LINC01963 (long intergenic non-protein coding RNA 1963) - Rat Genome Database

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Pathways
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Gene: LINC01963 (long intergenic non-protein coding RNA 1963) Homo sapiens
Analyze
Symbol: LINC01963
Name: long intergenic non-protein coding RNA 1963
RGD ID: 11569372
HGNC Page HGNC:25283
Description: INTERACTS WITH 4,4'-sulfonyldiphenol; aristolochic acid A; dorsomorphin
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: PKI55
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382216,216,889 - 216,220,192 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2216,217,045 - 216,220,192 (+)EnsemblGRCh38hg38GRCh38
GRCh372217,081,612 - 217,084,915 (+)NCBIGRCh37GRCh37hg19GRCh37
Celera2210,851,862 - 210,852,287 (+)NCBICelera
Cytogenetic Map2q35NCBI
HuRef2208,938,309 - 208,941,616 (+)NCBIHuRef
CHM1_12217,087,545 - 217,090,852 (+)NCBICHM1_1
T2T-CHM13v2.02216,702,311 - 216,705,618 (+)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:14562957   PMID:14702039   PMID:16344560   PMID:17467651   PMID:18167144   PMID:19095038   PMID:20644913   PMID:32559621  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2q35(chr2:215079289-216799770)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052731]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052731]|See cases [RCV000052731] Chr2:215079289..216799770 [GRCh38]
Chr2:215944012..217664493 [GRCh37]
Chr2:215652257..217372738 [NCBI36]
Chr2:2q35		 uncertain significance
GRCh38/hg38 2q35(chr2:215908412-216680325)x3 copy number gain See cases [RCV000139191] Chr2:215908412..216680325 [GRCh38]
Chr2:216773135..217545048 [GRCh37]
Chr2:216481380..217253293 [NCBI36]
Chr2:2q35		 likely benign
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 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 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 2q34-36.3(chr2:212614422-227121230)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052964]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052964]|See cases [RCV000052964] Chr2:212614422..227121230 [GRCh38]
Chr2:213479146..227985946 [GRCh37]
Chr2:213187391..227694190 [NCBI36]
Chr2:2q34-36.3		 pathogenic
GRCh38/hg38 2q31.3-36.2(chr2:180513793-224302848)x3 copy number gain See cases [RCV000139446] Chr2:180513793..224302848 [GRCh38]
Chr2:181378520..225167565 [GRCh37]
Chr2:181086765..224875809 [NCBI36]
Chr2:2q31.3-36.2		 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
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:366
Count of miRNA genes:177
Interacting mature miRNAs:182
Transcripts:ENST00000562038, ENST00000597904
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 entire extraembryonic component
High
Medium 115 387 479 21 267 22 1003 486 2706 97 271 415 3 10 912
Low 2314 2391 1142 499 1481 340 3351 1698 1002 321 1177 1192 168 1193 1876 4
Below cutoff 3 206 101 101 199 101 1 9 1 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000562038
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2216,217,045 - 216,220,192 (+)Ensembl
RefSeq Acc Id: NR_037701
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382216,216,889 - 216,220,192 (+)NCBI
CHM1_12217,087,545 - 217,090,852 (+)NCBI
T2T-CHM13v2.02216,702,311 - 216,705,618 (+)NCBI
Sequence:
Protein Sequences
GenBank Protein CAB70797 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences

Promoters
RGD ID:15095531
Promoter ID:EPDNEWNC_H368
Type:initiation region
Name:LINC01963_1
Description:long intergenic non-protein coding RNA 1963 [Source:HGNCSymbol;Acc:HGNC:25283]
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
GRCh382216,217,082 - 216,217,142EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC01963 COSMIC
Ensembl Genes ENSG00000260804 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000562038 ENTREZGENE
GTEx ENSG00000260804 GTEx
HGNC ID HGNC:25283 ENTREZGENE
Human Proteome Map LINC01963 Human Proteome Map
NCBI Gene LINC01963 ENTREZGENE
RNAcentral URS000075B935 RNACentral