LIFR-AS1 (LIFR antisense RNA 1) - Rat Genome Database

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Gene: LIFR-AS1 (LIFR antisense RNA 1) Homo sapiens
Analyze
Symbol: LIFR-AS1
Name: LIFR antisense RNA 1
RGD ID: 7246675
HGNC Page HGNC:43600
Description: ASSOCIATED WITH Stuve-Wiedemann Syndrome; INTERACTS WITH benzo[e]pyrene; bisphenol A; methapyrilene
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
GRCh38538,556,786 - 38,671,216 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl538,556,765 - 38,671,216 (+)EnsemblGRCh38hg38GRCh38
GRCh37538,556,888 - 38,671,318 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map5p13.1NCBI
HuRef538,508,673 - 38,623,021 (+)NCBIHuRef
CHM1_1538,558,833 - 38,673,200 (+)NCBICHM1_1
T2T-CHM13v2.0538,805,863 - 38,920,283 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:12477932   PMID:26725846   PMID:29807108   PMID:31127025   PMID:32495872   PMID:33070767   PMID:33355363   PMID:34658294   PMID:34781815   PMID:35071590   PMID:35778954   PMID:36316703  


Genomics

Variants

.
Variants in LIFR-AS1
11 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 5p15.33-11(chr5:49978-46114984)x3 copy number gain See cases [RCV000135453] Chr5:49978..46114984 [GRCh38]
Chr5:50093..46115086 [GRCh37]
Chr5:103093..46150843 [NCBI36]
Chr5:5p15.33-11		 pathogenic
GRCh38/hg38 5p13.2-q12.1(chr5:35201559-61903141)x3 copy number gain See cases [RCV000137302] Chr5:35201559..61903141 [GRCh38]
Chr5:35201661..61198968 [GRCh37]
Chr5:35237418..61234725 [NCBI36]
Chr5:5p13.2-q12.1		 pathogenic
GRCh38/hg38 5p15.33-q13.3(chr5:22149-74412725)x3 copy number gain See cases [RCV000138780] Chr5:22149..74412725 [GRCh38]
Chr5:22149..73708550 [GRCh37]
Chr5:75149..73744306 [NCBI36]
Chr5:5p15.33-q13.3		 pathogenic
GRCh38/hg38 5p13.1(chr5:38542122-38760928)x3 copy number gain See cases [RCV000138979] Chr5:38542122..38760928 [GRCh38]
Chr5:38542224..38761030 [GRCh37]
Chr5:38577981..38796787 [NCBI36]
Chr5:5p13.1		 likely benign
GRCh38/hg38 5p13.1(chr5:38400157-38593979)x3 copy number gain See cases [RCV000140372] Chr5:38400157..38593979 [GRCh38]
Chr5:38400259..38594081 [GRCh37]
Chr5:38436016..38629838 [NCBI36]
Chr5:5p13.1		 uncertain significance
GRCh38/hg38 5p15.33-12(chr5:54839-45649861)x3 copy number gain See cases [RCV000051810] Chr5:54839..45649861 [GRCh38]
Chr5:54954..45649963 [GRCh37]
Chr5:107954..45685720 [NCBI36]
Chr5:5p15.33-12		 pathogenic
GRCh38/hg38 5p14.1-q11.1(chr5:26593632-50288555)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051834]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051834]|See cases [RCV000051834] Chr5:26593632..50288555 [GRCh38]
Chr5:26593741..49584389 [GRCh37]
Chr5:26629498..49620146 [NCBI36]
Chr5:5p14.1-q11.1		 pathogenic
GRCh38/hg38 5p13.2-12(chr5:35700480-45260029)x3 copy number gain See cases [RCV000051835] Chr5:35700480..45260029 [GRCh38]
Chr5:35700582..45260131 [GRCh37]
Chr5:35736339..45295888 [NCBI36]
Chr5:5p13.2-12		 pathogenic
GRCh38/hg38 5p13.2-q11.1(chr5:36374107-51103841)x3 copy number gain See cases [RCV000051836] Chr5:36374107..51103841 [GRCh38]
Chr5:36374209..50399675 [GRCh37]
Chr5:36409966..50435432 [NCBI36]
Chr5:5p13.2-q11.1		 pathogenic
GRCh38/hg38 5p13.2-13.1(chr5:37016043-39383281)x3 copy number gain See cases [RCV000051837] Chr5:37016043..39383281 [GRCh38]
Chr5:37016145..39383383 [GRCh37]
Chr5:37051902..39419140 [NCBI36]
Chr5:5p13.2-13.1		 pathogenic
NM_002310.6(LIFR):c.-129T>G single nucleotide variant Stuve-Wiedemann syndrome [RCV000261179] Chr5:38595370 [GRCh38]
Chr5:38595472 [GRCh37]
Chr5:5p13.1		 uncertain significance
NM_002310.6(LIFR):c.-139G>A single nucleotide variant Stuve-Wiedemann syndrome [RCV000316474] Chr5:38595380 [GRCh38]
Chr5:38595482 [GRCh37]
Chr5:5p13.1		 uncertain significance
NM_002310.6(LIFR):c.-118G>A single nucleotide variant Stuve-Wiedemann syndrome [RCV000379086] Chr5:38595359 [GRCh38]
Chr5:38595461 [GRCh37]
Chr5:5p13.1		 uncertain significance
NM_002310.6(LIFR):c.-90T>C single nucleotide variant Stuve-Wiedemann syndrome [RCV000324586] Chr5:38595331 [GRCh38]
Chr5:38595433 [GRCh37]
Chr5:5p13.1		 uncertain significance
NM_002310.6(LIFR):c.-28G>A single nucleotide variant Stuve-Wiedemann syndrome [RCV000264901] Chr5:38595269 [GRCh38]
Chr5:38595371 [GRCh37]
Chr5:5p13.1		 uncertain significance
NM_002310.6(LIFR):c.-20+294A>T single nucleotide variant Stuve-Wiedemann syndrome [RCV000507167] Chr5:38594967 [GRCh38]
Chr5:38595069 [GRCh37]
Chr5:5p13.1		 benign
GRCh38/hg38 5p13.3-12(chr5:29299893-45899898)x3 copy number gain See cases [RCV003482191] Chr5:29299893..45899898 [GRCh38]
Chr5:5p13.3-12		 likely pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:201
Count of miRNA genes:186
Interacting mature miRNAs:189
Transcripts:ENST00000500733, ENST00000500817, ENST00000514291
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.

Markers in Region
RH65436  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37538,569,007 - 38,569,131UniSTSGRCh37
Build 36538,604,764 - 38,604,888RGDNCBI36
Celera538,455,598 - 38,455,722RGD
Cytogenetic Map5p13-p12UniSTS
HuRef538,520,792 - 38,520,916UniSTS
D5S2614  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37538,606,065 - 38,606,206UniSTSGRCh37
Build 36538,641,822 - 38,641,963RGDNCBI36
Celera538,492,624 - 38,492,765RGD
HuRef538,557,816 - 38,557,957UniSTS
Stanford-G3 RH Map51525.0UniSTS
NCBI RH Map5178.9UniSTS


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 2 1 1 7 4 17 9
Low 1804 1829 1219 174 369 30 3787 1569 3673 347 1339 1475 154 1 1108 2447 5 2
Below cutoff 568 632 466 411 549 396 555 624 54 63 101 121 20 96 341

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000500733
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl538,556,786 - 38,608,862 (+)Ensembl
RefSeq Acc Id: ENST00000500817
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl538,558,830 - 38,671,216 (+)Ensembl
RefSeq Acc Id: ENST00000514291
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl538,558,942 - 38,579,594 (+)Ensembl
RefSeq Acc Id: ENST00000652922
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl538,556,792 - 38,615,729 (+)Ensembl
RefSeq Acc Id: ENST00000657740
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl538,557,739 - 38,601,314 (+)Ensembl
RefSeq Acc Id: ENST00000658674
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl538,556,805 - 38,644,912 (+)Ensembl
RefSeq Acc Id: ENST00000660661
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl538,556,772 - 38,647,937 (+)Ensembl
RefSeq Acc Id: ENST00000661968
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl538,558,169 - 38,644,798 (+)Ensembl
RefSeq Acc Id: ENST00000666123
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl538,556,792 - 38,645,005 (+)Ensembl
RefSeq Acc Id: ENST00000669394
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl538,558,792 - 38,579,594 (+)Ensembl
RefSeq Acc Id: ENST00000670079
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl538,556,765 - 38,647,931 (+)Ensembl
RefSeq Acc Id: ENST00000670215
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl538,556,961 - 38,647,628 (+)Ensembl
RefSeq Acc Id: ENST00000671056
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl538,556,823 - 38,567,382 (+)Ensembl
RefSeq Acc Id: ENST00000671098
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl538,557,075 - 38,641,670 (+)Ensembl
RefSeq Acc Id: NR_103553
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38538,556,786 - 38,608,862 (+)NCBI
HuRef538,508,673 - 38,623,021 (+)NCBI
CHM1_1538,558,833 - 38,610,890 (+)NCBI
T2T-CHM13v2.0538,805,863 - 38,857,906 (+)NCBI
Sequence:
RefSeq Acc Id: NR_103554
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38538,556,786 - 38,671,216 (+)NCBI
HuRef538,508,673 - 38,623,021 (+)NCBI
CHM1_1538,558,833 - 38,673,200 (+)NCBI
T2T-CHM13v2.0538,805,863 - 38,920,283 (+)NCBI
Sequence:
Promoters
RGD ID:15095927
Promoter ID:EPDNEWNC_H717
Type:multiple initiation site
Name:LIFR-AS1_1
Description:LIFR antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:43600]
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
GRCh38538,556,775 - 38,556,835EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LIFR-AS1 COSMIC
Ensembl Genes ENSG00000244968 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000500733 ENTREZGENE
GTEx ENSG00000244968 GTEx
HGNC ID HGNC:43600 ENTREZGENE
Human Proteome Map LIFR-AS1 Human Proteome Map
NCBI Gene LIFR-AS1 ENTREZGENE
RNAcentral URS0000490DBB RNACentral
  URS000075EF6E RNACentral