LINC02146 (long intergenic non-protein coding RNA 2146) - Rat Genome Database

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Gene: LINC02146 (long intergenic non-protein coding RNA 2146) Homo sapiens
Analyze
Symbol: LINC02146
Name: long intergenic non-protein coding RNA 2146
RGD ID: 11576927
HGNC Page HGNC:53006
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
GRCh38520,612,625 - 20,615,535 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl520,606,710 - 20,616,441 (-)EnsemblGRCh38hg38GRCh38
GRCh37520,612,734 - 20,615,644 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map5p14.3NCBI
CHM1_1520,607,467 - 20,616,333 (-)NCBICHM1_1
T2T-CHM13v2.0520,614,730 - 20,617,640 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 5p14.3(chr5:19857388-20747378)x3 copy number gain See cases [RCV000051703] Chr5:19857388..20747378 [GRCh38]
Chr5:19857497..20747487 [GRCh37]
Chr5:19893254..20783244 [NCBI36]
Chr5:5p14.3		 uncertain significance
GRCh38/hg38 5p15.33-12(chr5:54839-45649861)x3 copy number gain See cases [RCV000051810] Chr5:54839..45649861 [GRCh38]
Chr5:54954..45649963 [GRCh37]
Chr5:107954..45685720 [NCBI36]
Chr5:5p15.33-12		 pathogenic
GRCh38/hg38 5p15.33-13.2(chr5:54839-35680845)x3 copy number gain See cases [RCV000051811] Chr5:54839..35680845 [GRCh38]
Chr5:54954..35680947 [GRCh37]
Chr5:107954..35716704 [NCBI36]
Chr5:5p15.33-13.2		 pathogenic
GRCh38/hg38 5p15.33-14.3(chr5:22149-23132046)x1 copy number loss See cases [RCV000053398] Chr5:22149..23132046 [GRCh38]
Chr5:22149..23132155 [GRCh37]
Chr5:75149..23167912 [NCBI36]
Chr5:5p15.33-14.3		 pathogenic
GRCh38/hg38 5p15.33-14.1(chr5:547757-26541238)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053445]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053445]|See cases [RCV000053445] Chr5:547757..26541238 [GRCh38]
Chr5:547872..26541347 [GRCh37]
Chr5:600872..26577104 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic
GRCh38/hg38 5p15.33-14.1(chr5:22149-25699605)x1 copy number loss See cases [RCV000133768] Chr5:22149..25699605 [GRCh38]
Chr5:22149..25699714 [GRCh37]
Chr5:75149..25735471 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic
GRCh38/hg38 5p15.33-13.3(chr5:22149-33418188)x3 copy number gain See cases [RCV000133788] Chr5:22149..33418188 [GRCh38]
Chr5:22149..33418294 [GRCh37]
Chr5:75149..33454051 [NCBI36]
Chr5:5p15.33-13.3		 pathogenic
GRCh38/hg38 5p15.33-14.1(chr5:22149-27788616)x1 copy number loss See cases [RCV000134873] Chr5:22149..27788616 [GRCh38]
Chr5:22149..27788723 [GRCh37]
Chr5:75149..27824480 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic
GRCh38/hg38 5p15.33-11(chr5:49978-46114984)x3 copy number gain See cases [RCV000135453] Chr5:49978..46114984 [GRCh38]
Chr5:50093..46115086 [GRCh37]
Chr5:103093..46150843 [NCBI36]
Chr5:5p15.33-11		 pathogenic
GRCh38/hg38 5p15.33-13.3(chr5:22149-32248010)x1 copy number loss See cases [RCV000135668] Chr5:22149..32248010 [GRCh38]
Chr5:22149..32248116 [GRCh37]
Chr5:75149..32283873 [NCBI36]
Chr5:5p15.33-13.3		 pathogenic
GRCh38/hg38 5p15.33-13.3(chr5:49978-30112535)x1 copy number loss See cases [RCV000135878] Chr5:49978..30112535 [GRCh38]
Chr5:50093..30112642 [GRCh37]
Chr5:103093..30148399 [NCBI36]
Chr5:5p15.33-13.3		 pathogenic
GRCh38/hg38 5p15.33-14.1(chr5:22149-27485619)x1 copy number loss See cases [RCV000137072] Chr5:22149..27485619 [GRCh38]
Chr5:22149..27485726 [GRCh37]
Chr5:75149..27521483 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic
GRCh38/hg38 5p15.33-14.1(chr5:22149-28429241)x1 copy number loss See cases [RCV000137165] Chr5:22149..28429241 [GRCh38]
Chr5:22149..28429348 [GRCh37]
Chr5:75149..28465105 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic
GRCh38/hg38 5p15.33-14.2(chr5:22149-23607053)x3 copy number gain See cases [RCV000137806] Chr5:22149..23607053 [GRCh38]
Chr5:22149..23607162 [GRCh37]
Chr5:75149..23642919 [NCBI36]
Chr5:5p15.33-14.2		 pathogenic
GRCh38/hg38 5p15.33-14.1(chr5:22149-27187950)x1 copy number loss See cases [RCV000138099] Chr5:22149..27187950 [GRCh38]
Chr5:22149..27188057 [GRCh37]
Chr5:75149..27223814 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic
GRCh38/hg38 5p15.33-14.3(chr5:22149-22775295)x1 copy number loss See cases [RCV000138116] Chr5:22149..22775295 [GRCh38]
Chr5:22149..22775404 [GRCh37]
Chr5:75149..22811161 [NCBI36]
Chr5:5p15.33-14.3		 pathogenic
GRCh38/hg38 5p15.33-14.3(chr5:22149-21217120)x1 copy number loss See cases [RCV000138553] Chr5:22149..21217120 [GRCh38]
Chr5:22149..21217229 [GRCh37]
Chr5:75149..21252986 [NCBI36]
Chr5:5p15.33-14.3		 pathogenic
GRCh38/hg38 5p15.33-q13.3(chr5:22149-74412725)x3 copy number gain See cases [RCV000138780] Chr5:22149..74412725 [GRCh38]
Chr5:22149..73708550 [GRCh37]
Chr5:75149..73744306 [NCBI36]
Chr5:5p15.33-q13.3		 pathogenic
GRCh38/hg38 5p15.33-13.2(chr5:22149-35831538)x1 copy number loss See cases [RCV000138888] Chr5:22149..35831538 [GRCh38]
Chr5:22149..35831640 [GRCh37]
Chr5:75149..35867397 [NCBI36]
Chr5:5p15.33-13.2		 pathogenic
GRCh38/hg38 5p15.33-14.1(chr5:22149-28589192)x1 copy number loss See cases [RCV000141225] Chr5:22149..28589192 [GRCh38]
Chr5:22149..28589299 [GRCh37]
Chr5:75149..28625056 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic
GRCh38/hg38 5p15.32-13.2(chr5:4849498-36818719)x3 copy number gain See cases [RCV000141246] Chr5:4849498..36818719 [GRCh38]
Chr5:4849611..36818821 [GRCh37]
Chr5:4902611..36854578 [NCBI36]
Chr5:5p15.32-13.2		 pathogenic
GRCh38/hg38 5p14.3(chr5:20474639-20673991)x1 copy number loss See cases [RCV000141498] Chr5:20474639..20673991 [GRCh38]
Chr5:20474748..20674100 [GRCh37]
Chr5:20510505..20709857 [NCBI36]
Chr5:5p14.3		 benign
GRCh38/hg38 5p15.33-13.2(chr5:113461-33998289)x1 copy number loss See cases [RCV000141844] Chr5:113461..33998289 [GRCh38]
Chr5:113576..33998394 [GRCh37]
Chr5:166576..34034151 [NCBI36]
Chr5:5p15.33-13.2		 pathogenic
GRCh38/hg38 5p15.1-14.1(chr5:18379122-26803906)x1 copy number loss See cases [RCV000142584] Chr5:18379122..26803906 [GRCh38]
Chr5:18379231..26804015 [GRCh37]
Chr5:18414988..26839772 [NCBI36]
Chr5:5p15.1-14.1		 benign
GRCh38/hg38 5p15.33-14.1(chr5:22149-26593891)x1 copy number loss See cases [RCV000142645] Chr5:22149..26593891 [GRCh38]
Chr5:22149..26594000 [GRCh37]
Chr5:75149..26629757 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic
GRCh38/hg38 5p15.33-14.1(chr5:22149-27611163)x1 copy number loss See cases [RCV000142934] Chr5:22149..27611163 [GRCh38]
Chr5:22149..27611270 [GRCh37]
Chr5:75149..27647027 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic
GRCh38/hg38 5p15.33-14.3(chr5:22149-21726360)x1 copy number loss See cases [RCV000143022] Chr5:22149..21726360 [GRCh38]
Chr5:22149..21726469 [GRCh37]
Chr5:75149..21762226 [NCBI36]
Chr5:5p15.33-14.3		 pathogenic
GRCh38/hg38 5p14.3(chr5:19857588-20747237)x3 copy number gain See cases [RCV000143343] Chr5:19857588..20747237 [GRCh38]
Chr5:19857697..20747346 [GRCh37]
Chr5:19893454..20783103 [NCBI36]
Chr5:5p14.3		 uncertain significance
GRCh38/hg38 5p15.2-14.3(chr5:13609772-21930280)x1 copy number loss See cases [RCV000053447] Chr5:13609772..21930280 [GRCh38]
Chr5:13609881..21930389 [GRCh37]
Chr5:13662881..21966146 [NCBI36]
Chr5:5p15.2-14.3		 pathogenic
GRCh38/hg38 5p14.3(chr5:20474639-20711881)x1 copy number loss See cases [RCV000135017] Chr5:20474639..20711881 [GRCh38]
Chr5:20474748..20711990 [GRCh37]
Chr5:20510505..20747747 [NCBI36]
Chr5:5p14.3		 benign
GRCh38/hg38 5p15.33-14.1(chr5:22149-28075106)x3 copy number gain See cases [RCV000137682] Chr5:22149..28075106 [GRCh38]
Chr5:22149..28075213 [GRCh37]
Chr5:75149..28110970 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic|uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:54
Count of miRNA genes:51
Interacting mature miRNAs:51
Transcripts:ENST00000504244
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.


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 adipose tissue appendage entire extraembryonic component
High
Medium 6
Low 1 1 1 4 356 1
Below cutoff 31 16 20 8 26 8 37 22 43 14 37 34 6 15 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000504244
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl520,612,625 - 20,614,765 (-)Ensembl
RefSeq Acc Id: ENST00000657947
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl520,612,394 - 20,616,441 (-)Ensembl
RefSeq Acc Id: ENST00000659986
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl520,612,312 - 20,616,324 (-)Ensembl
RefSeq Acc Id: ENST00000664531
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl520,612,520 - 20,616,322 (-)Ensembl
RefSeq Acc Id: ENST00000668626
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl520,606,710 - 20,615,684 (-)Ensembl
RefSeq Acc Id: NR_147185
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38520,612,625 - 20,615,535 (-)NCBI
T2T-CHM13v2.0520,614,730 - 20,617,640 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC02146 COSMIC
Ensembl Genes ENSG00000249490 Ensembl
GTEx ENSG00000249490 GTEx
HGNC ID HGNC:53006 ENTREZGENE
Human Proteome Map LINC02146 Human Proteome Map
NCBI Gene LINC02146 ENTREZGENE
RNAcentral URS0000BC4468 RNACentral