LERFS (lncRNA negative regulator of fibroblast-like synoviocyte migration, SYNCRIP interacting) - Rat Genome Database

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Gene: LERFS (lncRNA negative regulator of fibroblast-like synoviocyte migration, SYNCRIP interacting) Homo sapiens
Analyze
Symbol: LERFS
Name: lncRNA negative regulator of fibroblast-like synoviocyte migration, SYNCRIP interacting
RGD ID: 1606066
HGNC Page HGNC:51182
Description: INTERACTS WITH bisphenol A; formaldehyde; lipopolysaccharide
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: LOC124906881; LOC403323; uncharacterized LOC124906881; uncharacterized LOC403323
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38962,857,856 - 62,898,087 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl962,856,999 - 62,898,095 (-)EnsemblGRCh38hg38GRCh38
GRCh37966,513,680 - 66,553,911 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36966,263,518 - 66,293,576 (-)NCBINCBI36Build 36hg18NCBI36
Cytogenetic Map9q13NCBI
CHM1_1966,657,157 - 66,663,039 (-)NCBICHM1_1
T2T-CHM13v2.0980,284,687 - 80,324,093 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:30198906  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 9p24.3-q34.3(chr9:204193-138179445) copy number gain See cases [RCV000133791] Chr9:204193..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q21.11(chr9:13997-68401065)x3 copy number gain See cases [RCV000135344] Chr9:13997..68401065 [GRCh38]
Chr9:13997..71015981 [GRCh37]
Chr9:3997..70205801 [NCBI36]
Chr9:9p24.3-q21.11		 pathogenic
GRCh38/hg38 9p24.3-q21.12(chr9:193412-70630731)x3 copy number gain See cases [RCV000136152] Chr9:193412..70630731 [GRCh38]
Chr9:220253..73245647 [GRCh37]
Chr9:210253..72435467 [NCBI36]
Chr9:9p24.3-q21.12		 pathogenic
GRCh38/hg38 9p24.3-q21.13(chr9:193412-74615913)x3 copy number gain See cases [RCV000135954] Chr9:193412..74615913 [GRCh38]
Chr9:204193..77230829 [GRCh37]
Chr9:194193..76420649 [NCBI36]
Chr9:9p24.3-q21.13		 pathogenic
GRCh38/hg38 9p24.3-q21.11(chr9:204104-66233120)x4 copy number gain See cases [RCV000137888] Chr9:204104..66233120 [GRCh38]
Chr9:204104..47212321 [GRCh37]
Chr9:194104..47002141 [NCBI36]
Chr9:9p24.3-q21.11		 pathogenic|conflicting data from submitters
GRCh38/hg38 9p13.3-q21.11(chr9:41747162-67217006)x3 copy number gain See cases [RCV000137784] Chr9:41747162..67217006 [GRCh38]
Chr9:33333162..71534501 [GRCh37]
Chr9:33323162..70724321 [NCBI36]
Chr9:9p13.3-q21.11		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138124524)x3 copy number gain See cases [RCV000138783] Chr9:193412..138124524 [GRCh38]
Chr9:204090..141018976 [GRCh37]
Chr9:194090..140138797 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q21.11(chr9:204104-67549861)x3 copy number gain See cases [RCV000139208] Chr9:204104..67549861 [GRCh38]
Chr9:204104..66516698 [GRCh37]
Chr9:194104..66256518 [NCBI36]
Chr9:9p24.3-q21.11		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138159073)x3 copy number gain See cases [RCV000138962] Chr9:193412..138159073 [GRCh38]
Chr9:204104..141053525 [GRCh37]
Chr9:194104..140173346 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic|conflicting data from submitters
GRCh38/hg38 9p11.2-q34.3(chr9:193412-138159073)x3 copy number gain See cases [RCV000139207] Chr9:193412..138159073 [GRCh38]
Chr9:68420641..141053525 [GRCh37]
Chr9:67910461..140173346 [NCBI36]
Chr9:9p11.2-q34.3		 pathogenic
GRCh38/hg38 9p22.2-q21.11(chr9:18344605-68257015) copy number gain See cases [RCV000140448] Chr9:18344605..68257015 [GRCh38]
Chr9:18344603..68995221 [GRCh37]
Chr9:18334603..68285041 [NCBI36]
Chr9:9p22.2-q21.11		 pathogenic
GRCh38/hg38 9p24.3-q22.1(chr9:203861-88130444)x4 copy number gain See cases [RCV000141904] Chr9:203861..88130444 [GRCh38]
Chr9:203861..90745359 [GRCh37]
Chr9:193861..89935179 [NCBI36]
Chr9:9p24.3-q22.1		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:203861-138125937)x3 copy number gain See cases [RCV000141876] Chr9:203861..138125937 [GRCh38]
Chr9:203861..141020389 [GRCh37]
Chr9:193861..140140210 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q12-21.11(chr9:61053889-67217006)x1 copy number loss See cases [RCV000141597] Chr9:61053889..67217006 [GRCh38]
Chr9:39140222..40940341 [GRCh37]
Chr9:39130222..40955573 [NCBI36]
Chr9:9q12-21.11		 benign
GRCh38/hg38 9p21.1-q21.11(chr9:31426827-68257015)x3 copy number gain See cases [RCV000141663] Chr9:31426827..68257015 [GRCh38]
Chr9:31426825..68330127 [GRCh37]
Chr9:31416825..67819947 [NCBI36]
Chr9:9p21.1-q21.11		 pathogenic
GRCh38/hg38 9p24.3-q21.31(chr9:193412-79877816)x3 copy number gain See cases [RCV000143012] Chr9:193412..79877816 [GRCh38]
Chr9:204104..82492731 [GRCh37]
Chr9:194104..81682551 [NCBI36]
Chr9:9p24.3-q21.31		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:203862-138125937)x3 copy number gain See cases [RCV000143476] Chr9:203862..138125937 [GRCh38]
Chr9:203862..141020389 [GRCh37]
Chr9:193862..140140210 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3 copy number gain See cases [RCV000148113] Chr9:193412..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3 copy number gain See cases [RCV000050348] Chr9:193412..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138124532)x3 copy number gain See cases [RCV000053745] Chr9:193412..138124532 [GRCh38]
Chr9:204193..141018984 [GRCh37]
Chr9:194193..140138805 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138114463)x3 copy number gain See cases [RCV000053746] Chr9:193412..138114463 [GRCh38]
Chr9:214367..141008915 [GRCh37]
Chr9:204367..140128736 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053748]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053748]|See cases [RCV000053748] Chr9:193412..138179445 [GRCh38]
Chr9:266045..141073897 [GRCh37]
Chr9:256045..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:644
Count of miRNA genes:515
Interacting mature miRNAs:565
Transcripts:ENST00000438699, ENST00000445604, ENST00000585533, ENST00000586625, ENST00000591993, ENST00000609749
Prediction methods:Microtar, 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 2 10 3
Low 603 602 516 139 380 95 1158 507 1327 147 739 487 46 289 717
Below cutoff 1612 1846 1083 360 935 254 2820 1537 2361 257 656 1023 116 781 1890 3

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000438699
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl962,867,708 - 62,876,614 (-)Ensembl
RefSeq Acc Id: ENST00000445604
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl962,865,597 - 62,898,095 (-)Ensembl
RefSeq Acc Id: ENST00000585533
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl962,868,141 - 62,897,707 (-)Ensembl
RefSeq Acc Id: ENST00000586625
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl962,856,999 - 62,897,713 (-)Ensembl
RefSeq Acc Id: ENST00000591993
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl962,857,833 - 62,897,707 (-)Ensembl
RefSeq Acc Id: ENST00000609749
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl962,868,137 - 62,880,632 (-)Ensembl
RefSeq Acc Id: ENST00000612590
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl962,868,197 - 62,869,868 (-)Ensembl
RefSeq Acc Id: ENST00000653936
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl962,868,141 - 62,880,632 (-)Ensembl
RefSeq Acc Id: ENST00000654225
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl962,856,999 - 62,897,709 (-)Ensembl
RefSeq Acc Id: ENST00000654882
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl962,867,203 - 62,898,095 (-)Ensembl
RefSeq Acc Id: ENST00000658257
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl962,865,335 - 62,880,641 (-)Ensembl
RefSeq Acc Id: ENST00000662817
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl962,856,999 - 62,898,087 (-)Ensembl
RefSeq Acc Id: ENST00000664229
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl962,868,137 - 62,880,632 (-)Ensembl
RefSeq Acc Id: ENST00000665356
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl962,868,209 - 62,898,093 (-)Ensembl
RefSeq Acc Id: ENST00000666775
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl962,857,034 - 62,897,770 (-)Ensembl
RefSeq Acc Id: ENST00000667349
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl962,865,335 - 62,880,620 (-)Ensembl
RefSeq Acc Id: ENST00000667498
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl962,856,999 - 62,897,705 (-)Ensembl
RefSeq Acc Id: ENST00000669453
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl962,867,874 - 62,870,079 (-)Ensembl
RefSeq Acc Id: ENST00000670636
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl962,868,129 - 62,880,632 (-)Ensembl
RefSeq Acc Id: NR_122076
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38962,857,856 - 62,898,087 (-)NCBI
CHM1_1966,647,131 - 66,687,479 (-)NCBI
T2T-CHM13v2.0980,284,687 - 80,324,093 (+)NCBI
Sequence:
RefSeq Acc Id: NR_122077
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38962,867,989 - 62,898,087 (-)NCBI
CHM1_1966,657,272 - 66,687,479 (-)NCBI
T2T-CHM13v2.0980,284,687 - 80,313,936 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LERFS COSMIC
Ensembl Genes ENSG00000234665 Ensembl
GTEx ENSG00000234665 GTEx
HGNC ID HGNC:51182 ENTREZGENE
Human Proteome Map LERFS Human Proteome Map
NCBI Gene 403323 ENTREZGENE
RNAcentral URS000075ABCF RNACentral
  URS000075DE51 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-03-23 LERFS  lncRNA negative regulator of fibroblast-like synoviocyte migration, SYNCRIP interacting  LOC124906881  uncharacterized LOC124906881  Data merged from RGD:151676031 737654 PROVISIONAL
2019-09-12 LERFS  lncRNA negative regulator of fibroblast-like synoviocyte migration, SYNCRIP interacting  LOC403323  uncharacterized LOC403323  Symbol and/or name change 5135510 APPROVED
2014-07-01 LOC403323  uncharacterized LOC403323  FLJ20444  hypothetical protein FLJ20444  Symbol and/or name change 5135510 APPROVED