LINC00996 (long intergenic non-protein coding RNA 996) - Rat Genome Database

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Gene: LINC00996 (long intergenic non-protein coding RNA 996) Homo sapiens
Analyze
Symbol: LINC00996
Name: long intergenic non-protein coding RNA 996
RGD ID: 7248139
HGNC Page HGNC:27800
Description: INTERACTS WITH bisphenol A; fulvestrant; nickel atom
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: RP11-511P7.2
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh387150,433,654 - 150,448,140 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl7150,433,654 - 150,448,141 (+)EnsemblGRCh38hg38GRCh38
GRCh377150,130,742 - 150,145,228 (+)NCBIGRCh37GRCh37hg19GRCh37
Celera7144,687,853 - 144,702,336 (+)NCBICelera
Cytogenetic Map7q36.1NCBI
HuRef7143,946,635 - 143,961,118 (+)NCBIHuRef
CHM1_17150,139,134 - 150,153,616 (+)NCBICHM1_1
T2T-CHM13v2.07151,612,008 - 151,626,492 (+)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v27149,468,573 - 149,483,057 (+)NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
bisphenol A  (EXP)
fulvestrant  (EXP)
nickel atom  (EXP)
propanal  (EXP)
propofol  (EXP)

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:12690205   PMID:14702039  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
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 7q35-36.2(chr7:147345844-153833351)x3 copy number gain See cases [RCV000135825] Chr7:147345844..153833351 [GRCh38]
Chr7:147042936..153530436 [GRCh37]
Chr7:146673869..153161369 [NCBI36]
Chr7:7q35-36.2		 pathogenic
GRCh38/hg38 7q33-36.2(chr7:137751200-154815582)x3 copy number gain See cases [RCV000136592] Chr7:137751200..154815582 [GRCh38]
Chr7:137435946..154607292 [GRCh37]
Chr7:137086486..154238225 [NCBI36]
Chr7:7q33-36.2		 pathogenic
GRCh38/hg38 7q21.3-36.3(chr7:97419852-158923762)x3 copy number gain See cases [RCV000136717] Chr7:97419852..158923762 [GRCh38]
Chr7:97049164..158716453 [GRCh37]
Chr7:96887100..158409214 [NCBI36]
Chr7:7q21.3-36.3		 pathogenic
GRCh38/hg38 7q34-36.3(chr7:141960861-159335866)x1 copy number loss See cases [RCV000137256] Chr7:141960861..159335866 [GRCh38]
Chr7:142528609..159128556 [GRCh37]
Chr7:141307130..158821317 [NCBI36]
Chr7:7q34-36.3		 pathogenic
GRCh38/hg38 7q35-36.3(chr7:145436544-159331441)x1 copy number loss See cases [RCV000137338] Chr7:145436544..159331441 [GRCh38]
Chr7:145133637..159124131 [GRCh37]
Chr7:144764570..158816892 [NCBI36]
Chr7:7q35-36.3		 pathogenic|likely pathogenic
GRCh38/hg38 7q35-36.3(chr7:145250254-159335866)x1 copy number loss See cases [RCV000138005] Chr7:145250254..159335866 [GRCh38]
Chr7:144947347..159128556 [GRCh37]
Chr7:144578280..158821317 [NCBI36]
Chr7:7q35-36.3		 pathogenic
GRCh38/hg38 7q33-36.3(chr7:134666829-158591882)x1 copy number loss See cases [RCV000138120] Chr7:134666829..158591882 [GRCh38]
Chr7:134351581..158384574 [GRCh37]
Chr7:134002121..158077335 [NCBI36]
Chr7:7q33-36.3		 pathogenic
GRCh38/hg38 7q35-36.3(chr7:146047157-157522158)x1 copy number loss See cases [RCV000137781] Chr7:146047157..157522158 [GRCh38]
Chr7:145744250..157314852 [GRCh37]
Chr7:145375183..157007613 [NCBI36]
Chr7:7q35-36.3		 pathogenic
GRCh38/hg38 7q31.32-36.3(chr7:121863759-159335865)x3 copy number gain See cases [RCV000138847] Chr7:121863759..159335865 [GRCh38]
Chr7:121503813..159128555 [GRCh37]
Chr7:121291049..158821316 [NCBI36]
Chr7:7q31.32-36.3		 pathogenic
GRCh38/hg38 7q36.1-36.2(chr7:150113232-154162779)x3 copy number gain See cases [RCV000138566] Chr7:150113232..154162779 [GRCh38]
Chr7:149810321..153859864 [GRCh37]
Chr7:149441254..153490797 [NCBI36]
Chr7:7q36.1-36.2		 likely pathogenic
GRCh38/hg38 7q32.3-36.3(chr7:132444095-159335866)x3 copy number gain See cases [RCV000139654] Chr7:132444095..159335866 [GRCh38]
Chr7:132128854..159128556 [GRCh37]
Chr7:131779394..158821317 [NCBI36]
Chr7:7q32.3-36.3		 pathogenic
GRCh38/hg38 7q36.1-36.2(chr7:150275734-153342804)x3 copy number gain See cases [RCV000139660] Chr7:150275734..153342804 [GRCh38]
Chr7:149972823..153039889 [GRCh37]
Chr7:149603756..152670822 [NCBI36]
Chr7:7q36.1-36.2		 uncertain significance
GRCh38/hg38 7q31.2-36.3(chr7:115459015-159325817)x3 copy number gain See cases [RCV000141413] Chr7:115459015..159325817 [GRCh38]
Chr7:115099069..159118507 [GRCh37]
Chr7:114886305..158811268 [NCBI36]
Chr7:7q31.2-36.3		 pathogenic
GRCh38/hg38 7q32.3-36.3(chr7:131228764-159335866)x3 copy number gain See cases [RCV000142802] Chr7:131228764..159335866 [GRCh38]
Chr7:130913523..159128556 [GRCh37]
Chr7:130564063..158821317 [NCBI36]
Chr7:7q32.3-36.3		 pathogenic
GRCh38/hg38 7q36.1-36.3(chr7:150260297-159325876)x1 copy number loss See cases [RCV000142592] Chr7:150260297..159325876 [GRCh38]
Chr7:149957386..159118566 [GRCh37]
Chr7:149588319..158811327 [NCBI36]
Chr7:7q36.1-36.3		 pathogenic
GRCh38/hg38 7q32.3-36.3(chr7:131171478-159327017)x3 copy number gain See cases [RCV000143754] Chr7:131171478..159327017 [GRCh38]
Chr7:130856237..159119707 [GRCh37]
Chr7:130506777..158812468 [NCBI36]
Chr7:7q32.3-36.3		 pathogenic
GRCh38/hg38 7q32.3-36.3(chr7:132438072-159327017)x3 copy number gain See cases [RCV000143707] Chr7:132438072..159327017 [GRCh38]
Chr7:132122831..159119707 [GRCh37]
Chr7:131773371..158812468 [NCBI36]
Chr7:7q32.3-36.3		 pathogenic
GRCh38/hg38 7q35-36.3(chr7:147144002-159327017)x1 copy number loss See cases [RCV000143503] Chr7:147144002..159327017 [GRCh38]
Chr7:146841094..159119707 [GRCh37]
Chr7:146472027..158812468 [NCBI36]
Chr7:7q35-36.3		 pathogenic
GRCh38/hg38 7q36.1(chr7:150319864-152674271)x1 copy number loss See cases [RCV000050552] Chr7:150319864..152674271 [GRCh38]
Chr7:150016953..152371356 [GRCh37]
Chr7:149647886..152002289 [NCBI36]
Chr7:7q36.1		 pathogenic
GRCh38/hg38 7q32.1-36.3(chr7:129310166-159282390)x3 copy number gain See cases [RCV000050876] Chr7:129310166..159282390 [GRCh38]
Chr7:128950007..159075079 [GRCh37]
Chr7:128737243..158767840 [NCBI36]
Chr7:7q32.1-36.3		 pathogenic
GRCh38/hg38 7q32.3-36.3(chr7:132850196-159325876)x3 copy number gain See cases [RCV000051101] Chr7:132850196..159325876 [GRCh38]
Chr7:132534956..159118566 [GRCh37]
Chr7:132185496..158811327 [NCBI36]
Chr7:7q32.3-36.3		 pathogenic
GRCh38/hg38 7q35-36.3(chr7:147250465-159325876)x1 copy number loss See cases [RCV000051108] Chr7:147250465..159325876 [GRCh38]
Chr7:146947557..159118566 [GRCh37]
Chr7:146578490..158811327 [NCBI36]
Chr7:7q35-36.3		 pathogenic
GRCh38/hg38 7q35-36.1(chr7:143884559-152674271)x1 copy number loss See cases [RCV000050750] Chr7:143884559..152674271 [GRCh38]
Chr7:143581652..152371356 [GRCh37]
Chr7:143212585..152002289 [NCBI36]
Chr7:7q35-36.1		 pathogenic
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 7q33-36.3(chr7:136309982-159307523)x3 copy number gain See cases [RCV000053576] Chr7:136309982..159307523 [GRCh38]
Chr7:135994730..159100212 [GRCh37]
Chr7:135645270..158792973 [NCBI36]
Chr7:7q33-36.3		 pathogenic
GRCh38/hg38 7q34-36.3(chr7:142021716-159325876)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053577]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053577]|See cases [RCV000053577] Chr7:142021716..159325876 [GRCh38]
Chr7:142528609..159118566 [GRCh37]
Chr7:141367985..158811327 [NCBI36]
Chr7:7q34-36.3		 pathogenic
GRCh38/hg38 7q34-36.3(chr7:139365967-159282531)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000054175]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000054175]|See cases [RCV000054175] Chr7:139365967..159282531 [GRCh38]
Chr7:139050713..159075220 [GRCh37]
Chr7:138701253..158767981 [NCBI36]
Chr7:7q34-36.3		 pathogenic
GRCh38/hg38 7q34-36.3(chr7:140754198-159307523)x1 copy number loss See cases [RCV000054176] Chr7:140754198..159307523 [GRCh38]
Chr7:140453998..159100212 [GRCh37]
Chr7:140100467..158792973 [NCBI36]
Chr7:7q34-36.3		 pathogenic
GRCh38/hg38 7q34-36.3(chr7:142358524-159282531)x1 copy number loss See cases [RCV000054177] Chr7:142358524..159282531 [GRCh38]
Chr7:142528609..159075220 [GRCh37]
Chr7:141726947..158767981 [NCBI36]
Chr7:7q34-36.3		 pathogenic
GRCh38/hg38 7q35-36.3(chr7:143884559-159282390)x1 copy number loss See cases [RCV000054178] Chr7:143884559..159282390 [GRCh38]
Chr7:143581652..159075079 [GRCh37]
Chr7:143212585..158767840 [NCBI36]
Chr7:7q35-36.3		 pathogenic
GRCh38/hg38 7q35-36.3(chr7:145699944-159296617)x1 copy number loss See cases [RCV000054188] Chr7:145699944..159296617 [GRCh38]
Chr7:145397037..159089306 [GRCh37]
Chr7:145027970..158782067 [NCBI36]
Chr7:7q35-36.3		 pathogenic
GRCh38/hg38 7q36.1(chr7:148256584-152332535)x1 copy number loss See cases [RCV000054189] Chr7:148256584..152332535 [GRCh38]
Chr7:147953676..152029620 [GRCh37]
Chr7:147584609..151660553 [NCBI36]
Chr7:7q36.1		 pathogenic
GRCh38/hg38 7q34-36.3(chr7:138620939-159233475)x3 copy number gain Neurodevelopmental disorder [RCV003327610] Chr7:138620939..159233475 [GRCh38]
Chr7:7q34-36.3		 likely pathogenic
GRCh38/hg38 7q33-36.3(chr7:137463392-159345973)x3 copy number gain Neurodevelopmental disorder [RCV003327609] Chr7:137463392..159345973 [GRCh38]
Chr7:7q33-36.3		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:558
Count of miRNA genes:431
Interacting mature miRNAs:450
Transcripts:ENST00000477392, ENST00000486954
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 pharyngeal arch
High
Medium 64 1 719 2 1 10
Low 683 302 327 138 570 108 122 86 659 118 319 693 30 142 60 1 1
Below cutoff 1382 1905 1201 451 586 332 2656 1334 2489 258 975 690 131 868 1632 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000477392
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7150,433,654 - 150,448,140 (+)Ensembl
RefSeq Acc Id: ENST00000486954
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7150,433,730 - 150,442,892 (+)Ensembl
RefSeq Acc Id: ENST00000692633
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7150,433,768 - 150,448,141 (+)Ensembl
RefSeq Acc Id: NR_034033
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh387150,433,654 - 150,448,140 (+)NCBI
GRCh377150,130,742 - 150,145,228 (+)NCBI
HuRef7143,946,635 - 143,961,118 (+)NCBI
CHM1_17150,139,134 - 150,153,616 (+)NCBI
T2T-CHM13v2.07151,612,008 - 151,626,492 (+)NCBI
CRA_TCAGchr7v27149,468,573 - 149,483,057 (+)NCBI
Sequence:
Protein Sequences
GenBank Protein EAL24478 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences

Promoters
RGD ID:15096192
Promoter ID:EPDNEWNC_H1007
Type:initiation region
Name:LINC00996_1
Description:long intergenic non-protein coding RNA 996 [Source:HGNCSymbol;Acc:HGNC:27800]
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
GRCh387150,433,730 - 150,433,790EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC00996 COSMIC
Ensembl Genes ENSG00000242258 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000477392 ENTREZGENE
GTEx ENSG00000242258 GTEx
HGNC ID HGNC:27800 ENTREZGENE
Human Proteome Map LINC00996 Human Proteome Map
NCBI Gene LINC00996 ENTREZGENE
RNAcentral URS000054D820 RNACentral