LINC02197 (long intergenic non-protein coding RNA 2197) - Rat Genome Database

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Gene: LINC02197 (long intergenic non-protein coding RNA 2197) Homo sapiens
Analyze
Symbol: LINC02197
Name: long intergenic non-protein coding RNA 2197
RGD ID: 11667431
HGNC Page HGNC:53063
Description: ASSOCIATED WITH amenorrhea; Primary amenorrhea
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
GRCh38571,321,031 - 71,446,756 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl571,337,182 - 71,446,772 (-)EnsemblGRCh38hg38GRCh38
GRCh37570,616,858 - 70,742,583 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map5q13.2NCBI
CHM1_1570,049,572 - 70,175,313 (-)NCBICHM1_1
T2T-CHM13v2.0571,802,345 - 71,928,080 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
amenorrhea  (IAGP)

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References
Additional References at PubMed
PMID:8889548   PMID:16344560  


Genomics

Variants

.
Variants in LINC02197
2 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 5q13.2(chr5:70436365-71420835)x1 copy number loss See cases [RCV000050656] Chr5:70436365..71420835 [GRCh38]
Chr5:69732192..70716662 [GRCh37]
Chr5:69767948..70752418 [NCBI36]
Chr5:5q13.2		 benign
GRCh38/hg38 5q13.2(chr5:71090743-71367241)x1 copy number loss See cases [RCV000136344] Chr5:71090743..71367241 [GRCh38]
Chr5:70386570..70663068 [GRCh37]
Chr5:70422326..70698824 [NCBI36]
Chr5:5q13.2		 benign
GRCh38/hg38 5q13.2(chr5:71074103-71361891)x1 copy number loss See cases [RCV000136420] Chr5:71074103..71361891 [GRCh38]
Chr5:70369930..70657718 [GRCh37]
Chr5:70405686..70693474 [NCBI36]
Chr5:5q13.2		 benign
GRCh38/hg38 5q13.2(chr5:71358232-71562995)x1 copy number loss See cases [RCV000142201] Chr5:71358232..71562995 [GRCh38]
Chr5:70654059..70858822 [GRCh37]
Chr5:70689815..70894578 [NCBI36]
Chr5:5q13.2		 uncertain significance
GRCh38/hg38 5p15.33-q13.3(chr5:22149-74412725)x3 copy number gain See cases [RCV000138780] Chr5:22149..74412725 [GRCh38]
Chr5:22149..73708550 [GRCh37]
Chr5:75149..73744306 [NCBI36]
Chr5:5p15.33-q13.3		 pathogenic
NC_000005.10:g.69553767_71361920dup duplication Primary amenorrhea [RCV000754422] Chr5:69553767..71361920 [GRCh38]
Chr5:68849594..70657747 [GRCh37]
Chr5:5q13.2		 benign
NC_000005.9:g.70308101_70657747del349647 deletion Primary amenorrhea [RCV000754425] Chr5:71012274..71361920 [GRCh38]
Chr5:70308101..70657747 [GRCh37]
Chr5:5q13.2		 benign
NC_000005.9:g.68818173_70657747del1839575 deletion Primary amenorrhea [RCV000754421] Chr5:69522346..71361920 [GRCh38]
Chr5:68818173..70657747 [GRCh37]
Chr5:5q13.2		 benign
GRCh38/hg38 5q11.2-13.2(chr5:58785203-73519962)x1 copy number loss Intellectual disability [RCV000984869] Chr5:58785203..73519962 [GRCh38]
Chr5:5q11.2-13.2		 likely pathogenic
GRCh38/hg38 5q13.2(chr5:71378409-72329454) copy number gain Autism spectrum disorder [RCV003883394] Chr5:71378409..72329454 [GRCh38]
Chr5:5q13.2		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:222
Count of miRNA genes:209
Interacting mature miRNAs:212
Transcripts:ENST00000502659, ENST00000517705
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 15 15 15 9 2 4 2 31
Low 14 9 441 307 20 308 9 18 84 73 162 119 4
Below cutoff 1260 913 795 156 414 104 1500 699 2214 177 885 1011 54 416 911 3

Sequence

Nucleotide Sequences
RefSeq Transcripts NR_134268 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_134269 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC138832 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC139463 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC145141 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC146949 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC244635 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC245931 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC277768 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC277825 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC277851 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC277918 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK123868 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK310013 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CF141492 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068273 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DA795384 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000502659
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl571,351,855 - 71,446,342 (-)Ensembl
RefSeq Acc Id: ENST00000517705
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl571,353,487 - 71,446,336 (-)Ensembl
RefSeq Acc Id: ENST00000671145
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl571,337,182 - 71,446,772 (-)Ensembl
RefSeq Acc Id: NR_134268
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38571,351,855 - 71,446,336 (-)NCBI
CHM1_1570,080,395 - 70,174,893 (-)NCBI
T2T-CHM13v2.0571,833,188 - 71,927,660 (-)NCBI
Sequence:
RefSeq Acc Id: NR_134269
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38571,321,031 - 71,446,756 (-)NCBI
CHM1_1570,049,572 - 70,175,313 (-)NCBI
T2T-CHM13v2.0571,802,345 - 71,928,080 (-)NCBI
Sequence:
Promoters
RGD ID:15095903
Promoter ID:EPDNEWNC_H733
Type:initiation region
Name:LINC02197_1
Description:long intergenic non-protein coding RNA 2197 [Source:HGNCSymbol;Acc:HGNC:53063]
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
GRCh38571,446,316 - 71,446,376EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC02197 COSMIC
Ensembl Genes ENSG00000250387 Ensembl
GTEx ENSG00000250387 GTEx
HGNC ID HGNC:53063 ENTREZGENE
Human Proteome Map LINC02197 Human Proteome Map
NCBI Gene LINC02197 ENTREZGENE
RNAcentral URS00008BC2AB RNACentral
  URS0000A76415 RNACentral