LINC00200 (long intergenic non-protein coding RNA 200) - Rat Genome Database

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Gene: LINC00200 (long intergenic non-protein coding RNA 200) Homo sapiens
Analyze
Symbol: LINC00200
Name: long intergenic non-protein coding RNA 200
RGD ID: 1605188
HGNC Page HGNC:30974
Description: INTERACTS WITH aflatoxin B1; arsenite(3-); benzo[a]pyrene
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: PREDICTED
Previously known as: C10orf139; FLJ40354; NCRNA00200; RP11-529L18.1
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38101,159,768 - 1,164,672 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl101,159,768 - 1,289,426 (+)EnsemblGRCh38hg38GRCh38
GRCh37101,205,708 - 1,210,612 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36101,195,708 - 1,200,612 (+)NCBINCBI36Build 36hg18NCBI36
Celera101,154,821 - 1,159,769 (+)NCBICelera
Cytogenetic Map10p15.3NCBI
HuRef101,144,310 - 1,149,225 (+)NCBIHuRef
CHM1_1101,205,717 - 1,210,708 (+)NCBICHM1_1
T2T-CHM13v2.0101,156,489 - 1,161,402 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
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:14702039   PMID:33822325  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 10p15.3-13(chr10:73856-12815915)x3 copy number gain See cases [RCV000135340] Chr10:73856..12815915 [GRCh38]
Chr10:119796..12857914 [GRCh37]
Chr10:109796..12897920 [NCBI36]
Chr10:10p15.3-13		 pathogenic
GRCh38/hg38 10p15.3-15.2(chr10:90421-3058742)x1 copy number loss See cases [RCV000135585] Chr10:90421..3058742 [GRCh38]
Chr10:224406..3100934 [GRCh37]
Chr10:126361..3090934 [NCBI36]
Chr10:10p15.3-15.2		 likely pathogenic
GRCh38/hg38 10p15.3-14(chr10:90421-11713049)x3 copy number gain See cases [RCV000135533] Chr10:90421..11713049 [GRCh38]
Chr10:224406..11755048 [GRCh37]
Chr10:126361..11795054 [NCBI36]
Chr10:10p15.3-14		 pathogenic|uncertain significance
GRCh38/hg38 10p15.3(chr10:918720-1843751)x4 copy number gain See cases [RCV000137589] Chr10:918720..1843751 [GRCh38]
Chr10:964660..1885945 [GRCh37]
Chr10:954660..1875945 [NCBI36]
Chr10:10p15.3		 likely benign|uncertain significance
GRCh38/hg38 10p15.3-13(chr10:70478-15373336)x3 copy number gain See cases [RCV000137384] Chr10:70478..15373336 [GRCh38]
Chr10:224406..15415335 [GRCh37]
Chr10:106418..15455341 [NCBI36]
Chr10:10p15.3-13		 uncertain significance
GRCh38/hg38 10p15.3(chr10:70478-1759743)x3 copy number gain See cases [RCV000138245] Chr10:70478..1759743 [GRCh38]
Chr10:224406..1801937 [GRCh37]
Chr10:106418..1791937 [NCBI36]
Chr10:10p15.3		 uncertain significance
GRCh38/hg38 10p15.3-12.1(chr10:90205-26339978)x3 copy number gain See cases [RCV000138428] Chr10:90205..26339978 [GRCh38]
Chr10:224406..26628907 [GRCh37]
Chr10:126145..26668913 [NCBI36]
Chr10:10p15.3-12.1		 pathogenic
GRCh38/hg38 10p15.3-15.2(chr10:538646-3636571)x1 copy number loss See cases [RCV000138321] Chr10:538646..3636571 [GRCh38]
Chr10:584586..3678763 [GRCh37]
Chr10:574586..3668763 [NCBI36]
Chr10:10p15.3-15.2		 uncertain significance
GRCh38/hg38 10p15.3-13(chr10:70478-13736564)x1 copy number loss See cases [RCV000138960] Chr10:70478..13736564 [GRCh38]
Chr10:224406..13778564 [GRCh37]
Chr10:106418..13818570 [NCBI36]
Chr10:10p15.3-13		 pathogenic
GRCh38/hg38 10p15.3-13(chr10:54086-13205916)x3 copy number gain See cases [RCV000142292] Chr10:54086..13205916 [GRCh38]
Chr10:100026..13247916 [GRCh37]
Chr10:90026..13287922 [NCBI36]
Chr10:10p15.3-13		 pathogenic
GRCh38/hg38 10p15.3(chr10:54086-1600803)x1 copy number loss See cases [RCV000142235] Chr10:54086..1600803 [GRCh38]
Chr10:100026..1642998 [GRCh37]
Chr10:90026..1632998 [NCBI36]
Chr10:10p15.3		 pathogenic
GRCh38/hg38 10p15.3(chr10:899498-1339873)x3 copy number gain See cases [RCV000142659] Chr10:899498..1339873 [GRCh38]
Chr10:945438..1382068 [GRCh37]
Chr10:935438..1372068 [NCBI36]
Chr10:10p15.3		 uncertain significance
GRCh38/hg38 10p15.3-12.31(chr10:54086-19336980)x1 copy number loss See cases [RCV000143703] Chr10:54086..19336980 [GRCh38]
Chr10:100026..19625909 [GRCh37]
Chr10:90026..19665915 [NCBI36]
Chr10:10p15.3-12.31		 pathogenic|likely pathogenic
GRCh38/hg38 10p15.3(chr10:730608-1358880)x3 copy number gain See cases [RCV000051593] Chr10:730608..1358880 [GRCh38]
Chr10:776548..1401075 [GRCh37]
Chr10:766548..1391075 [NCBI36]
Chr10:10p15.3		 uncertain significance
GRCh38/hg38 10p15.3(chr10:899498-1687440)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051594]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051594]|See cases [RCV000051594] Chr10:899498..1687440 [GRCh38]
Chr10:945438..1729634 [GRCh37]
Chr10:935438..1719634 [NCBI36]
Chr10:10p15.3		 uncertain significance
GRCh38/hg38 10p15.3-14(chr10:90421-8442783)x3 copy number gain See cases [RCV000051107] Chr10:90421..8442783 [GRCh38]
Chr10:224406..8484746 [GRCh37]
Chr10:126361..8524752 [NCBI36]
Chr10:10p15.3-14		 pathogenic
GRCh38/hg38 10p15.3-14(chr10:90421-6769994)x3 copy number gain See cases [RCV000051132] Chr10:90421..6769994 [GRCh38]
Chr10:224406..6811956 [GRCh37]
Chr10:126361..6851962 [NCBI36]
Chr10:10p15.3-14		 pathogenic
GRCh38/hg38 10p15.3-15.1(chr10:69260-6209368)x1 copy number loss See cases [RCV000052493] Chr10:69260..6209368 [GRCh38]
Chr10:224406..6251331 [GRCh37]
Chr10:105200..6291337 [NCBI36]
Chr10:10p15.3-15.1		 pathogenic
GRCh38/hg38 10p15.3(chr10:87458-2482736)x1 copy number loss See cases [RCV000052494] Chr10:87458..2482736 [GRCh38]
Chr10:224406..2524928 [GRCh37]
Chr10:123398..2514928 [NCBI36]
Chr10:10p15.3		 pathogenic
GRCh38/hg38 10p15.3(chr10:90221-1843892)x1 copy number loss See cases [RCV000052495] Chr10:90221..1843892 [GRCh38]
Chr10:224406..1886086 [GRCh37]
Chr10:126161..1876086 [NCBI36]
Chr10:10p15.3		 pathogenic
GRCh38/hg38 10p15.3-13(chr10:90421-15569528)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052496]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052496]|See cases [RCV000052496] Chr10:90421..15569528 [GRCh38]
Chr10:224406..15611527 [GRCh37]
Chr10:126361..15651533 [NCBI36]
Chr10:10p15.3-13		 pathogenic
GRCh38/hg38 10p15.3(chr10:90421-2894483)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052498]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052498]|See cases [RCV000052498] Chr10:90421..2894483 [GRCh38]
Chr10:224406..2936675 [GRCh37]
Chr10:126361..2926675 [NCBI36]
Chr10:10p15.3		 pathogenic
GRCh38/hg38 10p15.3-12.31(chr10:69261-19184047)x3 copy number gain See cases [RCV000053507] Chr10:69261..19184047 [GRCh38]
Chr10:224406..19472976 [GRCh37]
Chr10:105201..19512982 [NCBI36]
Chr10:10p15.3-12.31		 pathogenic
GRCh38/hg38 10p15.3-12.2(chr10:90221-22567425)x3 copy number gain See cases [RCV000053508] Chr10:90221..22567425 [GRCh38]
Chr10:224406..22856354 [GRCh37]
Chr10:126161..22896360 [NCBI36]
Chr10:10p15.3-12.2		 pathogenic
GRCh38/hg38 10p15.3-14(chr10:90421-7085100)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053511]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053511]|See cases [RCV000053511] Chr10:90421..7085100 [GRCh38]
Chr10:224406..7127062 [GRCh37]
Chr10:126361..7167068 [NCBI36]
Chr10:10p15.3-14		 pathogenic
GRCh38/hg38 10p15.3-12.1(chr10:90421-29058318)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053512]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053512]|See cases [RCV000053512] Chr10:90421..29058318 [GRCh38]
Chr10:224406..29347247 [GRCh37]
Chr10:126361..29387253 [NCBI36]
Chr10:10p15.3-12.1		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:251
Count of miRNA genes:235
Interacting mature miRNAs:243
Transcripts:ENST00000425630, ENST00000583117
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.

Markers in Region
SHGC-146377  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37101,206,562 - 1,206,867UniSTSGRCh37
Build 36101,196,562 - 1,196,867RGDNCBI36
Celera101,155,675 - 1,155,980RGD
Cytogenetic Map10p15.3UniSTS
HuRef101,145,170 - 1,145,475UniSTS
TNG Radiation Hybrid Map10172.0UniSTS


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 3 1 1 13 1 3 3 1 1 3 1
Low 19 5 25 5 46 5 16 6 23 3 391 21 1 12 11 2
Below cutoff 809 838 401 91 464 50 1344 720 1009 64 309 450 42 501 892 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000425630
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl101,159,768 - 1,165,112 (+)Ensembl
RefSeq Acc Id: ENST00000583117
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl101,159,804 - 1,160,997 (+)Ensembl
RefSeq Acc Id: ENST00000647993
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl101,159,812 - 1,164,789 (+)Ensembl
RefSeq Acc Id: ENST00000652683
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl101,159,811 - 1,180,923 (+)Ensembl
RefSeq Acc Id: ENST00000655745
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl101,159,812 - 1,289,426 (+)Ensembl
RefSeq Acc Id: ENST00000666348
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl101,159,833 - 1,202,982 (+)Ensembl
RefSeq Acc Id: NR_015376
RefSeq Status: PREDICTED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38101,159,768 - 1,164,672 (+)NCBI
GRCh37101,205,708 - 1,210,612 (+)RGD
Celera101,154,821 - 1,159,769 (+)RGD
HuRef101,144,310 - 1,149,225 (+)ENTREZGENE
CHM1_1101,205,717 - 1,210,708 (+)NCBI
T2T-CHM13v2.0101,156,489 - 1,161,402 (+)NCBI
Sequence:
Protein Sequences
GenBank Protein EAW86512 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences

Promoters
RGD ID:15096360
Promoter ID:EPDNEWNC_H1194
Type:initiation region
Name:LINC00200_1
Description:long intergenic non-protein coding RNA 200 [Source:HGNCSymbol;Acc:HGNC:30974]
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
GRCh38101,159,836 - 1,159,896EPDNEWNC
RGD ID:6787945
Promoter ID:HG_KWN:8336
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:K562
Transcripts:NR_015376,   UC009XHO.1
Position:
Human AssemblyChrPosition (strand)Source
Build 36101,195,426 - 1,195,926 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
COSMIC LINC00200 COSMIC
Ensembl Genes ENSG00000229205 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000425630 ENTREZGENE
GTEx ENSG00000229205 GTEx
HGNC ID HGNC:30974 ENTREZGENE
Human Proteome Map LINC00200 Human Proteome Map
NCBI Gene 399706 ENTREZGENE
PharmGKB PA165548929 PharmGKB
RNAcentral URS00003472D5 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-09-01 LINC00200  long intergenic non-protein coding RNA 200  NCRNA00200  non-protein coding RNA 200  Symbol and/or name change 5135510 APPROVED