LINC00528 (long intergenic non-protein coding RNA 528) - Rat Genome Database

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Gene: LINC00528 (long intergenic non-protein coding RNA 528) Homo sapiens
Analyze
Symbol: LINC00528
Name: long intergenic non-protein coding RNA 528
RGD ID: 7246732
HGNC Page HGNC:26875
Description: INTERACTS WITH aristolochic acid A; dieldrin; paracetamol
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: C22orf37
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382217,777,290 - 17,779,481 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2217,777,322 - 17,779,481 (+)EnsemblGRCh38hg38GRCh38
GRCh372218,260,056 - 18,262,247 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362216,640,056 - 16,640,933 (+)NCBINCBI36Build 36hg18NCBI36
Celera221,879,714 - 1,881,905 (+)NCBICelera
Cytogenetic Map22q11.21NCBI
HuRef222,074,257 - 2,076,448 (+)NCBIHuRef
CHM1_12218,259,648 - 18,261,839 (+)NCBICHM1_1
T2T-CHM13v2.02218,444,966 - 18,447,157 (+)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:14702039   PMID:16344560   PMID:24927568   PMID:31833800  


Genomics

Variants

.
Variants in LINC00528
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 22q11.1-13.33(chr22:16916608-50739836)x3 copy number gain See cases [RCV000133646] Chr22:16916608..50739836 [GRCh38]
Chr22:17397498..51178264 [GRCh37]
Chr22:15777498..49525130 [NCBI36]
Chr22:22q11.1-13.33		 pathogenic
GRCh38/hg38 22q11.1-11.21(chr22:16916608-20354644)x3 copy number gain See cases [RCV000133785] Chr22:16916608..20354644 [GRCh38]
Chr22:17397498..20708934 [GRCh37]
Chr22:15777498..19038934 [NCBI36]
Chr22:22q11.1-11.21		 pathogenic
GRCh38/hg38 22q11.1-11.21(chr22:16916608-20354644)x1 copy number loss See cases [RCV000133786] Chr22:16916608..20354644 [GRCh38]
Chr22:17397498..20708934 [GRCh37]
Chr22:15777498..19038934 [NCBI36]
Chr22:22q11.1-11.21		 pathogenic
GRCh38/hg38 22q11.1-11.21(chr22:16916608-20343532)x3 copy number gain See cases [RCV000133682] Chr22:16916608..20343532 [GRCh38]
Chr22:17397498..20659606 [GRCh37]
Chr22:15777498..18989606 [NCBI36]
Chr22:22q11.1-11.21		 pathogenic
GRCh38/hg38 22q11.1-13.33(chr22:16916743-50739785)x3 copy number gain See cases [RCV000134730] Chr22:16916743..50739785 [GRCh38]
Chr22:17397633..51178213 [GRCh37]
Chr22:15777633..49525079 [NCBI36]
Chr22:22q11.1-13.33		 pathogenic
GRCh38/hg38 22q11.1-11.21(chr22:16916743-19597367)x3 copy number gain See cases [RCV000134065] Chr22:16916743..19597367 [GRCh38]
Chr22:17397633..19584890 [GRCh37]
Chr22:15777633..17964890 [NCBI36]
Chr22:22q11.1-11.21		 pathogenic
GRCh38/hg38 22q11.1-11.21(chr22:16916743-18718546)x3 copy number gain See cases [RCV000138648] Chr22:16916743..18718546 [GRCh38]
Chr22:17397633..18706059 [GRCh37]
Chr22:15777633..17086059 [NCBI36]
Chr22:22q11.1-11.21		 pathogenic
GRCh38/hg38 22q11.1-11.21(chr22:16916743-18178991)x3 copy number gain See cases [RCV000138423] Chr22:16916743..18178991 [GRCh38]
Chr22:17397633..18661758 [GRCh37]
Chr22:15777633..17041758 [NCBI36]
Chr22:22q11.1-11.21		 pathogenic
GRCh38/hg38 22q11.1-11.21(chr22:16916743-18145439)x3 copy number gain See cases [RCV000139612] Chr22:16916743..18145439 [GRCh38]
Chr22:17397633..18628206 [GRCh37]
Chr22:15777633..17008206 [NCBI36]
Chr22:22q11.1-11.21		 pathogenic
GRCh38/hg38 22q11.1-11.21(chr22:16916608-18997006)x4 copy number gain See cases [RCV000142442] Chr22:16916608..18997006 [GRCh38]
Chr22:17397498..18984519 [GRCh37]
Chr22:15777498..17364519 [NCBI36]
Chr22:22q11.1-11.21		 pathogenic
GRCh38/hg38 22q11.1-11.21(chr22:16916608-18179006)x4 copy number gain See cases [RCV000142570] Chr22:16916608..18179006 [GRCh38]
Chr22:17397498..18661773 [GRCh37]
Chr22:15777498..17041773 [NCBI36]
Chr22:22q11.1-11.21		 pathogenic
GRCh38/hg38 22p11.2-q11.1(chr22:16367190-18178957)x4 copy number gain See cases [RCV000140776] Chr22:16367190..18178957 [GRCh38]
Chr22:16054691..18661724 [GRCh37]
Chr22:14434691..17041724 [NCBI36]
Chr22:22p11.2-q11.1		 pathogenic
GRCh38/hg38 22q11.1-11.21(chr22:16916608-20324240)x3 copy number gain See cases [RCV000050858] Chr22:16916608..20324240 [GRCh38]
Chr22:17397498..20311763 [GRCh37]
Chr22:15777498..18691763 [NCBI36]
Chr22:22q11.1-11.21		 pathogenic
GRCh38/hg38 22q11.1-11.21(chr22:16916608-21151128)x3 copy number gain See cases [RCV000050614] Chr22:16916608..21151128 [GRCh38]
Chr22:17397498..21505417 [GRCh37]
Chr22:15777498..19835417 [NCBI36]
Chr22:22q11.1-11.21		 pathogenic
GRCh38/hg38 22q11.1-11.21(chr22:16916608-20324240)x1 copy number loss See cases [RCV000050859] Chr22:16916608..20324240 [GRCh38]
Chr22:17397498..20311763 [GRCh37]
Chr22:15777498..18691763 [NCBI36]
Chr22:22q11.1-11.21		 pathogenic
GRCh38/hg38 22q11.1-11.21(chr22:16538125-20363937)x1 copy number loss See cases [RCV000051270] Chr22:16538125..20363937 [GRCh38]
Chr22:17019015..20718227 [GRCh37]
Chr22:15399015..19048227 [NCBI36]
Chr22:22q11.1-11.21		 pathogenic
GRCh38/hg38 22q11.1-11.21(chr22:16578056-18134332)x3 copy number gain See cases [RCV000051917] Chr22:16578056..18134332 [GRCh38]
Chr22:17058946..18617099 [GRCh37]
Chr22:15438946..16997099 [NCBI36]
Chr22:22q11.1-11.21		 pathogenic
GRCh38/hg38 22q11.1-11.21(chr22:11121452-18167952)x3 copy number gain See cases [RCV000053100] Chr22:11121452..18167952 [GRCh38]
Chr22:16230024..18650719 [GRCh37]
Chr22:14610024..17030719 [NCBI36]
Chr22:22q11.1-11.21		 pathogenic
GRCh38/hg38 22q11.1-11.21(chr22:16916608-20343532)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053103]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053103]|See cases [RCV000053103] Chr22:16916608..20343532 [GRCh38]
Chr22:17397498..20402677 [GRCh37]
Chr22:15777498..18782677 [NCBI36]
Chr22:22q11.1-11.21		 pathogenic
GRCh38/hg38 22q11.1-11.23(chr22:16916608-24358936)x3 copy number gain See cases [RCV000053104] Chr22:16916608..24358936 [GRCh38]
Chr22:17397498..24754904 [GRCh37]
Chr22:15777498..23084904 [NCBI36]
Chr22:22q11.1-11.23		 pathogenic
GRCh38/hg38 22q11.1-11.21(chr22:16916608-18718532)x3 copy number gain See cases [RCV000051127] Chr22:16916608..18718532 [GRCh38]
Chr22:17397498..18706045 [GRCh37]
Chr22:15777498..17086045 [NCBI36]
Chr22:22q11.1-11.21		 pathogenic
GRCh38/hg38 22q11.1-11.21(chr22:16804110-18162024) copy number gain Anomalous pulmonary venous return [RCV003223583] Chr22:16804110..18162024 [GRCh38]
Chr22:22q11.1-11.21		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:212
Count of miRNA genes:201
Interacting mature miRNAs:211
Transcripts:ENST00000600723
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
RH27783  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372218,260,305 - 18,260,451UniSTSGRCh37
Build 362216,640,305 - 16,640,451RGDNCBI36
Celera221,879,963 - 1,880,109RGD
Cytogenetic Map22q11.21UniSTS
HuRef222,074,506 - 2,074,652UniSTS
RH77734  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372218,262,012 - 18,262,137UniSTSGRCh37
Build 362216,642,012 - 16,642,137RGDNCBI36
Celera221,881,670 - 1,881,795RGD
Cytogenetic Map22q11.21UniSTS
HuRef222,076,213 - 2,076,338UniSTS
GeneMap99-GB4 RH Map2213.14UniSTS


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 37 326 6 2 985 2 3 1 1 8
Low 861 712 997 412 920 309 785 224 789 155 612 1197 105 668 319
Below cutoff 1456 1869 707 203 35 146 3297 1811 2831 224 737 300 61 536 2305 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000600723
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2217,777,322 - 17,779,481 (+)Ensembl
RefSeq Acc Id: NR_103718
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382217,777,290 - 17,779,481 (+)NCBI
HuRef222,074,257 - 2,076,448 (+)NCBI
CHM1_12218,259,648 - 18,261,839 (+)NCBI
T2T-CHM13v2.02218,444,966 - 18,447,157 (+)NCBI
Sequence:
Protein Sequences
GenBank Protein BAC05187 (Get FASTA)   NCBI Sequence Viewer  
  Q8N1L1 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8N1L1-F1-model_v2 AlphaFold Q8N1L1 1-170 view protein structure

Promoters
RGD ID:15097373
Promoter ID:EPDNEWNC_H2215
Type:initiation region
Name:LINC00528_1
Description:long intergenic non-protein coding RNA 528 [Source:HGNCSymbol;Acc:HGNC:26875]
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
GRCh382217,777,322 - 17,777,382EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC00528 COSMIC
Ensembl Genes ENSG00000269220 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000600723 ENTREZGENE
GTEx ENSG00000269220 GTEx
HGNC ID HGNC:26875 ENTREZGENE
Human Proteome Map LINC00528 Human Proteome Map
NCBI Gene LINC00528 ENTREZGENE
RNAcentral URS000075E032 RNACentral
UniProt CV037_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE