LINC01621 (long intergenic non-protein coding RNA 1621) - Rat Genome Database

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Gene: LINC01621 (long intergenic non-protein coding RNA 1621) Homo sapiens
Analyze
Symbol: LINC01621
Name: long intergenic non-protein coding RNA 1621
RGD ID: 1353600
HGNC Page HGNC:14109
Description: ASSOCIATED WITH maple syrup urine disease
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: C6orf7; hypothetical protein LOC89758; RP1-159G19.1; uncharacterized protein LOC89758
RGD Orthologs
Bonobo
Green Monkey
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38679,803,583 - 79,812,246 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl679,803,574 - 79,833,387 (-)EnsemblGRCh38hg38GRCh38
GRCh37680,513,300 - 80,521,963 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map6q14.1NCBI
HuRef677,733,281 - 77,800,097 (-)NCBIHuRef
CHM1_1680,610,818 - 80,677,625 (-)NCBICHM1_1
T2T-CHM13v2.0681,009,153 - 81,017,816 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References
Additional References at PubMed
PMID:20522523   PMID:23669352  


Genomics

Comparative Map Data
LINC01621
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38679,803,583 - 79,812,246 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl679,803,574 - 79,833,387 (-)EnsemblGRCh38hg38GRCh38
GRCh37680,513,300 - 80,521,963 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map6q14.1NCBI
HuRef677,733,281 - 77,800,097 (-)NCBIHuRef
CHM1_1680,610,818 - 80,677,625 (-)NCBICHM1_1
T2T-CHM13v2.0681,009,153 - 81,017,816 (-)NCBIT2T-CHM13v2.0
LOC100989047
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2599,886,744 - 99,894,788 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1697,766,831 - 97,774,113 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0677,686,578 - 77,694,637 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1680,955,812 - 80,964,446 (-)NCBIpanpan1.1PanPan1.1panPan2
LOC103239974
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1134,529,936 - 4,539,264 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666040180,764,937 - 180,767,487 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 6q14.1-14.2(chr6:78912019-84096427)x1 copy number loss See cases [RCV000137752] Chr6:78912019..84096427 [GRCh38]
Chr6:79621736..84806146 [GRCh37]
Chr6:79678455..84862865 [NCBI36]
Chr6:6q14.1-14.2		 uncertain significance
GRCh38/hg38 6q13-24.1(chr6:74382807-142040500)x3 copy number gain See cases [RCV000139729] Chr6:74382807..142040500 [GRCh38]
Chr6:75092523..142361637 [GRCh37]
Chr6:75149243..142403330 [NCBI36]
Chr6:6q13-24.1		 pathogenic
GRCh38/hg38 6q12-14.2(chr6:64549655-83426791)x1 copy number loss See cases [RCV000142527] Chr6:64549655..83426791 [GRCh38]
Chr6:65259548..84136510 [GRCh37]
Chr6:65316269..84193229 [NCBI36]
Chr6:6q12-14.2		 pathogenic
GRCh38/hg38 6q14.1(chr6:78661176-80245532)x1 copy number loss See cases [RCV000143199] Chr6:78661176..80245532 [GRCh38]
Chr6:79370893..80955249 [GRCh37]
Chr6:79427612..81011968 [NCBI36]
Chr6:6q14.1		 uncertain significance
GRCh38/hg38 6q14.1-16.1(chr6:75926199-92710793)x1 copy number loss See cases [RCV000143505] Chr6:75926199..92710793 [GRCh38]
Chr6:76635916..93420511 [GRCh37]
Chr6:76692636..93477232 [NCBI36]
Chr6:6q14.1-16.1		 pathogenic
NC_000006.12:g.79875437C>T single nucleotide variant Lung cancer [RCV000097194] Chr6:79875437 [GRCh38]
Chr6:80585154 [GRCh37]
Chr6:6q14.1		 uncertain significance
GRCh37/hg19 6p25.3-q27(chr6:156975-170919482)x3 copy number gain See cases [RCV000512067] Chr6:156975..170919482 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:156975-170919482) copy number gain See cases [RCV000510595] Chr6:156975..170919482 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p22.1-q14.1(chr6:29455465-81447367) copy number gain not provided [RCV000767714] Chr6:29455465..81447367 [GRCh37]
Chr6:6p22.1-q14.1		 pathogenic
GRCh37/hg19 6q13-14.2(chr6:73674612-84829774)x1 copy number loss not provided [RCV000682681] Chr6:73674612..84829774 [GRCh37]
Chr6:6q13-14.2		 pathogenic
GRCh37/hg19 6q14.1(chr6:80480799-81040515)x3 copy number gain not provided [RCV000682687] Chr6:80480799..81040515 [GRCh37]
Chr6:6q14.1		 uncertain significance
GRCh37/hg19 6p25.3-q27(chr6:108666-170980171)x3 copy number gain not provided [RCV000745403] Chr6:108666..170980171 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:60107-171054786)x3 copy number gain not provided [RCV000745400] Chr6:60107..171054786 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:165632-170919470)x3 copy number gain not provided [RCV000745404] Chr6:165632..170919470 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6q14.1(chr6:78216253-82753743)x3 copy number gain not provided [RCV000846973] Chr6:78216253..82753743 [GRCh37]
Chr6:6q14.1		 uncertain significance
GRCh37/hg19 6q14.1(chr6:80557845-80897919)x1 copy number loss not provided [RCV000845729] Chr6:80557845..80897919 [GRCh37]
Chr6:6q14.1		 uncertain significance
GRCh37/hg19 6q13-14.1(chr6:72799054-83275894)x1 copy number loss not provided [RCV001829197] Chr6:72799054..83275894 [GRCh37]
Chr6:6q13-14.1		 pathogenic
GRCh37/hg19 6q12-16.1(chr6:69938252-94379210) copy number gain not specified [RCV002053581] Chr6:69938252..94379210 [GRCh37]
Chr6:6q12-16.1		 pathogenic
NC_000006.11:g.(?_79650410)_(80912949_?)del deletion Maple syrup urine disease [RCV003122618]|not provided [RCV003111506] Chr6:79650410..80912949 [GRCh37]
Chr6:6q14.1		 pathogenic|no classifications from unflagged records
GRCh37/hg19 6q14.1-16.1(chr6:78911022-98909173)x1 copy number loss See cases [RCV002292710] Chr6:78911022..98909173 [GRCh37]
Chr6:6q14.1-16.1		 uncertain significance
GRCh37/hg19 6q14.1(chr6:77773778-80880138)x3 copy number gain not provided [RCV002473802] Chr6:77773778..80880138 [GRCh37]
Chr6:6q14.1		 uncertain significance
GRCh37/hg19 6q14.1(chr6:79199356-80915988)x1 copy number loss not provided [RCV003485515] Chr6:79199356..80915988 [GRCh37]
Chr6:6q14.1		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:142
Count of miRNA genes:137
Interacting mature miRNAs:141
Transcripts:ENST00000438797
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 4 4 4 1
Low 4 13 287 279 6 273 1000 12 898 38 278 29 6 541
Below cutoff 123 173 336 125 58 105 390 160 1551 148 222 137 20 59 205 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000438797
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl679,803,574 - 79,833,387 (-)Ensembl
RefSeq Acc Id: ENST00000669965
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl679,803,582 - 79,833,386 (-)Ensembl
RefSeq Acc Id: ENST00000693479
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl679,803,577 - 79,833,372 (-)Ensembl
RefSeq Acc Id: NR_131786
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38679,803,583 - 79,812,246 (-)NCBI
CHM1_1680,610,814 - 80,619,476 (-)NCBI
T2T-CHM13v2.0681,009,153 - 81,017,816 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC01621 COSMIC
Ensembl Genes ENSG00000235357 Ensembl
GTEx ENSG00000235357 GTEx
HGNC ID HGNC:14109 ENTREZGENE
Human Proteome Map LINC01621 Human Proteome Map
NCBI Gene 89758 ENTREZGENE
RNAcentral URS00008E3A26 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-10-20 LINC01621  long intergenic non-protein coding RNA 1621  C6orf7  chromosome 6 open reading frame 7  Symbol and/or name change 5135510 APPROVED