LINC01122 (long intergenic non-protein coding RNA 1122) - Rat Genome Database

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Gene: LINC01122 (long intergenic non-protein coding RNA 1122) Homo sapiens
Analyze
Symbol: LINC01122
Name: long intergenic non-protein coding RNA 1122
RGD ID: 7377872
HGNC Page HGNC:49267
Description: INTERACTS WITH aflatoxin B1; antirheumatic drug; benzo[a]pyrene
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: AC007092.1
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38258,520,753 - 59,063,766 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl258,427,738 - 59,063,766 (+)EnsemblGRCh38hg38GRCh38
GRCh37258,747,888 - 59,290,901 (+)NCBIGRCh37GRCh37hg19GRCh37
Celera258,591,257 - 59,134,274 (+)NCBICelera
Cytogenetic Map2p16.1NCBI
HuRef258,489,201 - 59,032,344 (+)NCBIHuRef
CHM1_1258,678,088 - 59,221,227 (+)NCBICHM1_1
T2T-CHM13v2.0258,525,587 - 59,068,770 (+)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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
Additional References at PubMed
PMID:14702039   PMID:21460842   PMID:21668797   PMID:23055271   PMID:23563607   PMID:24159190   PMID:25158072   PMID:25959816  


Genomics

Variants

.
Variants in LINC01122
78 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NR_033873.1(LINC01122):n.185+49733G>C single nucleotide variant Lung cancer [RCV000092228] Chr2:58570670 [GRCh38]
Chr2:58797805 [GRCh37]
Chr2:2p16.1		 uncertain significance
NR_033873.1(LINC01122):n.185+53064G>T single nucleotide variant Lung cancer [RCV000092230] Chr2:58574001 [GRCh38]
Chr2:58801136 [GRCh37]
Chr2:2p16.1		 uncertain significance
NR_033873.1(LINC01122):n.186-40768C>G single nucleotide variant Lung cancer [RCV000092231] Chr2:58615882 [GRCh38]
Chr2:58843017 [GRCh37]
Chr2:2p16.1		 uncertain significance
NR_033873.1(LINC01122):n.424+17599G>T single nucleotide variant Lung cancer [RCV000092232] Chr2:58868205 [GRCh38]
Chr2:59095340 [GRCh37]
Chr2:2p16.1		 uncertain significance
NR_033873.1(LINC01122):n.833+22569G>T single nucleotide variant Lung cancer [RCV000092233] Chr2:58948478 [GRCh38]
Chr2:59175613 [GRCh37]
Chr2:2p16.1		 uncertain significance
NR_033873.1(LINC01122):n.833+33926T>C single nucleotide variant Lung cancer [RCV000092234] Chr2:58959835 [GRCh38]
Chr2:59186970 [GRCh37]
Chr2:2p16.1		 uncertain significance
GRCh38/hg38 2p16.1-11.2(chr2:58279519-83586962)x3 copy number gain See cases [RCV000136053] Chr2:58279519..83586962 [GRCh38]
Chr2:58506654..83814086 [GRCh37]
Chr2:58360158..83667597 [NCBI36]
Chr2:2p16.1-11.2		 pathogenic
GRCh38/hg38 2p16.1(chr2:55570578-60519844)x1 copy number loss See cases [RCV000137092] Chr2:55570578..60519844 [GRCh38]
Chr2:55797714..60746979 [GRCh37]
Chr2:55651218..60600483 [NCBI36]
Chr2:2p16.1		 pathogenic|uncertain significance
GRCh38/hg38 2p16.3-11.2(chr2:47620388-86702722)x3 copy number gain See cases [RCV000137586] Chr2:47620388..86702722 [GRCh38]
Chr2:47847527..86929845 [GRCh37]
Chr2:47701031..86783356 [NCBI36]
Chr2:2p16.3-11.2		 uncertain significance
GRCh38/hg38 2p16.1(chr2:57802633-58951698)x3 copy number gain See cases [RCV000137145] Chr2:57802633..58951698 [GRCh38]
Chr2:58029768..59178833 [GRCh37]
Chr2:57883272..59032337 [NCBI36]
Chr2:2p16.1		 uncertain significance
GRCh38/hg38 2p16.1(chr2:58951639-59191685)x1 copy number loss See cases [RCV000140649] Chr2:58951639..59191685 [GRCh38]
Chr2:59178774..59418820 [GRCh37]
Chr2:59032278..59272324 [NCBI36]
Chr2:2p16.1		 uncertain significance
GRCh38/hg38 2p25.1-11.2(chr2:7495123-87705899)x3 copy number gain See cases [RCV000141494] Chr2:7495123..87705899 [GRCh38]
Chr2:7635254..88005418 [GRCh37]
Chr2:7552705..87786533 [NCBI36]
Chr2:2p25.1-11.2		 benign
GRCh38/hg38 2p16.1-15(chr2:58031916-63611810)x1 copy number loss See cases [RCV000143007] Chr2:58031916..63611810 [GRCh38]
Chr2:58259051..63838944 [GRCh37]
Chr2:58112555..63692448 [NCBI36]
Chr2:2p16.1-15		 pathogenic
GRCh38/hg38 2p16.1-15(chr2:56738054-62473668)x1 copy number loss See cases [RCV000054020] Chr2:56738054..62473668 [GRCh38]
Chr2:56965189..62700803 [GRCh37]
Chr2:56818693..62554307 [NCBI36]
Chr2:2p16.1-15		 pathogenic
GRCh38/hg38 2p16.1-15(chr2:57249378-61842734)x1 copy number loss See cases [RCV000054021] Chr2:57249378..61842734 [GRCh38]
Chr2:57476513..62069869 [GRCh37]
Chr2:57330017..61923373 [NCBI36]
Chr2:2p16.1-15		 pathogenic
GRCh38/hg38 2p16.1-14(chr2:58873039-64190332)x1 copy number loss See cases [RCV000054022] Chr2:58873039..64190332 [GRCh38]
Chr2:59100174..64417466 [GRCh37]
Chr2:58953678..64270970 [NCBI36]
Chr2:2p16.1-14		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1326
Count of miRNA genes:569
Interacting mature miRNAs:631
Transcripts:ENST00000422723, ENST00000422793, ENST00000427421, ENST00000429095, ENST00000429664, ENST00000449448, ENST00000452840, ENST00000455219
Prediction methods:Miranda, Rnahybrid, Targetscan
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 visual system adipose tissue appendage entire extraembryonic component
High
Medium 12
Low 7 5 86 6 25 6 178 6 1792 21 556 63 2 1
Below cutoff 1442 616 1177 252 649 112 1573 554 1533 152 740 1106 145 367 942 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000422723
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,427,799 - 58,925,701 (+)Ensembl
RefSeq Acc Id: ENST00000422793
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,428,412 - 58,931,081 (+)Ensembl
RefSeq Acc Id: ENST00000427421
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,520,753 - 59,061,653 (+)Ensembl
RefSeq Acc Id: ENST00000429095
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,428,338 - 58,925,701 (+)Ensembl
RefSeq Acc Id: ENST00000429664
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,428,338 - 58,931,156 (+)Ensembl
RefSeq Acc Id: ENST00000449448
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,428,385 - 59,003,992 (+)Ensembl
RefSeq Acc Id: ENST00000452840
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,428,338 - 59,063,766 (+)Ensembl
RefSeq Acc Id: ENST00000455219
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,614,326 - 58,696,327 (+)Ensembl
RefSeq Acc Id: ENST00000650056
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,428,412 - 59,061,649 (+)Ensembl
RefSeq Acc Id: ENST00000655072
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,460,932 - 58,657,757 (+)Ensembl
RefSeq Acc Id: ENST00000656135
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,428,301 - 58,930,289 (+)Ensembl
RefSeq Acc Id: ENST00000656193
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,460,952 - 58,628,521 (+)Ensembl
RefSeq Acc Id: ENST00000656381
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,427,880 - 58,932,162 (+)Ensembl
RefSeq Acc Id: ENST00000657130
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,428,412 - 58,931,081 (+)Ensembl
RefSeq Acc Id: ENST00000657378
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,460,932 - 58,697,131 (+)Ensembl
RefSeq Acc Id: ENST00000662396
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,633,714 - 58,697,041 (+)Ensembl
RefSeq Acc Id: ENST00000663407
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,428,385 - 58,697,130 (+)Ensembl
RefSeq Acc Id: ENST00000664741
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,607,102 - 58,931,072 (+)Ensembl
RefSeq Acc Id: ENST00000665429
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,460,928 - 58,931,076 (+)Ensembl
RefSeq Acc Id: ENST00000665478
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,428,373 - 58,932,127 (+)Ensembl
RefSeq Acc Id: ENST00000665525
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,428,412 - 58,931,079 (+)Ensembl
RefSeq Acc Id: ENST00000668410
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,460,985 - 58,931,072 (+)Ensembl
RefSeq Acc Id: ENST00000669630
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,460,948 - 58,696,476 (+)Ensembl
RefSeq Acc Id: ENST00000671194
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,925,609 - 58,930,766 (+)Ensembl
RefSeq Acc Id: ENST00000684946
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,428,406 - 58,931,081 (+)Ensembl
RefSeq Acc Id: ENST00000687108
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,614,315 - 58,931,078 (+)Ensembl
RefSeq Acc Id: ENST00000701416
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,428,402 - 58,919,001 (+)Ensembl
RefSeq Acc Id: ENST00000702114
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl258,427,738 - 58,428,292 (+)Ensembl
RefSeq Acc Id: NR_033873
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38258,520,753 - 59,063,766 (+)NCBI
GRCh37258,747,888 - 59,290,901 (+)NCBI
HuRef258,489,201 - 59,032,344 (+)NCBI
CHM1_1258,678,088 - 59,221,227 (+)NCBI
T2T-CHM13v2.0258,525,587 - 59,068,770 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC01122 COSMIC
Ensembl Genes ENSG00000233723 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000452840 ENTREZGENE
GTEx ENSG00000233723 GTEx
HGNC ID HGNC:49267 ENTREZGENE
Human Proteome Map LINC01122 Human Proteome Map
NCBI Gene LINC01122 ENTREZGENE
RNAcentral URS000075E2F0 RNACentral