LINC00508 (long intergenic non-protein coding RNA 508) - Rat Genome Database

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Gene: LINC00508 (long intergenic non-protein coding RNA 508) Homo sapiens
Analyze
Symbol: LINC00508
Name: long intergenic non-protein coding RNA 508
RGD ID: 9589886
HGNC Page HGNC:43559
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
GRCh3812127,883,989 - 127,983,891 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl12127,933,689 - 127,983,854 (-)EnsemblGRCh38hg38GRCh38
GRCh3712128,368,534 - 128,468,436 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map12q24.32NCBI
CHM1_112128,189,389 - 128,289,494 (-)NCBICHM1_1
T2T-CHM13v2.012127,912,358 - 128,012,371 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:12477932   PMID:16344560  


Genomics

Variants

.
Variants in LINC00508
2 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NC_000012.12:g.127972717G>T single nucleotide variant Lung cancer [RCV000110709] Chr12:127972717 [GRCh38]
Chr12:128457262 [GRCh37]
Chr12:12q24.32		 uncertain significance
GRCh38/hg38 12q24.32(chr12:126526398-127998599)x3 copy number gain See cases [RCV000139449] Chr12:126526398..127998599 [GRCh38]
Chr12:127010944..128483144 [GRCh37]
Chr12:125576897..127049097 [NCBI36]
Chr12:12q24.32		 uncertain significance|conflicting data from submitters
GRCh38/hg38 12q24.32-24.33(chr12:127900499-129778294)x3 copy number gain See cases [RCV000137094] Chr12:127900499..129778294 [GRCh38]
Chr12:128385044..130262839 [GRCh37]
Chr12:126950997..128828792 [NCBI36]
Chr12:12q24.32-24.33		 uncertain significance
GRCh38/hg38 12p13.33-q24.33(chr12:121271-133196807)x3 copy number gain See cases [RCV000139555] Chr12:121271..133196807 [GRCh38]
Chr12:282465..133773393 [GRCh37]
Chr12:100698..132283466 [NCBI36]
Chr12:12p13.33-q24.33		 pathogenic
GRCh38/hg38 12q24.31-24.33(chr12:120697672-133202490)x3 copy number gain See cases [RCV000137651] Chr12:120697672..133202490 [GRCh38]
Chr12:121135475..133779076 [GRCh37]
Chr12:119619858..132289149 [NCBI36]
Chr12:12q24.31-24.33		 pathogenic
GRCh38/hg38 12q24.32(chr12:127145342-128422497)x4 copy number gain See cases [RCV000138658] Chr12:127145342..128422497 [GRCh38]
Chr12:127629887..128907042 [GRCh37]
Chr12:126195840..127472995 [NCBI36]
Chr12:12q24.32		 uncertain significance
GRCh38/hg38 12q24.21-24.33(chr12:115131583-133166920)x3 copy number gain See cases [RCV000053689] Chr12:115131583..133166920 [GRCh38]
Chr12:115569388..133743506 [GRCh37]
Chr12:114053771..132253579 [NCBI36]
Chr12:12q24.21-24.33		 pathogenic
GRCh38/hg38 12q24.23-24.33(chr12:119417382-133191400)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053691]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053691]|See cases [RCV000053691] Chr12:119417382..133191400 [GRCh38]
Chr12:119855187..133767986 [GRCh37]
Chr12:118339570..132278059 [NCBI36]
Chr12:12q24.23-24.33		 pathogenic
GRCh38/hg38 12q24.32-24.33(chr12:126403612-133166920)x3 copy number gain See cases [RCV000053715] Chr12:126403612..133166920 [GRCh38]
Chr12:126888158..133743506 [GRCh37]
Chr12:125454111..132253579 [NCBI36]
Chr12:12q24.32-24.33		 pathogenic
GRCh38/hg38 12q24.31-24.33(chr12:123365769-133191400)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053693]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053693]|See cases [RCV000053693] Chr12:123365769..133191400 [GRCh38]
Chr12:123850316..133767986 [GRCh37]
Chr12:122416269..132278059 [NCBI36]
Chr12:12q24.31-24.33		 pathogenic
GRCh38/hg38 12q24.31-24.33(chr12:123509825-133191400)x3 copy number gain See cases [RCV000135535] Chr12:123509825..133191400 [GRCh38]
Chr12:123994372..133767986 [GRCh37]
Chr12:122560325..132278059 [NCBI36]
Chr12:12q24.31-24.33		 pathogenic
GRCh38/hg38 12q24.32(chr12:127802658-128663624)x3 copy number gain See cases [RCV000136702] Chr12:127802658..128663624 [GRCh38]
Chr12:128287203..129148169 [GRCh37]
Chr12:126853156..127714122 [NCBI36]
Chr12:12q24.32		 uncertain significance
GRCh38/hg38 12q24.32(chr12:126587447-127900558)x3 copy number gain See cases [RCV000136703] Chr12:126587447..127900558 [GRCh38]
Chr12:127071993..128385103 [GRCh37]
Chr12:125637946..126951056 [NCBI36]
Chr12:12q24.32		 uncertain significance
GRCh38/hg38 12q24.31-24.33(chr12:122985202-130714574)x1 copy number loss See cases [RCV000051345] Chr12:122985202..130714574 [GRCh38]
Chr12:123469749..131199119 [GRCh37]
Chr12:122035702..129765072 [NCBI36]
Chr12:12q24.31-24.33		 pathogenic
GRCh38/hg38 12q24.21-24.33(chr12:114268403-133201316)x3 copy number gain See cases [RCV000143656] Chr12:114268403..133201316 [GRCh38]
Chr12:114706208..133777902 [GRCh37]
Chr12:113190591..132287975 [NCBI36]
Chr12:12q24.21-24.33		 pathogenic
GRCh38/hg38 12q24.23-24.33(chr12:118165459-133182322)x3 copy number gain See cases [RCV000050866] Chr12:118165459..133182322 [GRCh38]
Chr12:118603264..133758908 [GRCh37]
Chr12:117087647..132268981 [NCBI36]
Chr12:12q24.23-24.33		 pathogenic
GRCh38/hg38 12q24.31-24.33(chr12:123444758-133191400)x3 copy number gain See cases [RCV000051151] Chr12:123444758..133191400 [GRCh38]
Chr12:123929305..133767986 [GRCh37]
Chr12:122495258..132278059 [NCBI36]
Chr12:12q24.31-24.33		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:60
Count of miRNA genes:59
Interacting mature miRNAs:60
Transcripts:ENST00000538901
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 4 7 5 8 5 3 3 2 8
Low 11 10 11 4 21 5 21 9 83 6 340 16 1 1 4
Below cutoff 36 35 15 7 18 4 41 23 191 12 52 21 3 8 27

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000538901
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl12127,940,595 - 127,950,160 (-)Ensembl
RefSeq Acc Id: ENST00000653038
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl12127,933,689 - 127,983,854 (-)Ensembl
RefSeq Acc Id: NR_126452
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh3812127,883,989 - 127,983,891 (-)NCBI
CHM1_112128,189,389 - 128,289,494 (-)NCBI
T2T-CHM13v2.012127,912,358 - 128,012,371 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC00508 COSMIC
Ensembl Genes ENSG00000256971 Ensembl
GTEx ENSG00000256971 GTEx
HGNC ID HGNC:43559 ENTREZGENE
Human Proteome Map LINC00508 Human Proteome Map
NCBI Gene LINC00508 ENTREZGENE
RNAcentral URS00007E4199 RNACentral