LINC01625 (long intergenic non-protein coding RNA 1625) - Rat Genome Database

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Gene: LINC01625 (long intergenic non-protein coding RNA 1625) Homo sapiens
Analyze
Symbol: LINC01625
Name: long intergenic non-protein coding RNA 1625
RGD ID: 10402663
HGNC Page HGNC:52052
Description: ASSOCIATED WITH familial Behcet-like autoinflammatory 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
GRCh386139,468,995 - 139,474,596 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6139,435,636 - 139,474,658 (-)EnsemblGRCh38hg38GRCh38
GRCh376139,790,132 - 139,795,733 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366139,831,825 - 139,837,426 (-)NCBINCBI36Build 36hg18NCBI36
Celera6140,530,179 - 140,535,781 (-)NCBICelera
Cytogenetic Map6q24.1NCBI
HuRef6137,351,337 - 137,356,931 (-)NCBIHuRef
CHM1_16140,053,170 - 140,058,771 (-)NCBICHM1_1
T2T-CHM13v2.06140,652,832 - 140,658,434 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References
Additional References at PubMed
PMID:11181995   PMID:14702039   PMID:23222517  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 6q24.1(chr6:139455977-140318558)x3 copy number gain See cases [RCV000137881] Chr6:139455977..140318558 [GRCh38]
Chr6:139777114..140639695 [GRCh37]
Chr6:139818807..140681388 [NCBI36]
Chr6:6q24.1		 likely benign
GRCh38/hg38 6q24.1(chr6:139002616-140199336)x3 copy number gain See cases [RCV000137989] Chr6:139002616..140199336 [GRCh38]
Chr6:139323753..140520473 [GRCh37]
Chr6:139365446..140562166 [NCBI36]
Chr6:6q24.1		 uncertain significance
GRCh38/hg38 6q13-24.1(chr6:74382807-142040500)x3 copy number gain See cases [RCV000139729] Chr6:74382807..142040500 [GRCh38]
Chr6:75092523..142361637 [GRCh37]
Chr6:75149243..142403330 [NCBI36]
Chr6:6q13-24.1		 pathogenic
GRCh38/hg38 6q24.1(chr6:139397617-139932971)x3 copy number gain See cases [RCV000143775] Chr6:139397617..139932971 [GRCh38]
Chr6:139718754..140254108 [GRCh37]
Chr6:139760447..140295801 [NCBI36]
Chr6:6q24.1		 uncertain significance
GRCh38/hg38 6q23.3-25.3(chr6:135358150-155455117)x3 copy number gain See cases [RCV000136826] Chr6:135358150..155455117 [GRCh38]
Chr6:135679288..155776251 [GRCh37]
Chr6:135720981..155817943 [NCBI36]
Chr6:6q23.3-25.3		 pathogenic
GRCh38/hg38 6q23.2-27(chr6:133537271-165875545)x3 copy number gain See cases [RCV000143444] Chr6:133537271..165875545 [GRCh38]
Chr6:133858409..166289033 [GRCh37]
Chr6:133900102..166209023 [NCBI36]
Chr6:6q23.2-27		 pathogenic
Single allele deletion Autoinflammatory syndrome, familial, Behcet-like [RCV002247731] Chr6:134838331..142160056 [GRCh38]
Chr6:6q23.3-24.1		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:95
Count of miRNA genes:93
Interacting mature miRNAs:94
Transcripts:ENST00000454788
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 19 1 1 1
Low 99 79 433 176 119 174 505 44 1282 193 307 95 2 394 205
Below cutoff 1722 1555 879 319 582 180 2918 1239 2233 120 715 975 141 736 1864 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000454788
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl6139,468,995 - 139,474,638 (-)Ensembl
RefSeq Acc Id: ENST00000654256
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl6139,456,895 - 139,474,658 (-)Ensembl
RefSeq Acc Id: ENST00000655740
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl6139,456,895 - 139,473,444 (-)Ensembl
RefSeq Acc Id: ENST00000658080
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl6139,456,895 - 139,474,638 (-)Ensembl
RefSeq Acc Id: ENST00000664461
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl6139,469,004 - 139,474,571 (-)Ensembl
RefSeq Acc Id: ENST00000665194
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl6139,469,004 - 139,473,456 (-)Ensembl
RefSeq Acc Id: ENST00000666511
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl6139,435,636 - 139,474,599 (-)Ensembl
RefSeq Acc Id: ENST00000668014
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl6139,435,647 - 139,474,598 (-)Ensembl
RefSeq Acc Id: NR_033919
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh386139,468,995 - 139,474,596 (-)NCBI
CHM1_16140,053,170 - 140,058,771 (-)NCBI
T2T-CHM13v2.06140,652,832 - 140,658,434 (-)NCBI
Sequence:
Protein Sequences
GenBank Protein EAW47890 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences

Promoters
RGD ID:15096071
Promoter ID:EPDNEWNC_H912
Type:initiation region
Name:LINC01625_1
Description:long intergenic non-protein coding RNA 1625 [Source:HGNCSymbol;Acc:HGNC:52052]
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
GRCh386139,474,598 - 139,474,658EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC01625 COSMIC
Ensembl Genes ENSG00000238099 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000454788 ENTREZGENE
GTEx ENSG00000238099 GTEx
HGNC ID HGNC:52052 ENTREZGENE
Human Proteome Map LINC01625 Human Proteome Map
NCBI Gene LINC01625 ENTREZGENE
RNAcentral URS000075EB79 RNACentral