LINC01007 (long intergenic non-protein coding RNA 1007) - Rat Genome Database

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Gene: LINC01007 (long intergenic non-protein coding RNA 1007) Homo sapiens
Analyze
Symbol: LINC01007
Name: long intergenic non-protein coding RNA 1007
RGD ID: 7248383
HGNC Page HGNC:48973
Description:
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: RP5-1059M17.1
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh387101,562,755 - 101,569,006 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl7101,562,779 - 101,569,006 (-)EnsemblGRCh38hg38GRCh38
GRCh377101,206,035 - 101,212,286 (-)NCBIGRCh37GRCh37hg19GRCh37
Celera796,216,642 - 96,220,275 (-)NCBICelera
Cytogenetic Map7q22.1NCBI
HuRef795,795,426 - 95,801,677 (-)NCBIHuRef
CHM1_17101,138,102 - 101,144,353 (-)NCBICHM1_1
T2T-CHM13v2.07102,882,655 - 102,888,905 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v27100,564,422 - 100,570,673 (-)NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:8619474   PMID:9110174   PMID:9847074   PMID:12477932   PMID:16344560  


Genomics

Variants

.
Variants in LINC01007
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 7q22.1(chr7:99195836-102258175)x1 copy number loss See cases [RCV000135782] Chr7:99195836..102258175 [GRCh38]
Chr7:98793459..101718950 [GRCh37]
Chr7:98631395..101688175 [NCBI36]
Chr7:7q22.1		 pathogenic|uncertain significance
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(chr7:99932610-102473188)x3 copy number gain See cases [RCV000138109] Chr7:99932610..102473188 [GRCh38]
Chr7:99530233..102113635 [GRCh37]
Chr7:99368169..101900640 [NCBI36]
Chr7:7q22.1		 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 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(chr7:100419914-102482826)x1 copy number loss See cases [RCV000054155] Chr7:100419914..102482826 [GRCh38]
Chr7:100017537..102123273 [GRCh37]
Chr7:99855473..101910278 [NCBI36]
Chr7:7q22.1		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:789
Count of miRNA genes:474
Interacting mature miRNAs:522
Transcripts:ENST00000434537, ENST00000437900, ENST00000451953
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 1 359
Low 1 1 1 1 1 1 446 19 4 1 1 2
Below cutoff 436 706 469 88 286 61 1060 377 1395 44 612 353 27 256 696 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000434537
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7101,565,306 - 101,568,976 (-)Ensembl
RefSeq Acc Id: ENST00000437900
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7101,565,306 - 101,569,006 (-)Ensembl
RefSeq Acc Id: ENST00000451953
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl7101,562,779 - 101,568,971 (-)Ensembl
RefSeq Acc Id: NR_103747
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh387101,565,306 - 101,569,006 (-)NCBI
HuRef795,795,426 - 95,801,677 (-)NCBI
CHM1_17101,140,653 - 101,144,353 (-)NCBI
T2T-CHM13v2.07102,885,205 - 102,888,905 (-)NCBI
CRA_TCAGchr7v27100,564,422 - 100,570,673 (-)NCBI
Sequence:
RefSeq Acc Id: NR_103748
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh387101,565,306 - 101,569,006 (-)NCBI
HuRef795,795,426 - 95,801,677 (-)NCBI
CHM1_17101,140,653 - 101,144,353 (-)NCBI
T2T-CHM13v2.07102,885,205 - 102,888,905 (-)NCBI
CRA_TCAGchr7v27100,564,422 - 100,570,673 (-)NCBI
Sequence:
RefSeq Acc Id: NR_103749
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh387101,562,755 - 101,569,006 (-)NCBI
HuRef795,795,426 - 95,801,677 (-)NCBI
CHM1_17101,138,102 - 101,144,353 (-)NCBI
T2T-CHM13v2.07102,882,655 - 102,888,905 (-)NCBI
Sequence:
Promoters
RGD ID:15096175
Promoter ID:EPDNEWNC_H985
Type:initiation region
Name:LINC01007_1
Description:long intergenic non-protein coding RNA 1007 [Source:HGNCSymbol;Acc:HGNC:48973]
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
GRCh387101,568,955 - 101,569,015EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC01007 COSMIC
Ensembl Genes ENSG00000233123 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000434537 ENTREZGENE
  ENST00000437900 ENTREZGENE
  ENST00000451953 ENTREZGENE
GTEx ENSG00000233123 GTEx
HGNC ID HGNC:48973 ENTREZGENE
Human Proteome Map LINC01007 Human Proteome Map
NCBI Gene LINC01007 ENTREZGENE
RNAcentral URS000075C2E4 RNACentral
  URS000075D3DA RNACentral
  URS000075E97E RNACentral