LINC00989 (long intergenic non-protein coding RNA 989) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: LINC00989 (long intergenic non-protein coding RNA 989) Homo sapiens
Analyze
Symbol: LINC00989
Name: long intergenic non-protein coding RNA 989
RGD ID: 7252253
HGNC Page HGNC:48918
Description: INTERACTS WITH aflatoxin B1; bisphenol A
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: RP11-234K19.2
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38479,492,593 - 79,576,460 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl479,491,802 - 79,623,479 (+)EnsemblGRCh38hg38GRCh38
GRCh37480,413,747 - 80,497,614 (+)NCBIGRCh37GRCh37hg19GRCh37
Celera477,709,255 - 77,793,302 (+)NCBICelera
Cytogenetic Map4q21.21NCBI
HuRef476,161,709 - 76,245,407 (+)NCBIHuRef
CHM1_1480,390,228 - 80,473,995 (+)NCBICHM1_1
T2T-CHM13v2.0482,828,341 - 82,912,097 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:14702039   PMID:25628894  


Genomics

Variants

.
Variants in LINC00989
2 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 4q13.3-21.3(chr4:72262258-86002147)x3 copy number gain See cases [RCV000138312] Chr4:72262258..86002147 [GRCh38]
Chr4:73127975..86923300 [GRCh37]
Chr4:73346839..87142324 [NCBI36]
Chr4:4q13.3-21.3		 pathogenic
GRCh38/hg38 4q13.2-22.3(chr4:68686088-95294456)x3 copy number gain See cases [RCV000143458] Chr4:68686088..95294456 [GRCh38]
Chr4:69551806..96215607 [GRCh37]
Chr4:69234401..96434630 [NCBI36]
Chr4:4q13.2-22.3		 pathogenic
GRCh38/hg38 4q12-22.3(chr4:51831622-97505618)x3 copy number gain See cases [RCV000051772] Chr4:51831622..97505618 [GRCh38]
Chr4:52697788..98426769 [GRCh37]
Chr4:52392545..98645792 [NCBI36]
Chr4:4q12-22.3		 pathogenic
GRCh38/hg38 4q21.1-21.23(chr4:75453111-84094295)x1 copy number loss See cases [RCV000050786] Chr4:75453111..84094295 [GRCh38]
Chr4:76378321..85015448 [GRCh37]
Chr4:76597345..85234472 [NCBI36]
Chr4:4q21.1-21.23		 pathogenic
GRCh38/hg38 4q13.2-21.23(chr4:67869564-85517308)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053294]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053294]|See cases [RCV000053294] Chr4:67869564..85517308 [GRCh38]
Chr4:68735282..86438461 [GRCh37]
Chr4:68417877..86657485 [NCBI36]
Chr4:4q13.2-21.23		 pathogenic
GRCh38/hg38 4q13.3-21.22(chr4:71079179-81802208)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053295]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053295]|See cases [RCV000053295] Chr4:71079179..81802208 [GRCh38]
Chr4:71944896..82723361 [GRCh37]
Chr4:72163760..82942385 [NCBI36]
Chr4:4q13.3-21.22		 pathogenic
GRCh38/hg38 4q13.3-22.1(chr4:74031395-90421127)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053296]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053296]|See cases [RCV000053296] Chr4:74031395..90421127 [GRCh38]
Chr4:74897112..91342278 [GRCh37]
Chr4:75115976..91561301 [NCBI36]
Chr4:4q13.3-22.1		 pathogenic
GRCh38/hg38 4q21.21-22.1(chr4:79575748-92412449)x1 copy number loss See cases [RCV000053297] Chr4:79575748..92412449 [GRCh38]
Chr4:80496902..93333600 [GRCh37]
Chr4:80715926..93552623 [NCBI36]
Chr4:4q21.21-22.1		 pathogenic
NM_033214.2(GK2):c.-269359_*167228dup duplication Normal pregnancy [RCV000161348] Chr4:79239311..79677559 [GRCh38]
Chr4:80160465..80598713 [GRCh37]
Chr4:4q21.21		 not provided
NC_000004.12:g.67833055_82716065del deletion See cases [RCV003313802] Chr4:67833055..82716065 [GRCh38]
Chr4:4q13.2-21.22		 pathogenic
GRCh38/hg38 4q21.21-23(chr4:79123548-99457773)x1 copy number loss Chromosome 4q21 deletion syndrome [RCV003327709] Chr4:79123548..99457773 [GRCh38]
Chr4:4q21.21-23		 pathogenic
GRCh38/hg38 4q21.21(chr4:78722180-79522307) copy number gain Autism spectrum disorder [RCV003883404] Chr4:78722180..79522307 [GRCh38]
Chr4:4q21.21		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:152
Count of miRNA genes:75
Interacting mature miRNAs:75
Transcripts:ENST00000508174, ENST00000515544
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 2 114 3 2 242 2 8 25 5 186 69
Low 1310 2133 852 65 837 11 3181 1203 638 184 798 879 55 1016 2232
Below cutoff 906 725 611 379 557 272 727 943 1372 160 440 493 108 2 486 3

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000508174
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl479,492,407 - 79,576,466 (+)Ensembl
RefSeq Acc Id: ENST00000515544
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl479,492,573 - 79,576,466 (+)Ensembl
RefSeq Acc Id: ENST00000654276
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl479,492,367 - 79,540,783 (+)Ensembl
RefSeq Acc Id: ENST00000654687
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl479,492,367 - 79,494,226 (+)Ensembl
RefSeq Acc Id: ENST00000656371
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl479,492,410 - 79,540,783 (+)Ensembl
RefSeq Acc Id: ENST00000661529
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl479,492,357 - 79,587,127 (+)Ensembl
RefSeq Acc Id: ENST00000661950
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl479,492,612 - 79,587,094 (+)Ensembl
RefSeq Acc Id: ENST00000664228
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl479,491,802 - 79,493,623 (+)Ensembl
RefSeq Acc Id: ENST00000668018
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl479,492,593 - 79,623,479 (+)Ensembl
RefSeq Acc Id: ENST00000670961
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl479,492,367 - 79,494,227 (+)Ensembl
RefSeq Acc Id: ENST00000671684
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl479,513,784 - 79,576,466 (+)Ensembl
RefSeq Acc Id: ENST00000685595
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl479,492,407 - 79,576,460 (+)Ensembl
RefSeq Acc Id: ENST00000685699
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl479,492,407 - 79,540,780 (+)Ensembl
RefSeq Acc Id: ENST00000685909
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl479,492,410 - 79,540,783 (+)Ensembl
RefSeq Acc Id: ENST00000691929
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl479,492,407 - 79,576,460 (+)Ensembl
RefSeq Acc Id: ENST00000692563
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl479,492,407 - 79,540,783 (+)Ensembl
RefSeq Acc Id: ENST00000702315
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl479,492,410 - 79,576,460 (+)Ensembl
RefSeq Acc Id: ENST00000702341
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl479,492,407 - 79,493,624 (+)Ensembl
RefSeq Acc Id: NR_038826
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38479,492,593 - 79,576,460 (+)NCBI
GRCh37480,413,747 - 80,497,614 (+)NCBI
HuRef476,161,709 - 76,245,407 (+)NCBI
CHM1_1480,390,228 - 80,473,995 (+)NCBI
T2T-CHM13v2.0482,828,341 - 82,912,097 (+)NCBI
Sequence:
Promoters
RGD ID:15095780
Promoter ID:EPDNEWNC_H618
Type:initiation region
Name:LINC00989_2
Description:long intergenic non-protein coding RNA 989 [Source:HGNCSymbol;Acc:HGNC:48918]
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
GRCh38479,492,410 - 79,492,470EPDNEWNC
RGD ID:15095777
Promoter ID:EPDNEWNC_H619
Type:initiation region
Name:LINC00989_1
Description:long intergenic non-protein coding RNA 989 [Source:HGNCSymbol;Acc:HGNC:48918]
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
GRCh38479,492,596 - 79,492,656EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC00989 COSMIC
Ensembl Genes ENSG00000250334 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000515544 ENTREZGENE
GTEx ENSG00000250334 GTEx
HGNC ID HGNC:48918 ENTREZGENE
Human Proteome Map LINC00989 Human Proteome Map
NCBI Gene LINC00989 ENTREZGENE
RNAcentral URS000075CD21 RNACentral