LINC02244 (long intergenic non-protein coding RNA 2244) - Rat Genome Database

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Gene: LINC02244 (long intergenic non-protein coding RNA 2244) Homo sapiens
Analyze
Symbol: LINC02244
Name: long intergenic non-protein coding RNA 2244
RGD ID: 13702999
HGNC Page HGNC:53929
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
GRCh381599,394,650 - 99,402,418 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1599,395,179 - 99,396,593 (-)EnsemblGRCh38hg38GRCh38
Cytogenetic Map15q26.3NCBI
CHM1_11599,775,824 - 99,783,970 (-)NCBICHM1_1
T2T-CHM13v2.01597,158,442 - 97,166,210 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:29884798  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 15q26.2-26.3(chr15:96913979-101843411)x1 copy number loss See cases [RCV000053245] Chr15:96913979..101843411 [GRCh38]
Chr15:97457209..102383614 [GRCh37]
Chr15:95258213..100201137 [NCBI36]
Chr15:15q26.2-26.3		 pathogenic
GRCh38/hg38 15q26.3(chr15:99299033-99997136)x1 copy number loss See cases [RCV000137279] Chr15:99299033..99997136 [GRCh38]
Chr15:99839238..100537341 [GRCh37]
Chr15:97656761..98354864 [NCBI36]
Chr15:15q26.3		 likely benign
GRCh38/hg38 15q26.2-26.3(chr15:97941427-101797926)x1 copy number loss See cases [RCV000139666] Chr15:97941427..101797926 [GRCh38]
Chr15:98484657..102338129 [GRCh37]
Chr15:96285661..100155652 [NCBI36]
Chr15:15q26.2-26.3		 pathogenic
GRCh38/hg38 15q26.2-26.3(chr15:97283711-101920998)x3 copy number gain See cases [RCV000140658] Chr15:97283711..101920998 [GRCh38]
Chr15:97826941..102461201 [GRCh37]
Chr15:95627945..100278724 [NCBI36]
Chr15:15q26.2-26.3		 likely pathogenic
GRCh38/hg38 15q26.2-26.3(chr15:97681713-101920998)x1 copy number loss See cases [RCV000143176] Chr15:97681713..101920998 [GRCh38]
Chr15:98224943..102461201 [GRCh37]
Chr15:96025947..100278724 [NCBI36]
Chr15:15q26.2-26.3		 pathogenic
GRCh38/hg38 15q26.3(chr15:98845807-101843270)x1 copy number loss See cases [RCV000053247] Chr15:98845807..101843270 [GRCh38]
Chr15:99389036..102383473 [GRCh37]
Chr15:97206559..100200996 [NCBI36]
Chr15:15q26.3		 pathogenic
GRCh38/hg38 15q26.3(chr15:98976591-99456909)x4 copy number gain See cases [RCV000136607] Chr15:98976591..99456909 [GRCh38]
Chr15:99519820..99997114 [GRCh37]
Chr15:97337343..97814637 [NCBI36]
Chr15:15q26.3		 uncertain significance
GRCh38/hg38 15q26.2-26.3(chr15:97783828-100780256)x3 copy number gain See cases [RCV000137352] Chr15:97783828..100780256 [GRCh38]
Chr15:98327058..101320461 [GRCh37]
Chr15:96128062..99137984 [NCBI36]
Chr15:15q26.2-26.3		 likely pathogenic
GRCh38/hg38 15q26.3(chr15:99338283-101843270)x3 copy number gain See cases [RCV000142579] Chr15:99338283..101843270 [GRCh38]
Chr15:99878488..102383473 [GRCh37]
Chr15:97696011..100200996 [NCBI36]
Chr15:15q26.3		 pathogenic
GRCh38/hg38 15q26.3(chr15:98280297-101888909)x3 copy number gain See cases [RCV000143526] Chr15:98280297..101888909 [GRCh38]
Chr15:98823526..102429112 [GRCh37]
Chr15:96641049..100246635 [NCBI36]
Chr15:15q26.3		 pathogenic
GRCh38/hg38 15q26.2-26.3(chr15:97172754-101920998)x1 copy number loss See cases [RCV000141263] Chr15:97172754..101920998 [GRCh38]
Chr15:97715984..102461201 [GRCh37]
Chr15:95516988..100278724 [NCBI36]
Chr15:15q26.2-26.3		 pathogenic
GRCh38/hg38 15q26.3(chr15:99155987-101843270)x1 copy number loss See cases [RCV000134969] Chr15:99155987..101843270 [GRCh38]
Chr15:99696192..102383473 [GRCh37]
Chr15:97513715..100200996 [NCBI36]
Chr15:15q26.3		 pathogenic
GRCh38/hg38 15q26.2-26.3(chr15:97014065-101843270)x1 copy number loss See cases [RCV000135397] Chr15:97014065..101843270 [GRCh38]
Chr15:97557295..102383473 [GRCh37]
Chr15:95358299..100200996 [NCBI36]
Chr15:15q26.2-26.3		 pathogenic
GRCh38/hg38 15q26.2-26.3(chr15:96329791-101849578)x1 copy number loss See cases [RCV000053244] Chr15:96329791..101849578 [GRCh38]
Chr15:96873020..102389781 [GRCh37]
Chr15:94674024..100207304 [NCBI36]
Chr15:15q26.2-26.3		 pathogenic
GRCh38/hg38 15q26.1-26.3(chr15:93041524-101941326)x3 copy number gain See cases [RCV000141431] Chr15:93041524..101941326 [GRCh38]
Chr15:93584754..102481529 [GRCh37]
Chr15:91385758..100299052 [NCBI36]
Chr15:15q26.1-26.3		 pathogenic
GRCh38/hg38 15q22.2-26.3(chr15:59828460-101920998)x3 copy number gain See cases [RCV000142915] Chr15:59828460..101920998 [GRCh38]
Chr15:60120659..102461201 [GRCh37]
Chr15:57907951..100278724 [NCBI36]
Chr15:15q22.2-26.3		 pathogenic
GRCh38/hg38 15q23-26.3(chr15:72154949-101920998)x3 copy number gain See cases [RCV000143019] Chr15:72154949..101920998 [GRCh38]
Chr15:72447290..102461201 [GRCh37]
Chr15:70234344..100278724 [NCBI36]
Chr15:15q23-26.3		 pathogenic
GRCh38/hg38 15q26.2-26.3(chr15:96024127-101920998)x1 copy number loss See cases [RCV000143088] Chr15:96024127..101920998 [GRCh38]
Chr15:96567356..102461201 [GRCh37]
Chr15:94368360..100278724 [NCBI36]
Chr15:15q26.2-26.3		 pathogenic
GRCh38/hg38 15q25.3-26.3(chr15:87904735-101843270)x3 copy number gain See cases [RCV000135568] Chr15:87904735..101843270 [GRCh38]
Chr15:88447966..102383473 [GRCh37]
Chr15:86248970..100200996 [NCBI36]
Chr15:15q25.3-26.3		 pathogenic
GRCh38/hg38 15q25.2-26.3(chr15:83711377-101843270)x3 copy number gain See cases [RCV000135858] Chr15:83711377..101843270 [GRCh38]
Chr15:84380129..102383473 [GRCh37]
Chr15:82171133..100200996 [NCBI36]
Chr15:15q25.2-26.3		 pathogenic
GRCh38/hg38 15q25.2-26.3(chr15:82859676-101810992)x3 copy number gain See cases [RCV000136849] Chr15:82859676..101810992 [GRCh38]
Chr15:83528428..102351195 [GRCh37]
Chr15:81325482..100168718 [NCBI36]
Chr15:15q25.2-26.3		 pathogenic
GRCh38/hg38 15q26.2-26.3(chr15:95770627-101810992)x1 copy number loss See cases [RCV000136864] Chr15:95770627..101810992 [GRCh38]
Chr15:96313856..102351195 [GRCh37]
Chr15:94114860..100168718 [NCBI36]
Chr15:15q26.2-26.3		 pathogenic
GRCh38/hg38 15q26.3(chr15:98976591-99598500)x3 copy number gain See cases [RCV000138661] Chr15:98976591..99598500 [GRCh38]
Chr15:99519820..100138705 [GRCh37]
Chr15:97337343..97956228 [NCBI36]
Chr15:15q26.3		 uncertain significance
GRCh38/hg38 15q26.3(chr15:98467297-101843270)x1 copy number loss See cases [RCV000142728] Chr15:98467297..101843270 [GRCh38]
Chr15:99010526..102383473 [GRCh37]
Chr15:96828049..100200996 [NCBI36]
Chr15:15q26.3		 pathogenic
GRCh38/hg38 15q26.2-26.3(chr15:97735430-101810992)x1 copy number loss See cases [RCV000053246] Chr15:97735430..101810992 [GRCh38]
Chr15:98278660..102351195 [GRCh37]
Chr15:96079664..100168718 [NCBI36]
Chr15:15q26.2-26.3		 pathogenic
GRCh38/hg38 15q26.2-26.3(chr15:94033008-101843270)x3 copy number gain See cases [RCV000050851] Chr15:94033008..101843270 [GRCh38]
Chr15:94576237..102383473 [GRCh37]
Chr15:92377241..100200996 [NCBI36]
Chr15:15q26.2-26.3		 pathogenic
GRCh38/hg38 15q25.2-26.3(chr15:84169153-101904929)x3 copy number gain See cases [RCV000052352] Chr15:84169153..101904929 [GRCh38]
Chr15:84837905..102445132 [GRCh37]
Chr15:82628909..100262655 [NCBI36]
Chr15:15q25.2-26.3		 pathogenic
GRCh38/hg38 15q26.1-26.3(chr15:89679237-101978958)x3 copy number gain See cases [RCV000052354] Chr15:89679237..101978958 [GRCh38]
Chr15:90222468..102519161 [GRCh37]
Chr15:88023472..100336684 [NCBI36]
Chr15:15q26.1-26.3		 pathogenic
GRCh38/hg38 15q26.2-26.3(chr15:96069425-101849578)x1 copy number loss See cases [RCV000053228] Chr15:96069425..101849578 [GRCh38]
Chr15:96612654..102389781 [GRCh37]
Chr15:94413658..100207304 [NCBI36]
Chr15:15q26.2-26.3		 pathogenic
GRCh38/hg38 15q25.3-26.3(chr15:85826665-101920998)x4 copy number gain See cases [RCV000137264] Chr15:85826665..101920998 [GRCh38]
Chr15:86369896..102461201 [GRCh37]
Chr15:84170900..100278724 [NCBI36]
Chr15:15q25.3-26.3		 pathogenic
GRCh38/hg38 15q26.3(chr15:99057691-99598500)x3 copy number gain See cases [RCV000137362] Chr15:99057691..99598500 [GRCh38]
Chr15:99621061..100138705 [GRCh37]
Chr15:97418443..97956228 [NCBI36]
Chr15:15q26.3		 likely benign
GRCh38/hg38 15q26.2-26.3(chr15:93805032-101326876)x1 copy number loss See cases [RCV000143687] Chr15:93805032..101326876 [GRCh38]
Chr15:94348261..101867081 [GRCh37]
Chr15:92149265..99684604 [NCBI36]
Chr15:15q26.2-26.3		 pathogenic
GRCh38/hg38 15q24.3-26.3(chr15:77543797-101843411)x3 copy number gain See cases [RCV000052347] Chr15:77543797..101843411 [GRCh38]
Chr15:77836139..102383614 [GRCh37]
Chr15:75623194..100201137 [NCBI36]
Chr15:15q24.3-26.3		 pathogenic
GRCh38/hg38 15q26.1-26.3(chr15:93198717-101843270)x1 copy number loss See cases [RCV000133733] Chr15:93198717..101843270 [GRCh38]
Chr15:93741946..102383473 [GRCh37]
Chr15:91542950..100200996 [NCBI36]
Chr15:15q26.1-26.3		 pathogenic
GRCh38/hg38 15q26.3(chr15:99248720-99456850)x1 copy number loss See cases [RCV000134436] Chr15:99248720..99456850 [GRCh38]
Chr15:99788925..99997055 [GRCh37]
Chr15:97606448..97814578 [NCBI36]
Chr15:15q26.3		 uncertain significance
GRCh38/hg38 15q25.3-26.3(chr15:85397539-101888909)x3 copy number gain See cases [RCV000141899] Chr15:85397539..101888909 [GRCh38]
Chr15:85940770..102429112 [GRCh37]
Chr15:83741774..100246635 [NCBI36]
Chr15:15q25.3-26.3		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:31
Count of miRNA genes:31
Interacting mature miRNAs:31
Transcripts:ENST00000561362
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 2 1 2 2 2 2 14 8 15 25 14
Low 290 296 199 95 297 83 877 98 593 225 249 531 13 518 384
Below cutoff 1285 1062 647 196 428 125 1789 1039 1796 114 608 522 73 437 1193 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000561362
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1599,395,179 - 99,396,593 (-)Ensembl
RefSeq Acc Id: NR_187226
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381599,394,650 - 99,402,418 (-)NCBI
T2T-CHM13v2.01597,158,442 - 97,166,210 (-)NCBI

Additional Information

Database Acc Id Source(s)
COSMIC LINC02244 COSMIC
Ensembl Genes ENSG00000259590 Ensembl
GTEx ENSG00000259590 GTEx
HGNC ID HGNC:53929 ENTREZGENE
Human Proteome Map LINC02244 Human Proteome Map
NCBI Gene LINC02244 ENTREZGENE
RNAcentral URS00026A1E80 RNACentral