LINC03016 (long intergenic non-protein coding RNA 3016) - Rat Genome Database

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Gene: LINC03016 (long intergenic non-protein coding RNA 3016) Homo sapiens
Analyze
Symbol: LINC03016
Name: long intergenic non-protein coding RNA 3016
RGD ID: 16554853
HGNC Page HGNC:56145
Description: INTERACTS WITH perfluorooctanoic acid
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: AC005532.1; LOC101927354; uncharacterized LOC101927354
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38.p14 Ensembl - Human Genome Assembly GRCh38 Ensembl
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3877,255,154 - 7,278,069 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl77,255,154 - 7,278,073 (+)EnsemblGRCh38hg38GRCh38
GRCh3777,294,785 - 7,317,700 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map7p21.3NCBI
HuRef77,155,040 - 7,166,085 (+)NCBIHuRef
CHM1_177,306,539 - 7,317,573 (+)NCBICHM1_1
T2T-CHM13v2.077,374,363 - 7,397,260 (+)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:22589738   PMID:24556642  


Genomics

Variants

.
Variants in LINC03016
4 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 7p22.1-21.3(chr7:6887830-7528189)x3 copy number gain See cases [RCV000137906] Chr7:6887830..7528189 [GRCh38]
Chr7:6927461..7567820 [GRCh37]
Chr7:6893986..7534345 [NCBI36]
Chr7:7p22.1-21.3		 likely benign
GRCh38/hg38 7p22.1-21.3(chr7:7097890-7295446)x3 copy number gain See cases [RCV000140271] Chr7:7097890..7295446 [GRCh38]
Chr7:7137521..7335077 [GRCh37]
Chr7:7104046..7301602 [NCBI36]
Chr7:7p22.1-21.3		 likely benign
GRCh38/hg38 7p22.3-q36.3(chr7:54185-159282390)x1 copy number loss See cases [RCV000135401] Chr7:54185..159282390 [GRCh38]
Chr7:54185..159075079 [GRCh37]
Chr7:149268..158767840 [NCBI36]
Chr7:7p22.3-q36.3		 pathogenic
GRCh38/hg38 7p22.3-15.3(chr7:53985-24361531)x3 copy number gain See cases [RCV000053528] Chr7:53985..24361531 [GRCh38]
Chr7:53985..24401150 [GRCh37]
Chr7:149068..24367675 [NCBI36]
Chr7:7p22.3-15.3		 pathogenic
GRCh38/hg38 7p21.3(chr7:7249455-10718595)x3 copy number gain See cases [RCV000139695] Chr7:7249455..10718595 [GRCh38]
Chr7:7289086..10758222 [GRCh37]
Chr7:7255611..10724747 [NCBI36]
Chr7:7p21.3		 likely benign
GRCh38/hg38 7p22.3-15.2(chr7:54185-26827634)x3 copy number gain See cases [RCV000136557] Chr7:54185..26827634 [GRCh38]
Chr7:54185..26867253 [GRCh37]
Chr7:149268..26833778 [NCBI36]
Chr7:7p22.3-15.2		 pathogenic
GRCh38/hg38 7p22.1-15.2(chr7:5682209-27230311)x3 copy number gain See cases [RCV000136649] Chr7:5682209..27230311 [GRCh38]
Chr7:5721840..27269930 [GRCh37]
Chr7:5688366..27236455 [NCBI36]
Chr7:7p22.1-15.2		 pathogenic
GRCh38/hg38 7p22.3-15.3(chr7:45130-25221165)x3 copy number gain See cases [RCV000137824] Chr7:45130..25221165 [GRCh38]
Chr7:45130..25260784 [GRCh37]
Chr7:140213..25227309 [NCBI36]
Chr7:7p22.3-15.3		 pathogenic
GRCh38/hg38 7p22.1-21.3(chr7:6831253-8010127)x3 copy number gain See cases [RCV000138318] Chr7:6831253..8010127 [GRCh38]
Chr7:6870884..8049757 [GRCh37]
Chr7:6837409..8016282 [NCBI36]
Chr7:7p22.1-21.3		 likely benign
GRCh38/hg38 7p22.1-21.3(chr7:6887830-8054546)x3 copy number gain See cases [RCV000137744] Chr7:6887830..8054546 [GRCh38]
Chr7:6927461..8094176 [GRCh37]
Chr7:6893986..8060701 [NCBI36]
Chr7:7p22.1-21.3		 uncertain significance
GRCh38/hg38 7p22.3-q36.3(chr7:53985-159282531)x1 copy number loss See cases [RCV000052250] Chr7:53985..159282531 [GRCh38]
Chr7:53985..159075220 [GRCh37]
Chr7:149068..158767981 [NCBI36]
Chr7:7p22.3-q36.3		 pathogenic
GRCh38/hg38 7p22.3-14.1(chr7:54185-41875885)x3 copy number gain See cases [RCV000051159] Chr7:54185..41875885 [GRCh38]
Chr7:54185..41915483 [GRCh37]
Chr7:149268..41882008 [NCBI36]
Chr7:7p22.3-14.1		 pathogenic
GRCh38/hg38 7p22.3-14.2(chr7:54185-37089712)x3 copy number gain See cases [RCV000053530] Chr7:54185..37089712 [GRCh38]
Chr7:54185..37129317 [GRCh37]
Chr7:149268..37095842 [NCBI36]
Chr7:7p22.3-14.2		 pathogenic
GRCh38/hg38 7p22.3-15.2(chr7:43360-27196404)x3 copy number gain See cases [RCV000143586] Chr7:43360..27196404 [GRCh38]
Chr7:43360..27236023 [GRCh37]
Chr7:138443..27202548 [NCBI36]
Chr7:7p22.3-15.2		 pathogenic
GRCh38/hg38 7p22.1-21.3(chr7:6106402-11012657)x1 copy number loss See cases [RCV000050923] Chr7:6106402..11012657 [GRCh38]
Chr7:6146033..11052284 [GRCh37]
Chr7:6112559..11018809 [NCBI36]
Chr7:7p22.1-21.3		 pathogenic
GRCh38/hg38 7p22.3-15.2(chr7:1698124-27207295)x3 copy number gain See cases [RCV000143060] Chr7:1698124..27207295 [GRCh38]
Chr7:1737760..27246914 [GRCh37]
Chr7:1704286..27213439 [NCBI36]
Chr7:7p22.3-15.2		 pathogenic
GRCh38/hg38 7p21.3(chr7:7249268-7417064)x1 copy number loss See cases [RCV000134334] Chr7:7249268..7417064 [GRCh38]
Chr7:7288899..7456695 [GRCh37]
Chr7:7255424..7423220 [NCBI36]
Chr7:7p21.3		 benign
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:677
Count of miRNA genes:286
Interacting mature miRNAs:298
Transcripts:ENST00000430266, ENST00000436578, ENST00000447039
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 19 5 2 1 8 19 1
Low 276 261 208 67 452 29 842 149 665 113 449 264 43 78 567 3
Below cutoff 1533 2033 1176 411 1108 316 2771 1407 2653 266 648 1096 100 907 1734

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000430266
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl77,255,154 - 7,278,071 (+)Ensembl
RefSeq Acc Id: ENST00000436578
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl77,266,908 - 7,277,724 (+)Ensembl
RefSeq Acc Id: ENST00000447039
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl77,271,408 - 7,277,773 (+)Ensembl
RefSeq Acc Id: ENST00000655022
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl77,269,813 - 7,278,073 (+)Ensembl
RefSeq Acc Id: ENST00000657192
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl77,255,345 - 7,278,071 (+)Ensembl
RefSeq Acc Id: ENST00000659742
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl77,255,154 - 7,278,071 (+)Ensembl
RefSeq Acc Id: NR_108073
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh3877,255,154 - 7,278,069 (+)NCBI
T2T-CHM13v2.077,374,363 - 7,397,260 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC03016 COSMIC
Ensembl Genes ENSG00000230825 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000430266 ENTREZGENE
GTEx ENSG00000230825 GTEx
HGNC ID HGNC:56145 ENTREZGENE
Human Proteome Map LINC03016 Human Proteome Map
NCBI Gene LOC101927354 ENTREZGENE
RNAcentral URS000075A852 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-01-17 LINC03016  long intergenic non-protein coding RNA 3016  AC005532.1  novel transcript  Symbol and/or name change 19259463 PROVISIONAL
2020-06-25 AC005532.1  novel transcript  LOC101927354  uncharacterized LOC101927354  Symbol and/or name change 19259462 PROVISIONAL
2020-06-18 LOC101927354  uncharacterized LOC101927354  AC005532.1  novel transcript  Symbol and/or name change 5135510 APPROVED