LINC01729 (long intergenic non-protein coding RNA 1729) - Rat Genome Database

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Gene: LINC01729 (long intergenic non-protein coding RNA 1729) Homo sapiens
Analyze
Symbol: LINC01729
Name: long intergenic non-protein coding RNA 1729
RGD ID: 11564235
HGNC Page HGNC:52517
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
GRCh38205,507,875 - 5,510,002 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl205,507,875 - 5,510,002 (-)EnsemblGRCh38hg38GRCh38
GRCh37205,488,521 - 5,490,648 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map20p12.3NCBI
HuRef205,444,188 - 5,446,426 (-)NCBIHuRef
CHM1_1205,489,214 - 5,491,452 (-)NCBICHM1_1
T2T-CHM13v2.0205,548,474 - 5,550,601 (-)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 20p13-12.3(chr20:4343033-6911730)x1 copy number loss See cases [RCV000137695] Chr20:4343033..6911730 [GRCh38]
Chr20:4323680..6892377 [GRCh37]
Chr20:4271680..6840377 [NCBI36]
Chr20:20p13-12.3		 pathogenic
GRCh38/hg38 20p13-q13.33(chr20:99557-64277321)x3 copy number gain See cases [RCV000135859] Chr20:99557..64277321 [GRCh38]
Chr20:80198..62908674 [GRCh37]
Chr20:28198..62379118 [NCBI36]
Chr20:20p13-q13.33		 pathogenic
GRCh38/hg38 20p13-12.1(chr20:80106-13029401)x3 copy number gain See cases [RCV000138677] Chr20:80106..13029401 [GRCh38]
Chr20:60747..13010049 [GRCh37]
Chr20:8747..12958049 [NCBI36]
Chr20:20p13-12.1		 pathogenic
GRCh38/hg38 20p13-12.3(chr20:80093-6386012)x3 copy number gain See cases [RCV000139597] Chr20:80093..6386012 [GRCh38]
Chr20:60734..6366659 [GRCh37]
Chr20:8734..6314659 [NCBI36]
Chr20:20p13-12.3		 pathogenic
GRCh38/hg38 20p13-12.3(chr20:5039774-5645855)x3 copy number gain See cases [RCV000137853] Chr20:5039774..5645855 [GRCh38]
Chr20:5020420..5626501 [GRCh37]
Chr20:4968420..5574501 [NCBI36]
Chr20:20p13-12.3		 uncertain significance
GRCh38/hg38 20p12.3(chr20:5491535-5781055)x3 copy number gain See cases [RCV000137218] Chr20:5491535..5781055 [GRCh38]
Chr20:5472181..5761701 [GRCh37]
Chr20:5420181..5709701 [NCBI36]
Chr20:20p12.3		 benign
GRCh38/hg38 20p13-11.23(chr20:80928-18688031)x3 copy number gain See cases [RCV000143426] Chr20:80928..18688031 [GRCh38]
Chr20:61569..18668675 [GRCh37]
Chr20:9569..18616675 [NCBI36]
Chr20:20p13-11.23		 pathogenic
GRCh38/hg38 20p13-12.3(chr20:84402-6159078)x3 copy number gain See cases [RCV000141348] Chr20:84402..6159078 [GRCh38]
Chr20:65043..6139725 [GRCh37]
Chr20:13043..6087725 [NCBI36]
Chr20:20p13-12.3		 pathogenic
GRCh38/hg38 20p13-11.1(chr20:80927-26324843)x3 copy number gain See cases [RCV000142017] Chr20:80927..26324843 [GRCh38]
Chr20:61568..26305479 [GRCh37]
Chr20:9568..26253479 [NCBI36]
Chr20:20p13-11.1		 pathogenic
GRCh38/hg38 20p13-12.3(chr20:1269303-8626911)x3 copy number gain See cases [RCV000142917] Chr20:1269303..8626911 [GRCh38]
Chr20:1249947..8607558 [GRCh37]
Chr20:1197947..8555558 [NCBI36]
Chr20:20p13-12.3		 pathogenic
GRCh38/hg38 20p13-12.3(chr20:4926195-5543771)x3 copy number gain See cases [RCV000139625] Chr20:4926195..5543771 [GRCh38]
Chr20:4906841..5524417 [GRCh37]
Chr20:4854841..5472417 [NCBI36]
Chr20:20p13-12.3		 uncertain significance
GRCh38/hg38 20p13-11.21(chr20:89939-25697564)x3 copy number gain See cases [RCV000051227] Chr20:89939..25697564 [GRCh38]
Chr20:70580..25678200 [GRCh37]
Chr20:18580..25626200 [NCBI36]
Chr20:20p13-11.21		 pathogenic
GRCh38/hg38 20p13-q11.1(chr20:80106-30227427)x3 copy number gain See cases [RCV000133996] Chr20:80106..30227427 [GRCh38]
Chr20:60747..29462103 [GRCh37]
Chr20:8747..28075764 [NCBI36]
Chr20:20p13-q11.1		 pathogenic
GRCh38/hg38 20p13-11.23(chr20:89939-19146279)x3 copy number gain See cases [RCV000051041] Chr20:89939..19146279 [GRCh38]
Chr20:70580..19126923 [GRCh37]
Chr20:18580..19074923 [NCBI36]
Chr20:20p13-11.23		 pathogenic
GRCh38/hg38 20p13-11.23(chr20:89939-19071495)x3 copy number gain See cases [RCV000052995] Chr20:89939..19071495 [GRCh38]
Chr20:70580..19052139 [GRCh37]
Chr20:18580..19000139 [NCBI36]
Chr20:20p13-11.23		 pathogenic
GRCh38/hg38 20p13-11.22(chr20:89939-21787252)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052996]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052996]|See cases [RCV000052996] Chr20:89939..21787252 [GRCh38]
Chr20:70580..21767890 [GRCh37]
Chr20:18580..21715890 [NCBI36]
Chr20:20p13-11.22		 pathogenic
GRCh38/hg38 20p13-12.1(chr20:89939-14818511)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052997]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052997]|See cases [RCV000052997] Chr20:89939..14818511 [GRCh38]
Chr20:70580..14799157 [GRCh37]
Chr20:18580..14747157 [NCBI36]
Chr20:20p13-12.1		 pathogenic
GRCh38/hg38 20p13-11.21(chr20:87153-23635465)x3 copy number gain Renal agenesis [RCV003327640] Chr20:87153..23635465 [GRCh38]
Chr20:20p13-11.21		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:199
Count of miRNA genes:178
Interacting mature miRNAs:183
Transcripts:ENST00000450640
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 sensory system adipose tissue appendage
High
Medium 309
Low 12 9 5 1 77 1 3 5 2 4 76 12 1 3
Below cutoff 130 302 102 28 380 16 196 149 176 28 65 137 13 74 130

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000450640
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl205,507,875 - 5,510,002 (-)Ensembl
RefSeq Acc Id: NR_109860
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38205,507,875 - 5,510,002 (-)NCBI
CHM1_1205,489,214 - 5,491,341 (-)NCBI
T2T-CHM13v2.0205,548,474 - 5,550,601 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC01729 COSMIC
Ensembl Genes ENSG00000225640 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000450640 ENTREZGENE
GTEx ENSG00000225640 GTEx
HGNC ID HGNC:52517 ENTREZGENE
Human Proteome Map LINC01729 Human Proteome Map
NCBI Gene LINC01729 ENTREZGENE
RNAcentral URS000075BE55 RNACentral