LINC00336 (long intergenic non-protein coding RNA 336) - Rat Genome Database

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Gene: LINC00336 (long intergenic non-protein coding RNA 336) Homo sapiens
Analyze
Symbol: LINC00336
Name: long intergenic non-protein coding RNA 336
RGD ID: 1602153
HGNC Page HGNC:33813
Description: INTERACTS WITH benzo[a]pyrene; cadmium atom; valproic acid
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: C6orf227; FLJ43752; NCRNA00336
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38633,586,104 - 33,593,338 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl633,586,104 - 33,593,338 (-)EnsemblGRCh38hg38GRCh38
GRCh37633,553,881 - 33,561,115 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36633,661,861 - 33,669,093 (-)NCBINCBI36Build 36hg18NCBI36
Celera635,108,262 - 35,115,494 (-)NCBICelera
Cytogenetic Map6p21.31NCBI
HuRef633,295,346 - 33,302,578 (-)NCBIHuRef
CHM1_1633,556,221 - 33,563,451 (-)NCBICHM1_1
T2T-CHM13v2.0633,407,294 - 33,414,528 (-)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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:19851445   PMID:30787392   PMID:32978449   PMID:36057605  


Genomics

Variants

.
Variants in LINC00336
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 6p25.3-12.3(chr6:156974-46789291)x3 copy number gain See cases [RCV000143497] Chr6:156974..46789291 [GRCh38]
Chr6:156974..46757028 [GRCh37]
Chr6:101974..46864987 [NCBI36]
Chr6:6p25.3-12.3		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:288
Count of miRNA genes:275
Interacting mature miRNAs:287
Transcripts:ENST00000477984
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
D6S1560  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37633,554,695 - 33,554,928UniSTSGRCh37
Build 36633,662,673 - 33,662,906RGDNCBI36
Celera635,109,074 - 35,109,307RGD
HuRef633,296,158 - 33,296,391UniSTS
HuRef1113,045,939 - 13,046,452UniSTS
HuRef11121,219,431 - 121,219,625UniSTS
Marshfield Genetic Map647.71RGD
Genethon Genetic Map647.6UniSTS
deCODE Assembly Map652.75UniSTS
Whitehead-YAC Contig Map6 UniSTS
D6S1560  
Human AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map6p21.31UniSTS
Cytogenetic Map6p21UniSTS
Marshfield Genetic Map647.71UniSTS
Genethon Genetic Map647.6UniSTS
deCODE Assembly Map652.75UniSTS
Whitehead-YAC Contig Map6 UniSTS


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
High
Medium
Low 103 1 747 4 167 4 4 3 397 87 478 637 3
Below cutoff 1280 1230 573 233 1180 108 2234 769 2801 240 609 640 132 514 1407

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000477984
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl633,586,106 - 33,593,338 (-)Ensembl
RefSeq Acc Id: ENST00000689377
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl633,586,104 - 33,593,316 (-)Ensembl
RefSeq Acc Id: NR_027908
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38633,586,104 - 33,593,338 (-)NCBI
GRCh37633,553,883 - 33,561,115 (-)RGD
Celera635,108,262 - 35,115,494 (-)RGD
HuRef633,295,346 - 33,302,578 (-)RGD
CHM1_1633,556,221 - 33,563,451 (-)NCBI
T2T-CHM13v2.0633,407,294 - 33,414,528 (-)NCBI
Sequence:
Protein Sequences
GenBank Protein BAC86269 (Get FASTA)   NCBI Sequence Viewer  
  Q6ZUF6 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6ZUF6-F1-model_v2 AlphaFold Q6ZUF6 1-198 view protein structure

Promoters
RGD ID:6803860
Promoter ID:HG_KWN:53218
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   K562,   Lymphoblastoid
Transcripts:NR_027908
Position:
Human AssemblyChrPosition (strand)Source
Build 36633,668,844 - 33,669,344 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
COSMIC LINC00336 COSMIC
Ensembl Genes ENSG00000197251 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000477984 ENTREZGENE
GTEx ENSG00000197251 GTEx
HGNC ID HGNC:33813 ENTREZGENE
Human Proteome Map LINC00336 Human Proteome Map
NCBI Gene 401253 ENTREZGENE
PharmGKB PA164717365 PharmGKB
PRINTS F138DOMAIN UniProtKB/Swiss-Prot
RNAcentral URS00022AE773 RNACentral
UniProt NC336_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-09-01 LINC00336  long intergenic non-protein coding RNA 336  NCRNA00336  non-protein coding RNA 336  Symbol and/or name change 5135510 APPROVED
2011-07-27 NCRNA00336  non-protein coding RNA 336  C6orf227  chromosome 6 open reading frame 227  Symbol and/or name change 5135510 APPROVED