LINC01608 (long intergenic non-protein coding RNA 1608) - Rat Genome Database

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Gene: LINC01608 (long intergenic non-protein coding RNA 1608) Homo sapiens
Analyze
Symbol: LINC01608
Name: long intergenic non-protein coding RNA 1608
RGD ID: 10002876
HGNC Page HGNC
Description: INTERACTS WITH aflatoxin B1; leflunomide
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 Ensembl8110,899,996 - 111,040,372 (-)EnsemblGRCh38hg38GRCh38
GRCh388110,937,690 - 111,027,433 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh378111,949,919 - 112,039,662 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map8q23.2NCBI
HuRef8107,339,327 - 107,362,108 (-)NCBIHuRef
CHM1_18111,990,340 - 112,080,035 (-)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:16344560  


Genomics

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:225
Count of miRNA genes:211
Interacting mature miRNAs:218
Transcripts:ENST00000523557, ENST00000524283
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 1 18 15 10 15 2 6 1 1 10
Low 12 9 103 24 11 25 485 5 2287 4 298 29 1 2 434 1
Below cutoff 281 167 279 60 132 33 523 290 1223 65 244 201 31 73 356 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000523557
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,982,983 - 111,027,401 (-)Ensembl
RefSeq Acc Id: ENST00000524283
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,937,690 - 111,027,433 (-)Ensembl
RefSeq Acc Id: ENST00000653924
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,981,557 - 111,027,498 (-)Ensembl
RefSeq Acc Id: ENST00000657323
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,981,194 - 111,027,599 (-)Ensembl
RefSeq Acc Id: ENST00000657532
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,982,369 - 111,027,525 (-)Ensembl
RefSeq Acc Id: ENST00000658028
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,900,058 - 111,027,337 (-)Ensembl
RefSeq Acc Id: ENST00000658081
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,932,777 - 111,027,468 (-)Ensembl
RefSeq Acc Id: ENST00000658119
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,932,870 - 111,027,498 (-)Ensembl
RefSeq Acc Id: ENST00000658508
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,981,789 - 111,027,593 (-)Ensembl
RefSeq Acc Id: ENST00000658597
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,899,998 - 111,027,599 (-)Ensembl
RefSeq Acc Id: ENST00000658733
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,982,361 - 111,027,432 (-)Ensembl
RefSeq Acc Id: ENST00000659834
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,981,615 - 111,027,443 (-)Ensembl
RefSeq Acc Id: ENST00000660015
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,946,981 - 111,027,511 (-)Ensembl
RefSeq Acc Id: ENST00000660667
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8111,014,387 - 111,027,424 (-)Ensembl
RefSeq Acc Id: ENST00000661561
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,931,710 - 111,027,593 (-)Ensembl
RefSeq Acc Id: ENST00000661954
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,931,003 - 111,027,432 (-)Ensembl
RefSeq Acc Id: ENST00000662310
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,899,998 - 111,027,599 (-)Ensembl
RefSeq Acc Id: ENST00000663408
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,981,296 - 111,027,615 (-)Ensembl
RefSeq Acc Id: ENST00000663666
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8111,004,559 - 111,027,434 (-)Ensembl
RefSeq Acc Id: ENST00000664704
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,923,653 - 111,027,424 (-)Ensembl
RefSeq Acc Id: ENST00000665011
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,982,983 - 111,027,525 (-)Ensembl
RefSeq Acc Id: ENST00000665803
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,900,003 - 111,027,420 (-)Ensembl
RefSeq Acc Id: ENST00000667145
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,932,801 - 111,027,498 (-)Ensembl
RefSeq Acc Id: ENST00000668858
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,899,999 - 111,027,435 (-)Ensembl
RefSeq Acc Id: ENST00000668936
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8111,022,204 - 111,027,711 (-)Ensembl
RefSeq Acc Id: ENST00000668956
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,969,628 - 111,027,517 (-)Ensembl
RefSeq Acc Id: ENST00000669698
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,900,001 - 111,027,443 (-)Ensembl
RefSeq Acc Id: ENST00000669744
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,982,361 - 111,037,388 (-)Ensembl
RefSeq Acc Id: ENST00000669893
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,946,979 - 111,040,372 (-)Ensembl
RefSeq Acc Id: ENST00000669997
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8111,002,555 - 111,027,430 (-)Ensembl
RefSeq Acc Id: ENST00000670392
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,899,996 - 111,027,420 (-)Ensembl
RefSeq Acc Id: ENST00000671489
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8110,899,999 - 111,027,529 (-)Ensembl
RefSeq Acc Id: NR_125416
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh388110,982,950 - 111,027,433 (-)NCBI
CHM1_18112,035,584 - 112,080,035 (-)NCBI
Sequence:
RefSeq Acc Id: NR_125417
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh388110,937,690 - 111,027,433 (-)NCBI
CHM1_18111,990,340 - 112,080,035 (-)NCBI
Sequence:
Promoters
RGD ID:15096255
Promoter ID:EPDNEWNC_H1088
Type:initiation region
Name:LINC01608_1
Description:long intergenic non-protein coding RNA 1608 [Source:HGNCSymbol;Acc:HGNC:51662]
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
GRCh388111,027,422 - 111,027,482EPDNEWNC

Clinical Variants
Name Type Condition(s) Position(s) Clinical 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
NC_000008.11:g.110938968G>T single nucleotide variant Lung cancer [RCV000106817] Chr8:110938968 [GRCh38]
Chr8:111951197 [GRCh37]
Chr8:8q23.2
uncertain significance
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 LINC01608 COSMIC
Ensembl Genes ENSG00000253877 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000524283 ENTREZGENE
GTEx ENSG00000253877 GTEx
HGNC ID HGNC:51662 ENTREZGENE
Human Proteome Map LINC01608 Human Proteome Map
NCBI Gene LINC01608 ENTREZGENE
RNAcentral URS000059D50D RNACentral
  URS00007E3D42 RNACentral