LINC01656 (long intergenic non-protein coding RNA 1656) - Rat Genome Database

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Gene: LINC01656 (long intergenic non-protein coding RNA 1656) Homo sapiens
Analyze
Symbol: LINC01656
Name: long intergenic non-protein coding RNA 1656
RGD ID: 11563947
HGNC Page HGNC:52444
Description: ASSOCIATED WITH Phelan-McDermid syndrome
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
GRCh382244,443,327 - 44,444,788 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2244,443,290 - 44,444,793 (+)EnsemblGRCh38hg38GRCh38
GRCh372244,839,207 - 44,840,668 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map22q13.31NCBI
HuRef2227,788,630 - 27,790,094 (+)NCBIHuRef
CHM1_12244,797,944 - 44,799,407 (+)NCBICHM1_1
T2T-CHM13v2.02244,927,164 - 44,928,626 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 22q13.2-13.31(chr22:42197923-47305564)x4 copy number gain See cases [RCV000135528] Chr22:42197923..47305564 [GRCh38]
Chr22:42593929..47701314 [GRCh37]
Chr22:40923873..46079978 [NCBI36]
Chr22:22q13.2-13.31		 pathogenic
GRCh38/hg38 22q13.31-13.33(chr22:43992879-50683114)x3 copy number gain See cases [RCV000136124] Chr22:43992879..50683114 [GRCh38]
Chr22:44388759..51121542 [GRCh37]
Chr22:42720092..49468408 [NCBI36]
Chr22:22q13.31-13.33		 benign
GRCh38/hg38 22q13.2-13.33(chr22:42493445-50268479)x1 copy number loss See cases [RCV000136786] Chr22:42493445..50268479 [GRCh38]
Chr22:42889451..50706908 [GRCh37]
Chr22:41219395..49049035 [NCBI36]
Chr22:22q13.2-13.33		 pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:41871143-50739836)x1 copy number loss See cases [RCV000136921] Chr22:41871143..50739836 [GRCh38]
Chr22:42267147..51178264 [GRCh37]
Chr22:40597093..49525130 [NCBI36]
Chr22:22q13.2-13.33		 pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:42710276-50739836)x3 copy number gain See cases [RCV000137136] Chr22:42710276..50739836 [GRCh38]
Chr22:43106282..51178264 [GRCh37]
Chr22:41436226..49525130 [NCBI36]
Chr22:22q13.2-13.33		 pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:43187980-50745444)x1 copy number loss See cases [RCV000140901] Chr22:43187980..50745444 [GRCh38]
Chr22:43583986..51183872 [GRCh37]
Chr22:41913930..49530738 [NCBI36]
Chr22:22q13.2-13.33		 pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:42837094-50735806)x1 copy number loss See cases [RCV000141415] Chr22:42837094..50735806 [GRCh38]
Chr22:43233100..51174234 [GRCh37]
Chr22:41563044..49521100 [NCBI36]
Chr22:22q13.2-13.33		 pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:42380961-50759410)x3 copy number gain See cases [RCV000141659] Chr22:42380961..50759410 [GRCh38]
Chr22:42776967..51197838 [GRCh37]
Chr22:41106911..49544704 [NCBI36]
Chr22:22q13.2-13.33		 pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:42433752-50738932)x1 copy number loss See cases [RCV000051371] Chr22:42433752..50738932 [GRCh38]
Chr22:42829758..51177360 [GRCh37]
Chr22:41159702..49524226 [NCBI36]
Chr22:22q13.2-13.33		 pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:42080077-50739836)x3 copy number gain See cases [RCV000142755] Chr22:42080077..50739836 [GRCh38]
Chr22:42476081..51178264 [GRCh37]
Chr22:40806027..49525130 [NCBI36]
Chr22:22q13.2-13.33		 pathogenic
GRCh38/hg38 22q13.31-13.33(chr22:43902561-50739836)x1 copy number loss See cases [RCV000135444] Chr22:43902561..50739836 [GRCh38]
Chr22:44298441..51178264 [GRCh37]
Chr22:42629774..49525130 [NCBI36]
Chr22:22q13.31-13.33		 pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:42138114-50739836)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051370]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051370]|See cases [RCV000051370] Chr22:42138114..50739836 [GRCh38]
Chr22:42513525..51178264 [GRCh37]
Chr22:40843471..49525130 [NCBI36]
Chr22:22q13.2-13.33		 pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:42826246-50739836)x1 copy number loss See cases [RCV000051407] Chr22:42826246..50739836 [GRCh38]
Chr22:43222252..51178264 [GRCh37]
Chr22:41552196..49525130 [NCBI36]
Chr22:22q13.2-13.33		 pathogenic
GRCh38/hg38 22q13.31-13.33(chr22:43807366-50739836)x1 copy number loss See cases [RCV000051408] Chr22:43807366..50739836 [GRCh38]
Chr22:44203246..51178264 [GRCh37]
Chr22:42534579..49525130 [NCBI36]
Chr22:22q13.31-13.33		 pathogenic
GRCh38/hg38 22q13.31-13.33(chr22:43993654-50739977)x1 copy number loss See cases [RCV000051409] Chr22:43993654..50739977 [GRCh38]
Chr22:44389534..51178405 [GRCh37]
Chr22:42720867..49525271 [NCBI36]
Chr22:22q13.31-13.33		 pathogenic
GRCh38/hg38 22q12.3-13.33(chr22:33768441-50739977)x3 copy number gain See cases [RCV000051682] Chr22:33768441..50739977 [GRCh38]
Chr22:34164428..51178405 [GRCh37]
Chr22:32494428..49525271 [NCBI36]
Chr22:22q12.3-13.33		 pathogenic
GRCh38/hg38 22q12.3-13.33(chr22:37061769-50738932)x3 copy number gain See cases [RCV000051684] Chr22:37061769..50738932 [GRCh38]
Chr22:37457809..51177360 [GRCh37]
Chr22:35787755..49524226 [NCBI36]
Chr22:22q12.3-13.33		 pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:42599757-50725241)x3 copy number gain See cases [RCV000051686] Chr22:42599757..50725241 [GRCh38]
Chr22:42995763..51163669 [GRCh37]
Chr22:41325707..49510535 [NCBI36]
Chr22:22q13.2-13.33		 pathogenic
GRCh38/hg38 22q13.2-13.33(chr22:42653747-50739836)x3 copy number gain See cases [RCV000051687] Chr22:42653747..50739836 [GRCh38]
Chr22:43049753..51178264 [GRCh37]
Chr22:41379697..49525130 [NCBI36]
Chr22:22q13.2-13.33		 pathogenic
GRCh38/hg38 22q13.1-13.33(chr22:40202014-50735806)x3 copy number gain See cases [RCV000134513] Chr22:40202014..50735806 [GRCh38]
Chr22:40598018..51174234 [GRCh37]
Chr22:38927964..49521100 [NCBI36]
Chr22:22q13.1-13.33		 pathogenic
GRCh38/hg38 22q11.1-13.33(chr22:16916743-50739785)x3 copy number gain See cases [RCV000134730] Chr22:16916743..50739785 [GRCh38]
Chr22:17397633..51178213 [GRCh37]
Chr22:15777633..49525079 [NCBI36]
Chr22:22q11.1-13.33		 pathogenic
GRCh38/hg38 22q11.1-13.33(chr22:16916608-50739836)x3 copy number gain See cases [RCV000133646] Chr22:16916608..50739836 [GRCh38]
Chr22:17397498..51178264 [GRCh37]
Chr22:15777498..49525130 [NCBI36]
Chr22:22q11.1-13.33		 pathogenic
NC_000022.11:g.43802117_50806121del deletion Phelan-McDermid syndrome [RCV001254364] Chr22:43802117..50806121 [GRCh38]
Chr22:22q13.31-13.33		 pathogenic
NC_000022.11:g.43032129_50739836del deletion Phelan-McDermid syndrome [RCV001254356] Chr22:43032129..50739836 [GRCh38]
Chr22:22q13.2-13.33		 pathogenic
NC_000022.11:g.44245760_50806121del deletion Phelan-McDermid syndrome [RCV001254369] Chr22:44245760..50806121 [GRCh38]
Chr22:22q13.31-13.33		 pathogenic
GRCh38/hg38 22q13.31(chr22:44184196-45239435) copy number gain Anomalous pulmonary venous return [RCV003223579] Chr22:44184196..45239435 [GRCh38]
Chr22:22q13.31		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:301
Count of miRNA genes:275
Interacting mature miRNAs:297
Transcripts:ENST00000415702
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

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
273 648 1103 626 859 473 436 1 56 177 29 448 1808 1422 3 835 253 931 306 28

Sequence


Ensembl Acc Id: ENST00000415702
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2244,443,327 - 44,444,788 (+)Ensembl
Ensembl Acc Id: ENST00000735573
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2244,443,290 - 44,444,793 (+)Ensembl
Ensembl Acc Id: ENST00000735574
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2244,443,307 - 44,444,790 (+)Ensembl
RefSeq Acc Id: NR_109966
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382244,443,327 - 44,444,788 (+)NCBI
CHM1_12244,797,944 - 44,799,405 (+)NCBI
T2T-CHM13v2.02244,927,164 - 44,928,626 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC01656 COSMIC
Ensembl Genes ENSG00000232655 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000415702 ENTREZGENE
GTEx ENSG00000232655 GTEx
HGNC ID HGNC:52444 ENTREZGENE
Human Proteome Map LINC01656 Human Proteome Map
NCBI Gene LINC01656 ENTREZGENE
RNAcentral URS000075D9E3 RNACentral