LINC01609 (long intergenic non-protein coding RNA 1609) - Rat Genome Database

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Gene: LINC01609 (long intergenic non-protein coding RNA 1609) Homo sapiens
Analyze
Symbol: LINC01609
Name: long intergenic non-protein coding RNA 1609
RGD ID: 10002985
HGNC Page HGNC
Description: INTERACTS WITH aflatoxin B2; benzo[a]pyrene
Type: ncrna
RefSeq Status: VALIDATED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl8111,093,263 - 111,236,203 (-)EnsemblGRCh38hg38GRCh38
GRCh388111,098,961 - 111,236,203 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh378112,111,190 - 112,248,432 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map8q23.2-q23.3NCBI
HuRef8107,448,114 - 107,570,339 (-)NCBIHuRef
CHM1_18112,151,688 - 112,288,585 (-)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

Genomics

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:234
Count of miRNA genes:210
Interacting mature miRNAs:213
Transcripts:ENST00000519506, ENST00000522778
Prediction methods:Microtar, 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 1 1 3 6 1
Low 124 9 43 24 189 28 243 56 88 66 468 234 8 3 4
Below cutoff 51 19 103 36 33 33 76 28 75 76 58 92 3 8 24

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000519506
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8111,098,961 - 111,236,171 (-)Ensembl
RefSeq Acc Id: ENST00000522778
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8111,183,292 - 111,236,203 (-)Ensembl
RefSeq Acc Id: ENST00000653374
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8111,098,498 - 111,236,203 (-)Ensembl
RefSeq Acc Id: ENST00000653400
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8111,093,264 - 111,236,198 (-)Ensembl
RefSeq Acc Id: ENST00000653848
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8111,183,514 - 111,236,198 (-)Ensembl
RefSeq Acc Id: ENST00000654293
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8111,168,696 - 111,236,198 (-)Ensembl
RefSeq Acc Id: ENST00000655136
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8111,182,455 - 111,236,179 (-)Ensembl
RefSeq Acc Id: ENST00000663639
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8111,183,514 - 111,236,190 (-)Ensembl
RefSeq Acc Id: ENST00000669352
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8111,093,264 - 111,236,156 (-)Ensembl
RefSeq Acc Id: ENST00000671497
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8111,093,263 - 111,236,190 (-)Ensembl
RefSeq Acc Id: NR_125418
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh388111,098,961 - 111,236,203 (-)NCBI
CHM1_18112,151,688 - 112,288,585 (-)NCBI
Sequence:
Promoters
RGD ID:15096246
Promoter ID:EPDNEWNC_H1089
Type:initiation region
Name:LINC01609_1
Description:long intergenic non-protein coding RNA 1609 [Source:HGNCSymbol;Acc:HGNC:51663]
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
GRCh388111,236,179 - 111,236,239EPDNEWNC

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NR_125418.1(LINC01609):n.277+4442T>A single nucleotide variant Lung cancer [RCV000106819] Chr8:111108990 [GRCh38]
Chr8:112121219 [GRCh37]
Chr8:8q23.3
uncertain significance
NR_125418.1(LINC01609):n.123-36745C>A single nucleotide variant Lung cancer [RCV000106820] Chr8:111153345 [GRCh38]
Chr8:112165574 [GRCh37]
Chr8:8q23.3
uncertain significance
NR_125418.1(LINC01609):n.122+32739C>A single nucleotide variant Lung cancer [RCV000106821] Chr8:111203343 [GRCh38]
Chr8:112215572 [GRCh37]
Chr8:8q23.3
uncertain significance
NR_125418.1(LINC01609):n.122+3253A>T single nucleotide variant Lung cancer [RCV000106822] Chr8:111232829 [GRCh38]
Chr8:112245058 [GRCh37]
Chr8:8q23.3
uncertain significance
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145049449)x3 copy number gain See cases [RCV000051206] Chr8:241530..145049449 [GRCh38]
Chr8:191530..146274835 [GRCh37]
Chr8:181530..146245639 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145054634)x3 copy number gain See cases [RCV000053602] Chr8:241530..145054634 [GRCh38]
Chr8:191530..146280020 [GRCh37]
Chr8:181530..146250824 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:244417-145054775)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053604]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053604]|See cases [RCV000053604] Chr8:244417..145054775 [GRCh38]
Chr8:194417..146280161 [GRCh37]
Chr8:184417..146250965 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q23.2-23.3(chr8:110718242-112097796)x3 copy number gain See cases [RCV000141508] Chr8:110718242..112097796 [GRCh38]
Chr8:111730471..113110025 [GRCh37]
Chr8:111799647..113179201 [NCBI36]
Chr8:8q23.2-23.3
benign
GRCh38/hg38 8q22.3-24.3(chr8:100867343-145070385)x3 copy number gain See cases [RCV000141694] Chr8:100867343..145070385 [GRCh38]
Chr8:101879571..146295771 [GRCh37]
Chr8:101948747..146266575 [NCBI36]
Chr8:8q22.3-24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:208048-145070385)x3 copy number gain See cases [RCV000141808] Chr8:208048..145070385 [GRCh38]
Chr8:158048..146295771 [GRCh37]
Chr8:148048..146266575 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8p21.3-q24.3(chr8:21291522-145070385)x3 copy number gain See cases [RCV000142021] Chr8:21291522..145070385 [GRCh38]
Chr8:21149033..146295771 [GRCh37]
Chr8:21193313..146266575 [NCBI36]
Chr8:8p21.3-q24.3
pathogenic
GRCh38/hg38 8q21.13-24.3(chr8:78614077-145054634)x3 copy number gain See cases [RCV000142597] Chr8:78614077..145054634 [GRCh38]
Chr8:79526312..146280020 [GRCh37]
Chr8:79688867..146250824 [NCBI36]
Chr8:8q21.13-24.3
pathogenic
GRCh38/hg38 8q22.3-24.3(chr8:103306336-145068712)x3 copy number gain See cases [RCV000142810] Chr8:103306336..145068712 [GRCh38]
Chr8:104318564..146294098 [GRCh37]
Chr8:104387740..146264902 [NCBI36]
Chr8:8q22.3-24.3
pathogenic|likely pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:226452-145068712)x3 copy number gain See cases [RCV000142858] Chr8:226452..145068712 [GRCh38]
Chr8:176452..146294098 [GRCh37]
Chr8:166452..146264902 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q21.2-24.3(chr8:85765999-145070385)x3 copy number gain See cases [RCV000143659] Chr8:85765999..145070385 [GRCh38]
Chr8:86778228..146295771 [GRCh37]
Chr8:86863079..146266575 [NCBI36]
Chr8:8q21.2-24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145054634)x3 copy number gain See cases [RCV000148092] Chr8:241530..145054634 [GRCh38]
Chr8:191530..146280020 [GRCh37]
Chr8:181530..146250824 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q22.1-24.3(chr8:95606052-145054775)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053677]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053677]|See cases [RCV000053677] Chr8:95606052..145054775 [GRCh38]
Chr8:96618280..146280161 [GRCh37]
Chr8:96687456..146250965 [NCBI36]
Chr8:8q22.1-24.3
pathogenic
GRCh38/hg38 8q22.1-24.3(chr8:94682154-145068656)x3 copy number gain See cases [RCV000134353] Chr8:94682154..145068656 [GRCh38]
Chr8:95694382..146294042 [GRCh37]
Chr8:95763558..146264846 [NCBI36]
Chr8:8q22.1-24.3
pathogenic
GRCh38/hg38 8q21.3-24.23(chr8:86300584-137022587)x3 copy number gain See cases [RCV000135621] Chr8:86300584..137022587 [GRCh38]
Chr8:87312813..138034830 [GRCh37]
Chr8:87381929..138104012 [NCBI36]
Chr8:8q21.3-24.23
pathogenic|likely pathogenic
GRCh38/hg38 8q21.3-24.3(chr8:87931152-145068712)x3 copy number gain See cases [RCV000138551] Chr8:87931152..145068712 [GRCh38]
Chr8:88943380..146294098 [GRCh37]
Chr8:89012496..146264902 [NCBI36]
Chr8:8q21.3-24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241605-145054781)x3 copy number gain See cases [RCV000138643] Chr8:241605..145054781 [GRCh38]
Chr8:191605..146280167 [GRCh37]
Chr8:181605..146250971 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q21.13-24.3(chr8:77480050-145068712)x3 copy number gain See cases [RCV000139036] Chr8:77480050..145068712 [GRCh38]
Chr8:78392286..146294098 [GRCh37]
Chr8:78554841..146264902 [NCBI36]
Chr8:8q21.13-24.3
pathogenic
GRCh38/hg38 8q11.1-24.3(chr8:46031340-139285494)x3 copy number gain See cases [RCV000139539] Chr8:46031340..139285494 [GRCh38]
Chr8:46942962..140297737 [GRCh37]
Chr8:47062127..140366919 [NCBI36]
Chr8:8q11.1-24.3
pathogenic
GRCh38/hg38 8q22.1-24.3(chr8:97382873-145070385)x3 copy number gain See cases [RCV000140447] Chr8:97382873..145070385 [GRCh38]
Chr8:98395101..146295771 [GRCh37]
Chr8:98464277..146266575 [NCBI36]
Chr8:8q22.1-24.3
pathogenic

Additional Information

Database Acc Id Source(s)
COSMIC LINC01609 COSMIC
Ensembl Genes ENSG00000253103 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000519506 ENTREZGENE
GTEx ENSG00000253103 GTEx
HGNC ID HGNC:51663 ENTREZGENE
Human Proteome Map LINC01609 Human Proteome Map
NCBI Gene LINC01609 ENTREZGENE
RNAcentral URS00007E43B4 RNACentral