LINC00029 (long intergenic non-protein coding RNA 29) - Rat Genome Database

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Gene: LINC00029 (long intergenic non-protein coding RNA 29) Homo sapiens
Analyze
Symbol: LINC00029
Name: long intergenic non-protein coding RNA 29
RGD ID: 1351750
HGNC Page HGNC:16184
Description: INTERACTS WITH aflatoxin B1; benzo[a]pyrene; valproic acid
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: PREDICTED
Previously known as: bA305P22.4; C20orf51; DKFZp434E222; MGC133148; NCRNA00029
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382063,034,217 - 63,037,028 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2063,034,217 - 63,037,028 (-)EnsemblGRCh38hg38GRCh38
GRCh372061,665,569 - 61,668,380 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 342061,136,013 - 61,138,360NCBI
Celera2058,342,168 - 58,344,979 (-)NCBICelera
Cytogenetic Map20q13.33NCBI
HuRef2058,383,888 - 58,386,663 (-)NCBIHuRef
CHM1_12061,566,589 - 61,569,232 (-)NCBICHM1_1
T2T-CHM13v2.02064,835,829 - 64,838,604 (-)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:11181995   PMID:11780052   PMID:12477932   PMID:22219177  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 20q13.33(chr20:62561794-64277321)x1 copy number loss See cases [RCV000133842] Chr20:62561794..64277321 [GRCh38]
Chr20:61211869..62908674 [GRCh37]
Chr20:60569446..62379118 [NCBI36]
Chr20:20q13.33		 pathogenic
GRCh38/hg38 20q13.32-13.33(chr20:59041966-64277321)x3 copy number gain See cases [RCV000135805] Chr20:59041966..64277321 [GRCh38]
Chr20:57617021..62908674 [GRCh37]
Chr20:57050416..62379118 [NCBI36]
Chr20:20q13.32-13.33		 pathogenic
GRCh38/hg38 20p13-q13.33(chr20:99557-64277321)x3 copy number gain See cases [RCV000135859] Chr20:99557..64277321 [GRCh38]
Chr20:80198..62908674 [GRCh37]
Chr20:28198..62379118 [NCBI36]
Chr20:20p13-q13.33		 pathogenic
GRCh38/hg38 20q13.2-13.33(chr20:56198032-64277321)x3 copy number gain See cases [RCV000138035] Chr20:56198032..64277321 [GRCh38]
Chr20:54773088..62908674 [GRCh37]
Chr20:54206495..62379118 [NCBI36]
Chr20:20q13.2-13.33		 pathogenic
GRCh38/hg38 20q13.33(chr20:61326549-64277326)x3 copy number gain See cases [RCV000139100] Chr20:61326549..64277326 [GRCh38]
Chr20:59901605..62908679 [GRCh37]
Chr20:59335000..62379123 [NCBI36]
Chr20:20q13.33		 pathogenic
GRCh38/hg38 20q13.33(chr20:62939140-63198970)x3 copy number gain See cases [RCV000139758] Chr20:62939140..63198970 [GRCh38]
Chr20:61570492..61830322 [GRCh37]
Chr20:61040937..61300767 [NCBI36]
Chr20:20q13.33		 likely benign
GRCh38/hg38 20q13.31-13.33(chr20:57229415-64273089)x3 copy number gain See cases [RCV000141347] Chr20:57229415..64273089 [GRCh38]
Chr20:55804471..62904442 [GRCh37]
Chr20:55237878..62374886 [NCBI36]
Chr20:20q13.31-13.33		 pathogenic
GRCh38/hg38 20q13.33(chr20:62582073-64284202)x1 copy number loss See cases [RCV000141744] Chr20:62582073..64284202 [GRCh38]
Chr20:61179280..62915555 [GRCh37]
Chr20:60589725..62385999 [NCBI36]
Chr20:20q13.33		 pathogenic
GRCh38/hg38 20q13.33(chr20:62663307-64284202)x1 copy number loss See cases [RCV000141676] Chr20:62663307..64284202 [GRCh38]
Chr20:61294659..62915555 [GRCh37]
Chr20:60765104..62385999 [NCBI36]
Chr20:20q13.33		 pathogenic
GRCh38/hg38 20q13.2-13.33(chr20:53236165-64284202)x3 copy number gain See cases [RCV000143584] Chr20:53236165..64284202 [GRCh38]
Chr20:51852704..62915555 [GRCh37]
Chr20:51286111..62385999 [NCBI36]
Chr20:20q13.2-13.33		 likely pathogenic
GRCh38/hg38 20q13.33(chr20:62455231-63839491)x1 copy number loss See cases [RCV000052768] Chr20:62455231..63839491 [GRCh38]
Chr20:61030287..62470844 [GRCh37]
Chr20:60463682..61941288 [NCBI36]
Chr20:20q13.33		 pathogenic
GRCh38/hg38 20q13.33(chr20:62545370-64241486)x1 copy number loss See cases [RCV000052769] Chr20:62545370..64241486 [GRCh38]
Chr20:61142577..62872839 [GRCh37]
Chr20:60553022..62343283 [NCBI36]
Chr20:20q13.33		 pathogenic
GRCh38/hg38 20q13.33(chr20:62561794-63331723)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052770]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052770]|See cases [RCV000052770] Chr20:62561794..63331723 [GRCh38]
Chr20:61211869..61963075 [GRCh37]
Chr20:60569446..61433519 [NCBI36]
Chr20:20q13.33		 pathogenic
GRCh38/hg38 20q13.12-13.33(chr20:44787704-64277321)x3 copy number gain See cases [RCV000053035] Chr20:44787704..64277321 [GRCh38]
Chr20:43416345..62908674 [GRCh37]
Chr20:42849759..62379118 [NCBI36]
Chr20:20q13.12-13.33		 pathogenic
Single allele duplication not provided [RCV002266602] Chr20:62941782..63658260 [GRCh38]
Chr20:20q13.33		 uncertain significance
Single allele duplication not specified [RCV002286379] Chr20:61800345..63644611 [GRCh38]
Chr20:20q13.33		 uncertain significance
GRCh38/hg38 20q13.33(chr20:62632017-63794804)x1 copy number loss Neurodevelopmental disorder [RCV003327727] Chr20:62632017..63794804 [GRCh38]
Chr20:20q13.33		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:966
Count of miRNA genes:498
Interacting mature miRNAs:553
Transcripts:ENST00000370341, ENST00000414668, ENST00000456634
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
High
Medium 204
Low 8 3 2 383 2 50 2 6 1 172 6
Below cutoff 445 507 363 86 300 47 990 466 1347 28 207 310 40 209 607

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000370341
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2063,034,217 - 63,037,028 (-)Ensembl
RefSeq Acc Id: ENST00000414668
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2063,034,217 - 63,036,396 (-)Ensembl
RefSeq Acc Id: ENST00000456634
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2063,034,383 - 63,036,353 (-)Ensembl
RefSeq Acc Id: NR_028295
RefSeq Status: PREDICTED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382063,034,217 - 63,037,028 (-)NCBI
GRCh372061,665,569 - 61,668,380 (-)RGD
Celera2058,342,168 - 58,344,979 (-)RGD
HuRef2058,383,888 - 58,386,663 (-)RGD
CHM1_12061,566,589 - 61,569,232 (-)NCBI
T2T-CHM13v2.02064,835,829 - 64,838,604 (-)NCBI
Sequence:
Protein Sequences
GenBank Protein EAW75309 (Get FASTA)   NCBI Sequence Viewer  
  EAW75310 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences


Additional Information

Database Acc Id Source(s)
COSMIC LINC00029 COSMIC
Ensembl Genes ENSG00000125514 Ensembl
GTEx ENSG00000125514 GTEx
HGNC ID HGNC:16184 ENTREZGENE
Human Proteome Map LINC00029 Human Proteome Map
NCBI Gene 100144596 ENTREZGENE
PharmGKB PA164723570 PharmGKB
RNAcentral URS0000759F6B RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-09-01 LINC00029  long intergenic non-protein coding RNA 29  NCRNA00029  non-protein coding RNA 29  Symbol and/or name change 5135510 APPROVED