LINC00626 (long intergenic non-protein coding RNA 626) - 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: LINC00626 (long intergenic non-protein coding RNA 626) Homo sapiens
Analyze
Symbol: LINC00626
Name: long intergenic non-protein coding RNA 626
RGD ID: 6776596
HGNC Page HGNC:44257
Description: INTERACTS WITH benzo[a]pyrene; entinostat; propofol
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: RP1-10C16.2
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381168,786,941 - 168,792,888 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1168,784,012 - 168,792,886 (+)EnsemblGRCh38hg38GRCh38
GRCh371168,756,179 - 168,762,126 (+)NCBIGRCh37GRCh37hg19GRCh37
Celera1141,865,988 - 141,871,935 (+)NCBICelera
Cytogenetic Map1q24.2NCBI
HuRef1140,002,232 - 140,008,179 (+)NCBIHuRef
CHM1_11170,178,358 - 170,184,268 (+)NCBICHM1_1
T2T-CHM13v2.01168,142,138 - 168,148,089 (+)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:12477932  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1q24.2(chr1:168673294-168952481)x3 copy number gain See cases [RCV000135227] Chr1:168673294..168952481 [GRCh38]
Chr1:168642532..168921719 [GRCh37]
Chr1:166909156..167188343 [NCBI36]
Chr1:1q24.2		 likely benign
GRCh38/hg38 1q24.2(chr1:168498046-169184625)x4 copy number gain See cases [RCV000138211] Chr1:168498046..169184625 [GRCh38]
Chr1:168467284..169153863 [GRCh37]
Chr1:166733908..167420487 [NCBI36]
Chr1:1q24.2		 uncertain significance
GRCh38/hg38 1q23.3-25.1(chr1:163382523-175877022)x1 copy number loss See cases [RCV000143292] Chr1:163382523..175877022 [GRCh38]
Chr1:163352313..175846158 [GRCh37]
Chr1:161618937..174112781 [NCBI36]
Chr1:1q23.3-25.1		 pathogenic
GRCh38/hg38 1q21.2-25.2(chr1:149854269-180267197)x3 copy number gain See cases [RCV000143515] Chr1:149854269..180267197 [GRCh38]
Chr1:149825831..180236332 [GRCh37]
Chr1:148092455..178502955 [NCBI36]
Chr1:1q21.2-25.2		 pathogenic
GRCh38/hg38 1q23.1-25.1(chr1:157747246-176021247)x3 copy number gain See cases [RCV000051854] Chr1:157747246..176021247 [GRCh38]
Chr1:157717036..175990383 [GRCh37]
Chr1:155983660..174257006 [NCBI36]
Chr1:1q23.1-25.1		 pathogenic
GRCh38/hg38 1q23.3-25.2(chr1:164922655-180061589)x3 copy number gain See cases [RCV000051856] Chr1:164922655..180061589 [GRCh38]
Chr1:164891892..180030724 [GRCh37]
Chr1:163158516..178297347 [NCBI36]
Chr1:1q23.3-25.2		 pathogenic
GRCh38/hg38 1q24.2-25.1(chr1:168314822-175299299)x1 copy number loss See cases [RCV000053918] Chr1:168314822..175299299 [GRCh38]
Chr1:168284060..175268435 [GRCh37]
Chr1:166550684..173535058 [NCBI36]
Chr1:1q24.2-25.1		 pathogenic
GRCh38/hg38 1q23.3-25.1(chr1:161740907-173965154)x1 copy number loss See cases [RCV000053914] Chr1:161740907..173965154 [GRCh38]
Chr1:161710697..173934292 [GRCh37]
Chr1:159977321..172200915 [NCBI36]
Chr1:1q23.3-25.1		 pathogenic
GRCh38/hg38 1q23.3-24.3(chr1:164036599-171252077)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053916]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053916]|See cases [RCV000053916] Chr1:164036599..171252077 [GRCh38]
Chr1:164005836..171221216 [GRCh37]
Chr1:162272460..169487840 [NCBI36]
Chr1:1q23.3-24.3		 pathogenic
GRCh38/hg38 1q24.1-25.1(chr1:166762832-175327423)x1 copy number loss See cases [RCV000053917] Chr1:166762832..175327423 [GRCh38]
Chr1:166732069..175296559 [GRCh37]
Chr1:164998693..173563182 [NCBI36]
Chr1:1q24.1-25.1		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:83
Count of miRNA genes:83
Interacting mature miRNAs:83
Transcripts:ENST00000420691
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
High
Medium 1 2 1 10 8 19
Low 3 10 171 30 14 11 41 14 144 101 88 108 20 18 13
Below cutoff 304 201 684 141 182 40 979 271 750 172 479 606 103 448 469

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000420691
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1168,786,939 - 168,792,886 (+)Ensembl
RefSeq Acc Id: ENST00000663134
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1168,784,012 - 168,792,886 (+)Ensembl
RefSeq Acc Id: ENST00000665467
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1168,790,072 - 168,792,886 (+)Ensembl
RefSeq Acc Id: ENST00000667346
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1168,786,754 - 168,792,886 (+)Ensembl
RefSeq Acc Id: ENST00000669234
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1168,786,723 - 168,792,886 (+)Ensembl
RefSeq Acc Id: ENST00000670921
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1168,786,754 - 168,792,886 (+)Ensembl
RefSeq Acc Id: NR_024160
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381168,786,941 - 168,792,888 (+)NCBI
GRCh371168,756,179 - 168,762,126 (+)NCBI
HuRef1140,002,232 - 140,008,179 (+)NCBI
CHM1_11170,178,358 - 170,184,268 (+)NCBI
T2T-CHM13v2.01168,142,138 - 168,148,089 (+)NCBI
Sequence:
Promoters
RGD ID:15095301
Promoter ID:EPDNEWNC_H138
Type:initiation region
Name:LINC00626_1
Description:long intergenic non-protein coding RNA 626 [Source:HGNCSymbol;Acc:HGNC:44257]
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
GRCh381168,786,922 - 168,786,982EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC00626 COSMIC
Ensembl Genes ENSG00000225826 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000420691 ENTREZGENE
GTEx ENSG00000225826 GTEx
HGNC ID HGNC:44257 ENTREZGENE
Human Proteome Map LINC00626 Human Proteome Map
NCBI Gene LINC00626 ENTREZGENE
RNAcentral URS000075C630 RNACentral