LINC01619 (long intergenic non-protein coding RNA 1619) - Rat Genome Database

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Gene: LINC01619 (long intergenic non-protein coding RNA 1619) Homo sapiens
Analyze
Symbol: LINC01619
Name: long intergenic non-protein coding RNA 1619
RGD ID: 7245856
HGNC Page HGNC:27409
Description: INTERACTS WITH aflatoxin B1; all-trans-retinoic acid; bisphenol A
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: C12orf79; uncharacterized protein C12orf79; uncharacterized protein LOC256021
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381291,984,976 - 92,142,831 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1291,984,976 - 92,142,914 (-)EnsemblGRCh38hg38GRCh38
GRCh371292,378,752 - 92,536,607 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map12q21.33NCBI
HuRef1289,446,263 - 89,603,827 (-)NCBIHuRef
CHM1_11292,343,657 - 92,501,473 (-)NCBICHM1_1
T2T-CHM13v2.01291,962,471 - 92,120,393 (-)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:16344560   PMID:25056061   PMID:29334763  


Genomics

Variants

.
Variants in LINC01619
8 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 12q21.33-22(chr12:90996508-94872818)x1 copy number loss See cases [RCV000138659] Chr12:90996508..94872818 [GRCh38]
Chr12:91390285..95266594 [GRCh37]
Chr12:89914416..93790725 [NCBI36]
Chr12:12q21.33-22		 likely pathogenic
GRCh38/hg38 12p13.33-q24.33(chr12:121271-133196807)x3 copy number gain See cases [RCV000139555] Chr12:121271..133196807 [GRCh38]
Chr12:282465..133773393 [GRCh37]
Chr12:100698..132283466 [NCBI36]
Chr12:12p13.33-q24.33		 pathogenic
GRCh38/hg38 12q21.33-24.11(chr12:91044318-109133210)x3 copy number gain See cases [RCV000142447] Chr12:91044318..109133210 [GRCh38]
Chr12:91438095..109571015 [GRCh37]
Chr12:89962226..108055398 [NCBI36]
Chr12:12q21.33-24.11		 pathogenic
GRCh38/hg38 12q21.1-22(chr12:73485697-92795805)x1 copy number loss See cases [RCV000143099] Chr12:73485697..92795805 [GRCh38]
Chr12:73879477..93189581 [GRCh37]
Chr12:72165744..91713712 [NCBI36]
Chr12:12q21.1-22		 pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:1-133851895)x3 copy number gain See cases [RCV000258805] Chr12:1..133851895 [GRCh37]
Chr12:12p13.33-q24.33		 pathogenic|likely pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:173787-133777902)x3 copy number gain See cases [RCV000510482] Chr12:173787..133777902 [GRCh37]
Chr12:12p13.33-q24.33		 pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:173787-133777902) copy number gain See cases [RCV000511643] Chr12:173787..133777902 [GRCh37]
Chr12:12p13.33-q24.33		 pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:191619-133777645)x3 copy number gain not provided [RCV000750246] Chr12:191619..133777645 [GRCh37]
Chr12:12p13.33-q24.33		 pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:621220-133779118)x3 copy number gain not provided [RCV000750253] Chr12:621220..133779118 [GRCh37]
Chr12:12p13.33-q24.33		 pathogenic
GRCh37/hg19 12q21.33-22(chr12:91621655-96014946)x1 copy number loss not provided [RCV000737994] Chr12:91621655..96014946 [GRCh37]
Chr12:12q21.33-22		 uncertain significance
GRCh37/hg19 12q21.2-22(chr12:77737623-94330526)x1 copy number loss not provided [RCV000848027] Chr12:77737623..94330526 [GRCh37]
Chr12:12q21.2-22		 pathogenic
GRCh37/hg19 12q21.33-22(chr12:91073628-92829926) copy number loss not specified [RCV002053010] Chr12:91073628..92829926 [GRCh37]
Chr12:12q21.33-22		 uncertain significance
GRCh37/hg19 12q21.33-22(chr12:92154559-93692934)x3 copy number gain not specified [RCV003986960] Chr12:92154559..93692934 [GRCh37]
Chr12:12q21.33-22		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:2376
Count of miRNA genes:851
Interacting mature miRNAs:975
Transcripts:ENST00000546975, ENST00000548552, ENST00000549802, ENST00000551306, ENST00000551563, ENST00000551764, ENST00000551843, ENST00000552106, ENST00000552277, ENST00000553207
Prediction methods:Microtar, 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.

Markers in Region
RH78863  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371292,378,947 - 92,379,077UniSTSGRCh37
Build 361290,903,078 - 90,903,208RGDNCBI36
Celera1292,050,115 - 92,050,245RGD
Cytogenetic Map12q21.33UniSTS
HuRef1289,446,458 - 89,446,588UniSTS
GeneMap99-GB4 RH Map12356.07UniSTS


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 5 2 4 1 216 1 5 30 1 4 6 1
Low 1079 1204 691 134 1119 95 2307 431 1230 184 736 881 40 862 1214 2
Below cutoff 1296 1754 986 463 583 344 1914 1664 2354 215 662 668 129 341 1496 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000546975
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1291,985,778 - 92,142,668 (-)Ensembl
RefSeq Acc Id: ENST00000548552
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1292,141,039 - 92,142,914 (-)Ensembl
RefSeq Acc Id: ENST00000549802
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1291,985,090 - 92,142,671 (-)Ensembl
RefSeq Acc Id: ENST00000551306
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1291,993,085 - 92,028,257 (-)Ensembl
RefSeq Acc Id: ENST00000551563
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1291,985,778 - 92,142,668 (-)Ensembl
RefSeq Acc Id: ENST00000551764
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1291,988,323 - 91,993,529 (-)Ensembl
RefSeq Acc Id: ENST00000551843
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1291,984,976 - 92,141,713 (-)Ensembl
RefSeq Acc Id: ENST00000552106
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1291,985,778 - 92,142,668 (-)Ensembl
RefSeq Acc Id: ENST00000552277
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1291,993,192 - 92,137,021 (-)Ensembl
RefSeq Acc Id: ENST00000553207
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1291,988,387 - 92,142,831 (-)Ensembl
RefSeq Acc Id: ENST00000664336
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1291,985,124 - 91,988,988 (-)Ensembl
RefSeq Acc Id: ENST00000671521
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1291,985,151 - 91,994,623 (-)Ensembl
RefSeq Acc Id: ENST00000689659
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1291,987,986 - 92,061,937 (-)Ensembl
RefSeq Acc Id: NR_046159
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381291,984,976 - 92,141,713 (-)NCBI
GRCh371292,378,752 - 92,536,447 (-)NCBI
HuRef1289,446,263 - 89,603,827 (-)NCBI
CHM1_11292,343,657 - 92,500,515 (-)NCBI
T2T-CHM13v2.01291,962,471 - 92,119,275 (-)NCBI
Sequence:
RefSeq Acc Id: NR_046160
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381291,984,976 - 92,142,831 (-)NCBI
GRCh371292,378,752 - 92,536,447 (-)NCBI
HuRef1289,446,263 - 89,603,827 (-)NCBI
CHM1_11292,343,657 - 92,501,633 (-)NCBI
T2T-CHM13v2.01291,962,471 - 92,120,393 (-)NCBI
Sequence:
RefSeq Acc Id: NR_132339
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381291,984,976 - 92,142,831 (-)NCBI
CHM1_11292,343,657 - 92,501,633 (-)NCBI
T2T-CHM13v2.01291,962,471 - 92,120,393 (-)NCBI
Sequence:
RefSeq Acc Id: NR_132340
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381291,984,976 - 92,142,831 (-)NCBI
CHM1_11292,343,657 - 92,501,633 (-)NCBI
T2T-CHM13v2.01291,962,471 - 92,120,393 (-)NCBI
Sequence:
RefSeq Acc Id: NR_132341
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381291,984,976 - 92,142,831 (-)NCBI
CHM1_11292,343,657 - 92,501,633 (-)NCBI
T2T-CHM13v2.01291,962,471 - 92,120,393 (-)NCBI
Sequence:
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V211-F1-model_v2 AlphaFold G3V211 1-115 view protein structure


Additional Information

Database Acc Id Source(s)
COSMIC LINC01619 COSMIC
Ensembl Genes ENSG00000257242 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000549802 ENTREZGENE
  ENST00000551843 ENTREZGENE
GTEx ENSG00000257242 GTEx
HGNC ID HGNC:27409 ENTREZGENE
Human Proteome Map LINC01619 Human Proteome Map
NCBI Gene C12orf79 ENTREZGENE
RNAcentral URS00008E3966 RNACentral
  URS00008E39CC RNACentral
  URS00008E3A0C RNACentral
  URS00008E3A2E RNACentral
  URS00008E3A34 RNACentral
UniProt CL079_HUMAN UniProtKB/Swiss-Prot
UniProt Secondary F8VRL5 UniProtKB/Swiss-Prot
  F8VVU4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-09-29 LINC01619  long intergenic non-protein coding RNA 1619  C12orf79  chromosome 12 open reading frame 79  Symbol and/or name change 5135510 APPROVED