LINC01502 (long intergenic non-protein coding RNA 1502) - Rat Genome Database

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Gene: LINC01502 (long intergenic non-protein coding RNA 1502) Homo sapiens
Analyze
Symbol: LINC01502
Name: long intergenic non-protein coding RNA 1502
RGD ID: 8699044
HGNC Page HGNC:51183
Description: INTERACTS WITH fipronil
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
GRCh389135,574,925 - 135,587,112 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9135,574,935 - 135,587,112 (+)EnsemblGRCh38hg38GRCh38
GRCh379138,466,771 - 138,478,958 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369137,606,618 - 137,616,928 (+)NCBINCBI36Build 36hg18NCBI36
Celera9108,983,678 - 108,995,864 (+)NCBICelera
Cytogenetic Map9q34.3NCBI
HuRef9107,928,580 - 107,940,339 (+)NCBIHuRef
CHM1_19138,615,365 - 138,627,546 (+)NCBICHM1_1
T2T-CHM13v2.09147,802,764 - 147,814,596 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
fipronil  (EXP)

References
Additional References at PubMed
PMID:14702039  


Genomics

Variants

.
Variants in LINC01502
4 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 9p24.3-q34.3(chr9:204193-138179445) copy number gain See cases [RCV000133791] Chr9:204193..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q34.11-34.3(chr9:130513207-138124532)x3 copy number gain See cases [RCV000133778] Chr9:130513207..138124532 [GRCh38]
Chr9:133388594..141018984 [GRCh37]
Chr9:132378415..140138805 [NCBI36]
Chr9:9q34.11-34.3		 pathogenic
GRCh38/hg38 9q34.3(chr9:135164984-136437047)x3 copy number gain See cases [RCV000134910] Chr9:135164984..136437047 [GRCh38]
Chr9:138056830..139331499 [GRCh37]
Chr9:137196651..138451320 [NCBI36]
Chr9:9q34.3		 uncertain significance
GRCh38/hg38 9q34.11-34.3(chr9:129068560-138179445)x3 copy number gain See cases [RCV000134916] Chr9:129068560..138179445 [GRCh38]
Chr9:131830839..141073897 [GRCh37]
Chr9:130870660..140193718 [NCBI36]
Chr9:9q34.11-34.3		 pathogenic
GRCh38/hg38 9q33.2-34.3(chr9:121073102-138179445)x3 copy number gain See cases [RCV000134920] Chr9:121073102..138179445 [GRCh38]
Chr9:123835380..141073897 [GRCh37]
Chr9:122875201..140193718 [NCBI36]
Chr9:9q33.2-34.3		 pathogenic
GRCh38/hg38 9q34.13-34.3(chr9:132986903-138114463)x3 copy number gain See cases [RCV000136790] Chr9:132986903..138114463 [GRCh38]
Chr9:135862290..141008915 [GRCh37]
Chr9:134852111..140128736 [NCBI36]
Chr9:9q34.13-34.3		 pathogenic
GRCh38/hg38 9q34.2-34.3(chr9:133504071-138159073)x3 copy number gain See cases [RCV000137825] Chr9:133504071..138159073 [GRCh38]
Chr9:136324358..141053525 [GRCh37]
Chr9:135314179..140173346 [NCBI36]
Chr9:9q34.2-34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138124524)x3 copy number gain See cases [RCV000138783] Chr9:193412..138124524 [GRCh38]
Chr9:204090..141018976 [GRCh37]
Chr9:194090..140138797 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138159073)x3 copy number gain See cases [RCV000138962] Chr9:193412..138159073 [GRCh38]
Chr9:204104..141053525 [GRCh37]
Chr9:194104..140173346 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic|conflicting data from submitters
GRCh38/hg38 9p11.2-q34.3(chr9:193412-138159073)x3 copy number gain See cases [RCV000139207] Chr9:193412..138159073 [GRCh38]
Chr9:68420641..141053525 [GRCh37]
Chr9:67910461..140173346 [NCBI36]
Chr9:9p11.2-q34.3		 pathogenic
GRCh38/hg38 9q34.2-34.3(chr9:133996227-138124524)x3 copy number gain See cases [RCV000139807] Chr9:133996227..138124524 [GRCh38]
Chr9:136861349..141018976 [GRCh37]
Chr9:135851170..140138797 [NCBI36]
Chr9:9q34.2-34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:203861-138125937)x3 copy number gain See cases [RCV000141876] Chr9:203861..138125937 [GRCh38]
Chr9:203861..141020389 [GRCh37]
Chr9:193861..140140210 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q34.2-34.3(chr9:133918071-138159073)x3 copy number gain See cases [RCV000142955] Chr9:133918071..138159073 [GRCh38]
Chr9:136783193..141053525 [GRCh37]
Chr9:135773014..140173346 [NCBI36]
Chr9:9q34.2-34.3		 pathogenic
GRCh38/hg38 9q34.13-34.3(chr9:132386553-138059695)x3 copy number gain See cases [RCV000142636] Chr9:132386553..138059695 [GRCh38]
Chr9:135261940..140954147 [GRCh37]
Chr9:134251761..140073968 [NCBI36]
Chr9:9q34.13-34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:203862-138125937)x3 copy number gain See cases [RCV000143476] Chr9:203862..138125937 [GRCh38]
Chr9:203862..141020389 [GRCh37]
Chr9:193862..140140210 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3 copy number gain See cases [RCV000148113] Chr9:193412..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q33.2-34.3(chr9:121112395-138075224)x3 copy number gain See cases [RCV000051009] Chr9:121112395..138075224 [GRCh38]
Chr9:123874673..140969676 [GRCh37]
Chr9:122914494..140089497 [NCBI36]
Chr9:9q33.2-34.3		 pathogenic
GRCh38/hg38 9q33.2-34.3(chr9:122792658-138124532)x3 copy number gain See cases [RCV000051040] Chr9:122792658..138124532 [GRCh38]
Chr9:125554937..141018984 [GRCh37]
Chr9:124594758..140138805 [NCBI36]
Chr9:9q33.2-34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3 copy number gain See cases [RCV000050348] Chr9:193412..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q34.2-34.3(chr9:134428674-138154922)x1 copy number loss See cases [RCV000052936] Chr9:134428674..138154922 [GRCh38]
Chr9:137320520..141049374 [GRCh37]
Chr9:136460341..140169195 [NCBI36]
Chr9:9q34.2-34.3		 pathogenic
GRCh38/hg38 9q34.3(chr9:135452016-137613738)x1 copy number loss See cases [RCV000052937] Chr9:135452016..137613738 [GRCh38]
Chr9:138343862..140508190 [GRCh37]
Chr9:137483683..139628011 [NCBI36]
Chr9:9q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138124532)x3 copy number gain See cases [RCV000053745] Chr9:193412..138124532 [GRCh38]
Chr9:204193..141018984 [GRCh37]
Chr9:194193..140138805 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138114463)x3 copy number gain See cases [RCV000053746] Chr9:193412..138114463 [GRCh38]
Chr9:214367..141008915 [GRCh37]
Chr9:204367..140128736 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053748]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053748]|See cases [RCV000053748] Chr9:193412..138179445 [GRCh38]
Chr9:266045..141073897 [GRCh37]
Chr9:256045..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q34.11-34.3(chr9:129068560-136495351)x3 copy number gain See cases [RCV000053779] Chr9:129068560..136495351 [GRCh38]
Chr9:131830839..139389803 [GRCh37]
Chr9:130870660..138509624 [NCBI36]
Chr9:9q34.11-34.3		 pathogenic
GRCh38/hg38 9q34.2-34.3(chr9:134174698-138138735)x3 copy number gain See cases [RCV000053814] Chr9:134174698..138138735 [GRCh38]
Chr9:137091194..141033187 [GRCh37]
Chr9:136029641..140153008 [NCBI36]
Chr9:9q34.2-34.3		 pathogenic
GRCh38/hg38 9q33.2-34.3(chr9:121586837-138179445)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053776]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053776]|See cases [RCV000053776] Chr9:121586837..138179445 [GRCh38]
Chr9:124349116..141073897 [GRCh37]
Chr9:123388937..140193718 [NCBI36]
Chr9:9q33.2-34.3		 pathogenic
GRCh38/hg38 9q34.3(chr9:134962336-137240181)x1 copy number loss See cases [RCV002640756] Chr9:134962336..137240181 [GRCh38]
Chr9:9q34.3		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:716
Count of miRNA genes:521
Interacting mature miRNAs:571
Transcripts:ENST00000445997, ENST00000447497, ENST00000447907
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 8 1 7 1 4 4
Low 10 1 317 3 33 1 19 7 36 7 75 84 2 1 2
Below cutoff 702 470 589 147 582 76 864 328 1493 130 620 765 82 200 415 3

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000445997
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl9135,574,951 - 135,587,112 (+)Ensembl
RefSeq Acc Id: ENST00000447497
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl9135,583,743 - 135,585,272 (+)Ensembl
RefSeq Acc Id: ENST00000447907
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl9135,574,935 - 135,585,364 (+)Ensembl
RefSeq Acc Id: NR_034016
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh389135,574,925 - 135,587,112 (+)NCBI
HuRef9107,928,580 - 107,940,339 (+)NCBI
CHM1_19138,615,365 - 138,627,546 (+)NCBI
T2T-CHM13v2.09147,802,764 - 147,814,596 (+)NCBI
Sequence:
RefSeq Acc Id: NR_034017
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh389135,574,925 - 135,587,112 (+)NCBI
HuRef9107,928,580 - 107,940,339 (+)NCBI
CHM1_19138,615,365 - 138,627,546 (+)NCBI
T2T-CHM13v2.09147,802,764 - 147,814,596 (+)NCBI
Sequence:
RefSeq Acc Id: NR_109814
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh389135,574,925 - 135,587,112 (+)NCBI
HuRef9107,928,580 - 107,940,339 (+)NCBI
CHM1_19138,615,365 - 138,627,546 (+)NCBI
T2T-CHM13v2.09147,802,764 - 147,814,596 (+)NCBI
Sequence:
Promoters
RGD ID:15096346
Promoter ID:EPDNEWNC_H1187
Type:multiple initiation site
Name:LINC01502_1
Description:long intergenic non-protein coding RNA 1502 [Source:HGNCSymbol;Acc:HGNC:51183]
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
GRCh389135,574,951 - 135,575,011EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC01502 COSMIC
Ensembl Genes ENSG00000237339 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000445997 ENTREZGENE
GTEx ENSG00000237339 GTEx
HGNC ID HGNC:51183 ENTREZGENE
Human Proteome Map LINC01502 Human Proteome Map
NCBI Gene LINC01502 ENTREZGENE
RNAcentral URS0000759FD6 RNACentral
  URS000075A52E RNACentral
  URS000075B1BA RNACentral