(chr2:12770-2310816)x1 copy number loss See cases [RCV000140900] Chr2:12770..2310816 [GRCh38]
Chr2:12770..2314588 [GRCh37]
Chr2:2770..2293595 [NCBI36]
Chr2:2p25.3		 likely pathogenic
GRCh38/hg38 2p25.3-25.2(chr2:17019-4957745)x3 copy number gain See cases [RCV000140981] Chr2:17019..4957745 [GRCh38]
Chr2:17019..5005335 [GRCh37]
Chr2:7019..4983210 [NCBI36]
Chr2:2p25.3-25.2		 likely pathogenic
GRCh38/hg38 2p25.3-25.2(chr2:30341-4932359)x3 copy number gain See cases [RCV000133936] Chr2:30341..4932359 [GRCh38]
Chr2:30341..4979949 [GRCh37]
Chr2:20341..4957824 [NCBI36]
Chr2:2p25.3-25.2		 pathogenic
GRCh38/hg38 2p25.3-24.1(chr2:17019-20001056)x3 copy number gain See cases [RCV000141226] Chr2:17019..20001056 [GRCh38]
Chr2:17019..20200817 [GRCh37]
Chr2:7019..20064298 [NCBI36]
Chr2:2p25.3-24.1		 pathogenic
GRCh38/hg38 2p25.3(chr2:17019-2305267)x1 copy number loss See cases [RCV000141392] Chr2:17019..2305267 [GRCh38]
Chr2:17019..2309039 [GRCh37]
Chr2:7019..2288046 [NCBI36]
Chr2:2p25.3		 pathogenic
GRCh38/hg38 2p25.3(chr2:39193-992648)x1 copy number loss See cases [RCV000141588] Chr2:39193..992648 [GRCh38]
Chr2:39193..988334 [GRCh37]
Chr2:29193..978334 [NCBI36]
Chr2:2p25.3		 uncertain significance
GRCh38/hg38 2p25.3-22.3(chr2:12770-33711509)x3 copy number gain See cases [RCV000141829] Chr2:12770..33711509 [GRCh38]
Chr2:12770..33936576 [GRCh37]
Chr2:2770..33790080 [NCBI36]
Chr2:2p25.3-22.3		 pathogenic
GRCh38/hg38 2p25.3(chr2:330108-1021300)x3 copy number gain See cases [RCV000141841] Chr2:330108..1021300 [GRCh38]
Chr2:330108..1016986 [GRCh37]
Chr2:320108..1006986 [NCBI36]
Chr2:2p25.3		 uncertain significance
GRCh38/hg38 2p25.3(chr2:30341-2656139)x1 copy number loss See cases [RCV000137250] Chr2:30341..2656139 [GRCh38]
Chr2:30341..2659911 [GRCh37]
Chr2:20341..2638918 [NCBI36]
Chr2:2p25.3		 pathogenic|likely benign
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:163
Count of miRNA genes:155
Interacting mature miRNAs:157
Transcripts:ENST00000430529, ENST00000436808
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.


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 1
Low 3 11 2 1 13 1 9 6 97 1 295 14 3 1 2
Below cutoff 673 770 470 122 518 77 1311 363 2487 99 337 454 48 396 906 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000430529
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2317,912 - 336,465 (+)Ensembl
RefSeq Acc Id: ENST00000431911
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2388,412 - 416,885 (+)Ensembl
RefSeq Acc Id: ENST00000436808
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2318,053 - 342,118 (+)Ensembl
RefSeq Acc Id: ENST00000449119
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2421,057 - 422,156 (+)Ensembl
RefSeq Acc Id: ENST00000449621
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2421,133 - 422,303 (+)Ensembl
RefSeq Acc Id: ENST00000715298
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2317,823 - 422,312 (+)Ensembl
RefSeq Acc Id: ENST00000715299
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2317,845 - 376,526 (+)Ensembl
RefSeq Acc Id: ENST00000715300
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2317,898 - 416,954 (+)Ensembl
RefSeq Acc Id: ENST00000715301
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2386,933 - 416,996 (+)Ensembl
RefSeq Acc Id: ENST00000715302
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2386,933 - 416,996 (+)Ensembl
RefSeq Acc Id: ENST00000715303
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2386,947 - 416,996 (+)Ensembl
RefSeq Acc Id: ENST00000715304
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2386,961 - 416,996 (+)Ensembl
RefSeq Acc Id: ENST00000715335
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2386,938 - 416,996 (+)Ensembl
RefSeq Acc Id: ENST00000715336
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2386,970 - 416,996 (+)Ensembl
RefSeq Acc Id: NR_146953
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382316,284 - 337,054 (+)NCBI
T2T-CHM13v2.02315,119 - 335,870 (+)NCBI
Sequence:
Promoters
RGD ID:15095369
Promoter ID:EPDNEWNC_H201
Type:initiation region
Name:LINC01865_1
Description:long intergenic non-protein coding RNA 1865 [Source:HGNCSymbol;Acc:HGNC:52684]
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
GRCh382317,898 - 317,958EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC01865 COSMIC
Ensembl Genes ENSG00000233684 Ensembl
GTEx ENSG00000233684 GTEx
HGNC ID HGNC:52684 ENTREZGENE
Human Proteome Map LINC01865 Human Proteome Map
NCBI Gene LINC01865 ENTREZGENE
RNAcentral URS0000BC4460 RNACentral