LINC01004 (long intergenic non-protein coding RNA 1004) - Rat Genome Database

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Gene: LINC01004 (long intergenic non-protein coding RNA 1004) Homo sapiens
Analyze
Symbol: LINC01004
Name: long intergenic non-protein coding RNA 1004
RGD ID: 7247744
HGNC Page HGNC:48961
Description: Predicted to be a structural constituent of ribosome. Predicted to be located in ribosome; INTERACTS WITH (+)-catechin; 2-hydroxypropanoic acid; aristolochic acid A.
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
GRCh387104,981,747 - 104,991,165 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl7104,950,315 - 105,013,068 (-)EnsemblGRCh38hg38GRCh38
GRCh377104,622,194 - 104,631,612 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map7q22.3NCBI
HuRef798,981,769 - 98,991,189 (-)NCBIHuRef
CHM1_17104,555,506 - 104,564,924 (-)NCBICHM1_1
T2T-CHM13v2.07106,296,452 - 106,305,868 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v27103,982,885 - 103,992,302 (-)NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Cellular Component
ribosome  (IEA)

Molecular Function

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:35490653   PMID:36688997   PMID:36721155  


Genomics

Variants

.
Variants in LINC01004
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 7p22.3-q36.3(chr7:54185-159282390)x1 copy number loss See cases [RCV000135401] Chr7:54185..159282390 [GRCh38]
Chr7:54185..159075079 [GRCh37]
Chr7:149268..158767840 [NCBI36]
Chr7:7p22.3-q36.3		 pathogenic
GRCh38/hg38 7q21.3-36.3(chr7:97419852-158923762)x3 copy number gain See cases [RCV000136717] Chr7:97419852..158923762 [GRCh38]
Chr7:97049164..158716453 [GRCh37]
Chr7:96887100..158409214 [NCBI36]
Chr7:7q21.3-36.3		 pathogenic
GRCh38/hg38 7q22.1-31.31(chr7:102196924-121278641)x1 copy number loss See cases [RCV000137522] Chr7:102196924..121278641 [GRCh38]
Chr7:101912320..120918695 [GRCh37]
Chr7:101626924..120705931 [NCBI36]
Chr7:7q22.1-31.31		 pathogenic
GRCh38/hg38 7q22.2-22.3(chr7:104434729-106134635)x3 copy number gain See cases [RCV000140728] Chr7:104434729..106134635 [GRCh38]
Chr7:104075177..105775081 [GRCh37]
Chr7:103862413..105562317 [NCBI36]
Chr7:7q22.2-22.3		 uncertain significance
GRCh38/hg38 7q22.1-22.3(chr7:101525795-105432462)x3 copy number gain See cases [RCV000050705] Chr7:101525795..105432462 [GRCh38]
Chr7:101169076..105072909 [GRCh37]
Chr7:100955796..104860145 [NCBI36]
Chr7:7q22.1-22.3		 pathogenic
GRCh38/hg38 7q22.1-31.1(chr7:101807149-112414850)x1 copy number loss See cases [RCV000050924] Chr7:101807149..112414850 [GRCh38]
Chr7:101450429..112054905 [GRCh37]
Chr7:101237149..111842141 [NCBI36]
Chr7:7q22.1-31.1		 pathogenic
GRCh38/hg38 7p22.3-q36.3(chr7:53985-159282531)x1 copy number loss See cases [RCV000052250] Chr7:53985..159282531 [GRCh38]
Chr7:53985..159075220 [GRCh37]
Chr7:149068..158767981 [NCBI36]
Chr7:7p22.3-q36.3		 pathogenic
GRCh38/hg38 7q22.1-22.3(chr7:101700341-105162893)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000054156]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000054156]|See cases [RCV000054156] Chr7:101700341..105162893 [GRCh38]
Chr7:101343621..104803340 [GRCh37]
Chr7:101130341..104590576 [NCBI36]
Chr7:7q22.1-22.3		 pathogenic
GRCh38/hg38 7q22.1-22.3(chr7:102808199-105701108)x1 copy number loss See cases [RCV000054157] Chr7:102808199..105701108 [GRCh38]
Chr7:102448646..105341555 [GRCh37]
Chr7:102235882..105128791 [NCBI36]
Chr7:7q22.1-22.3		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:200
Count of miRNA genes:148
Interacting mature miRNAs:158
Transcripts:ENST00000445184, ENST00000450686
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 pharyngeal arch
High
Medium 327 233 733 21 224 19 155 134 556 52 394 594 3 1 147 1
Low 2110 2568 967 580 1561 423 4164 2019 3164 361 1063 1013 171 1 1198 2609 5 2
Below cutoff 2 187 25 22 161 22 38 44 14 6 3 5 5 32

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000445184
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7104,982,099 - 105,013,024 (-)Ensembl
RefSeq Acc Id: ENST00000450686
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7104,950,315 - 105,013,044 (-)Ensembl
RefSeq Acc Id: ENST00000655204
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7104,981,745 - 105,013,047 (-)Ensembl
RefSeq Acc Id: ENST00000684783
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7105,011,712 - 105,013,062 (-)Ensembl
RefSeq Acc Id: ENST00000684829
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7105,011,803 - 105,013,042 (-)Ensembl
RefSeq Acc Id: ENST00000685115
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7105,011,712 - 105,013,062 (-)Ensembl
RefSeq Acc Id: ENST00000687259
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7105,011,712 - 105,013,053 (-)Ensembl
RefSeq Acc Id: ENST00000687367
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7104,981,743 - 104,983,894 (-)Ensembl
RefSeq Acc Id: ENST00000687408
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7105,011,712 - 105,013,047 (-)Ensembl
RefSeq Acc Id: ENST00000687790
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7104,981,738 - 104,983,926 (-)Ensembl
RefSeq Acc Id: ENST00000687900
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7105,011,802 - 105,013,062 (-)Ensembl
RefSeq Acc Id: ENST00000688097
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7105,011,712 - 105,013,044 (-)Ensembl
RefSeq Acc Id: ENST00000688127
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7105,011,712 - 105,013,062 (-)Ensembl
RefSeq Acc Id: ENST00000688692
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7105,011,712 - 105,013,064 (-)Ensembl
RefSeq Acc Id: ENST00000689371
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7105,011,711 - 105,013,068 (-)Ensembl
RefSeq Acc Id: ENST00000689586
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7105,011,712 - 105,013,047 (-)Ensembl
RefSeq Acc Id: ENST00000690819
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7105,011,710 - 105,013,068 (-)Ensembl
RefSeq Acc Id: ENST00000693045
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7105,011,712 - 105,013,062 (-)Ensembl
RefSeq Acc Id: ENST00000693130
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7105,011,712 - 105,013,059 (-)Ensembl
RefSeq Acc Id: ENST00000702542
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7104,982,262 - 105,013,053 (-)Ensembl
RefSeq Acc Id: NR_039981
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh387104,981,747 - 104,991,165 (-)NCBI
GRCh377104,622,194 - 104,631,612 (-)NCBI
HuRef798,981,769 - 98,991,189 (-)NCBI
CHM1_17104,555,506 - 104,564,924 (-)NCBI
T2T-CHM13v2.07106,296,452 - 106,305,868 (-)NCBI
CRA_TCAGchr7v27103,982,885 - 103,992,302 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC01004 COSMIC
Ensembl Genes ENSG00000228393 Ensembl
GTEx ENSG00000228393 GTEx
HGNC ID HGNC:48961 ENTREZGENE
Human Proteome Map LINC01004 Human Proteome Map
NCBI Gene LINC01004 ENTREZGENE
RNAcentral URS0000759B65 RNACentral