LINC03123 (long intergenic non-protein coding RNA 3123) - Rat Genome Database

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Pathways
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Gene: LINC03123 (long intergenic non-protein coding RNA 3123) Homo sapiens
Analyze
Symbol: LINC03123 (Ensembl: C5orf64-AS1)
Name: long intergenic non-protein coding RNA 3123 (Ensembl:C5orf64 antisense RNA 1)
RGD ID: 11575159
HGNC Page HGNC:52969
Description:
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: C5orf64 antisense RNA 1; C5orf64-AS1
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38561,732,790 - 61,735,698 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl561,732,774 - 61,735,715 (-)EnsemblGRCh38hg38GRCh38
GRCh37561,028,617 - 61,031,525 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map5q12.1NCBI
HuRef557,985,124 - 57,988,017 (-)NCBIHuRef
CHM1_1561,028,299 - 61,031,192 (-)NCBICHM1_1
T2T-CHM13v2.0562,551,901 - 62,554,809 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:12477932   PMID:33309768  


Genomics

Variants

.
Variants in LINC03123
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 5q12.1(chr5:61610054-62739543)x3 copy number gain See cases [RCV000138210] Chr5:61610054..62739543 [GRCh38]
Chr5:60905881..62035370 [GRCh37]
Chr5:60941638..62071126 [NCBI36]
Chr5:5q12.1		 uncertain significance
GRCh38/hg38 5p13.2-q12.1(chr5:35201559-61903141)x3 copy number gain See cases [RCV000137302] Chr5:35201559..61903141 [GRCh38]
Chr5:35201661..61198968 [GRCh37]
Chr5:35237418..61234725 [NCBI36]
Chr5:5p13.2-q12.1		 pathogenic
GRCh38/hg38 5p15.33-q13.3(chr5:22149-74412725)x3 copy number gain See cases [RCV000138780] Chr5:22149..74412725 [GRCh38]
Chr5:22149..73708550 [GRCh37]
Chr5:75149..73744306 [NCBI36]
Chr5:5p15.33-q13.3		 pathogenic
GRCh38/hg38 5q11.1-12.1(chr5:50288355-63149770)x1 copy number loss See cases [RCV000050797] Chr5:50288355..63149770 [GRCh38]
Chr5:49584189..62445597 [GRCh37]
Chr5:49619946..62481353 [NCBI36]
Chr5:5q11.1-12.1		 pathogenic
GRCh38/hg38 5q12.1-12.3(chr5:60499077-63927783)x1 copy number loss See cases [RCV000133749] Chr5:60499077..63927783 [GRCh38]
Chr5:59794904..63223610 [GRCh37]
Chr5:59830661..63259366 [NCBI36]
Chr5:5q12.1-12.3		 pathogenic
GRCh38/hg38 5q11.2-13.2(chr5:58785203-73519962)x1 copy number loss Intellectual disability [RCV000984869] Chr5:58785203..73519962 [GRCh38]
Chr5:5q11.2-13.2		 likely pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:206
Count of miRNA genes:202
Interacting mature miRNAs:202
Transcripts:ENST00000506550, ENST00000512882
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 4 262
Low 2 31 27 27 8 3 1442 22 110 5 8
Below cutoff 777 298 568 204 131 191 904 408 1762 169 208 400 13 226 655

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000506550
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl561,732,774 - 61,735,668 (-)Ensembl
RefSeq Acc Id: ENST00000512882
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl561,735,138 - 61,735,669 (-)Ensembl
RefSeq Acc Id: ENST00000669357
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl561,732,791 - 61,735,715 (-)Ensembl
RefSeq Acc Id: NR_105000
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38561,732,790 - 61,735,698 (-)NCBI
CHM1_1561,028,299 - 61,031,207 (-)NCBI
T2T-CHM13v2.0562,551,901 - 62,554,809 (-)NCBI
Sequence:
Promoters
RGD ID:15095888
Promoter ID:EPDNEWNC_H730
Type:initiation region
Name:C5orf64-AS1_1
Description:C5orf64 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:52969]
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
GRCh38561,735,678 - 61,735,738EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC03123 COSMIC
Ensembl Genes ENSG00000251575 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000669357 ENTREZGENE
GTEx ENSG00000251575 GTEx
HGNC ID HGNC:52969 ENTREZGENE
Human Proteome Map LINC03123 Human Proteome Map
NCBI Gene C5orf64-AS1 ENTREZGENE
RNAcentral URS000075E6FE RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-12-18 LINC03123  long intergenic non-protein coding RNA 3123  C5orf64-AS1  C5orf64 antisense RNA 1  Symbol and/or name change 19259463 PROVISIONAL