LINC00471 (long intergenic non-protein coding RNA 471) - Rat Genome Database

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Gene: LINC00471 (long intergenic non-protein coding RNA 471) Homo sapiens
Analyze
Symbol: LINC00471
Name: long intergenic non-protein coding RNA 471
RGD ID: 1605277
HGNC Page HGNC:28668
Description: INTERACTS WITH Aflatoxin B2 alpha; benzo[a]pyrene; N-Nitrosopyrrolidine
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: PREDICTED
Previously known as: C2orf52; MGC43122
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382231,508,426 - 231,514,339 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2231,508,420 - 231,514,396 (-)EnsemblGRCh38hg38GRCh38
GRCh372232,373,137 - 232,379,050 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362232,081,381 - 232,087,294 (-)NCBINCBI36Build 36hg18NCBI36
Celera2226,149,538 - 226,155,456 (-)NCBICelera
Cytogenetic Map2q37.1NCBI
HuRef2224,214,585 - 224,220,504 (-)NCBIHuRef
CHM1_12232,378,939 - 232,384,852 (-)NCBICHM1_1
T2T-CHM13v2.02231,992,865 - 231,998,778 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
Additional References at PubMed
PMID:12477932   PMID:23563607   PMID:30021884  


Genomics

Variants

.
Variants in LINC00471
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NR_024079.1(LINC00471):n.581C>T single nucleotide variant Malignant melanoma [RCV000065467] Chr2:231509127 [GRCh38]
Chr2:232373838 [GRCh37]
Chr2:232082082 [NCBI36]
Chr2:2q37.1		 not provided
GRCh38/hg38 2q36.3-37.3(chr2:228723579-241404867)x3 copy number gain See cases [RCV000134169] Chr2:228723579..241404867 [GRCh38]
Chr2:229588295..242344282 [GRCh37]
Chr2:229296539..241992955 [NCBI36]
Chr2:2q36.3-37.3		 pathogenic
GRCh38/hg38 2q34-37.3(chr2:210579676-242126245)x3 copy number gain See cases [RCV000135934] Chr2:210579676..242126245 [GRCh38]
Chr2:211444400..243059659 [GRCh37]
Chr2:211152645..242717069 [NCBI36]
Chr2:2q34-37.3		 pathogenic
GRCh38/hg38 2q36.3-37.2(chr2:228014149-234976424)x3 copy number gain See cases [RCV000136967] Chr2:228014149..234976424 [GRCh38]
Chr2:228878865..235885068 [GRCh37]
Chr2:228587109..235549807 [NCBI36]
Chr2:2q36.3-37.2		 pathogenic
GRCh38/hg38 2q32.2-37.3(chr2:189436149-241841232)x3 copy number gain See cases [RCV000142307] Chr2:189436149..241841232 [GRCh38]
Chr2:190300875..242783384 [GRCh37]
Chr2:190009120..242432057 [NCBI36]
Chr2:2q32.2-37.3		 pathogenic
GRCh38/hg38 2q35-37.3(chr2:218101759-242126245)x3 copy number gain See cases [RCV000143216] Chr2:218101759..242126245 [GRCh38]
Chr2:218966482..243059659 [GRCh37]
Chr2:218674727..242717069 [NCBI36]
Chr2:2q35-37.3		 pathogenic
GRCh38/hg38 2q32.3-37.3(chr2:194898783-236473913)x3 copy number gain See cases [RCV000051119] Chr2:194898783..236473913 [GRCh38]
Chr2:195763507..237382556 [GRCh37]
Chr2:195471752..237047295 [NCBI36]
Chr2:2q32.3-37.3		 pathogenic
GRCh38/hg38 2q36.3-37.3(chr2:226978129-236886599)x1 copy number loss See cases [RCV000052637] Chr2:226978129..236886599 [GRCh38]
Chr2:227842845..237795242 [GRCh37]
Chr2:227551089..237459981 [NCBI36]
Chr2:2q36.3-37.3		 pathogenic
GRCh38/hg38 2q36.3-37.2(chr2:227343278-235339168)x1 copy number loss See cases [RCV000052638] Chr2:227343278..235339168 [GRCh38]
Chr2:228207994..236247812 [GRCh37]
Chr2:227916238..235912551 [NCBI36]
Chr2:2q36.3-37.2		 pathogenic
GRCh38/hg38 2q37.1-37.3(chr2:231375505-242065208)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052639]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052639]|See cases [RCV000052639] Chr2:231375505..242065208 [GRCh38]
Chr2:232240216..243007359 [GRCh37]
Chr2:231948460..242656032 [NCBI36]
Chr2:2q37.1-37.3		 pathogenic
GRCh38/hg38 2q32.2-37.3(chr2:188818195-242065208)x3 copy number gain See cases [RCV000052958] Chr2:188818195..242065208 [GRCh38]
Chr2:189682921..243007359 [GRCh37]
Chr2:189391166..242656032 [NCBI36]
Chr2:2q32.2-37.3		 pathogenic
GRCh38/hg38 2q32.2-37.3(chr2:190310736-241892770)x3 copy number gain See cases [RCV000052959] Chr2:190310736..241892770 [GRCh38]
Chr2:191175462..242834921 [GRCh37]
Chr2:190883707..242483594 [NCBI36]
Chr2:2q32.2-37.3		 pathogenic
GRCh38/hg38 2q32.3-37.3(chr2:193122313-241074980)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052960]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052960]|See cases [RCV000052960] Chr2:193122313..241074980 [GRCh38]
Chr2:193987039..242014395 [GRCh37]
Chr2:193695284..241663068 [NCBI36]
Chr2:2q32.3-37.3		 pathogenic
GRCh38/hg38 2q36.1-37.3(chr2:223992431-242126245)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052972]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052972]|See cases [RCV000052972] Chr2:223992431..242126245 [GRCh38]
Chr2:224857148..243059659 [GRCh37]
Chr2:224565392..242717069 [NCBI36]
Chr2:2q36.1-37.3		 pathogenic
GRCh38/hg38 2q36.3-37.3(chr2:227803148-242086301)x3 copy number gain See cases [RCV000052973] Chr2:227803148..242086301 [GRCh38]
Chr2:228667864..243028452 [GRCh37]
Chr2:228376108..242677125 [NCBI36]
Chr2:2q36.3-37.3		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:202
Count of miRNA genes:197
Interacting mature miRNAs:201
Transcripts:ENST00000313064
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 visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 2 10 1 1 24 15
Low 535 721 1118 163 823 113 2360 661 2882 248 1163 1096 64 1 358 1520 3 2
Below cutoff 1811 1815 561 415 725 308 1930 1466 848 163 262 485 108 819 1217 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000313064
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2231,508,425 - 231,514,396 (-)Ensembl
RefSeq Acc Id: ENST00000668648
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2231,508,420 - 231,514,385 (-)Ensembl
RefSeq Acc Id: NR_024079
RefSeq Status: PREDICTED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382231,508,426 - 231,514,339 (-)NCBI
GRCh372232,373,137 - 232,379,050 (-)RGD
Celera2226,149,538 - 226,155,456 (-)RGD
HuRef2224,214,585 - 224,220,504 (-)ENTREZGENE
CHM1_12232,378,939 - 232,384,852 (-)NCBI
T2T-CHM13v2.02231,992,865 - 231,998,778 (-)NCBI
Sequence:
Protein Sequences
GenBank Protein AAY24248 (Get FASTA)   NCBI Sequence Viewer  
  EAW70965 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8N535-F1-model_v2 AlphaFold Q8N535 1-108 view protein structure

Promoters
RGD ID:15095540
Promoter ID:EPDNEWNC_H379
Type:initiation region
Name:LINC00471_1
Description:long intergenic non-protein coding RNA 471 [Source:HGNCSymbol;Acc:HGNC:28668]
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
GRCh382231,514,364 - 231,514,424EPDNEWNC
RGD ID:6796900
Promoter ID:HG_KWN:37707
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:NR_024079
Position:
Human AssemblyChrPosition (strand)Source
Build 362232,087,191 - 232,087,691 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
COSMIC LINC00471 COSMIC
Ensembl Genes ENSG00000181798 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000668648 ENTREZGENE
GTEx ENSG00000181798 GTEx
HGNC ID HGNC:28668 ENTREZGENE
Human Proteome Map LINC00471 Human Proteome Map
NCBI Gene 151477 ENTREZGENE
PharmGKB PA162379204 PharmGKB
RNAcentral URS000075E41B RNACentral
UniProt CB052_HUMAN UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-09-13 LINC00471  long intergenic non-protein coding RNA 471  C2orf52  chromosome 2 open reading frame 52  Symbol and/or name change 5135510 APPROVED