C1RL-AS1 (C1RL antisense RNA 1) - Rat Genome Database

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Gene: C1RL-AS1 (C1RL antisense RNA 1) Homo sapiens
Analyze
Symbol: C1RL-AS1
Name: C1RL antisense RNA 1
RGD ID: 6769130
HGNC Page HGNC:27461
Description: ASSOCIATED WITH Hyperphosphatemic Familial Tumoral Calcinosis 1; INTERACTS WITH 4,4'-sulfonyldiphenol; antirheumatic drug; aristolochic acid A
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: PREDICTED
Previously known as: MATL2963
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38127,108,308 - 7,121,851 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl127,108,052 - 7,122,524 (+)EnsemblGRCh38hg38GRCh38
GRCh37127,260,904 - 7,274,447 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36127,162,884 - 7,165,720 (+)NCBINCBI36Build 36hg18NCBI36
Celera128,837,117 - 8,850,658 (+)NCBICelera
Cytogenetic Map12p13.31NCBI
HuRef127,073,787 - 7,087,232 (+)NCBIHuRef
CHM1_1127,259,941 - 7,273,471 (+)NCBICHM1_1
T2T-CHM13v2.0127,121,492 - 7,135,036 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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:12975309   PMID:14702039   PMID:29507755   PMID:36745681  


Genomics

Variants

.
Variants in C1RL-AS1
6 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 12p13.33-11.1(chr12:121255-34603274)x3 copy number gain See cases [RCV000136611] Chr12:121255..34603274 [GRCh38]
Chr12:282465..34756209 [GRCh37]
Chr12:100682..34647476 [NCBI36]
Chr12:12p13.33-11.1		 pathogenic
GRCh38/hg38 12p13.33-12.3(chr12:2871741-14987348)x3 copy number gain See cases [RCV000137694] Chr12:2871741..14987348 [GRCh38]
Chr12:2980907..15140282 [GRCh37]
Chr12:2851168..15031549 [NCBI36]
Chr12:12p13.33-12.3		 pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:121271-34603261)x3 copy number gain See cases [RCV000139052] Chr12:121271..34603261 [GRCh38]
Chr12:282465..34756196 [GRCh37]
Chr12:100698..34647463 [NCBI36]
Chr12:12p13.33-11.1		 pathogenic
GRCh38/hg38 12p13.33-q24.33(chr12:121271-133196807)x3 copy number gain See cases [RCV000139555] Chr12:121271..133196807 [GRCh38]
Chr12:282465..133773393 [GRCh37]
Chr12:100698..132283466 [NCBI36]
Chr12:12p13.33-q24.33		 pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:54427-34608071)x4 copy number gain See cases [RCV000139787] Chr12:54427..34608071 [GRCh38]
Chr12:282465..34761006 [GRCh37]
Chr12:33854..34652273 [NCBI36]
Chr12:12p13.33-11.1		 pathogenic
GRCh38/hg38 12p13.31(chr12:7055795-7428473)x3 copy number gain See cases [RCV000141432] Chr12:7055795..7428473 [GRCh38]
Chr12:7163099..7581069 [GRCh37]
Chr12:7033360..7472336 [NCBI36]
Chr12:12p13.31		 uncertain significance
GRCh38/hg38 12p13.33-12.2(chr12:1258274-20657577)x3 copy number gain See cases [RCV000141905] Chr12:1258274..20657577 [GRCh38]
Chr12:1367440..20810511 [GRCh37]
Chr12:1237701..20701778 [NCBI36]
Chr12:12p13.33-12.2		 pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:64620-34682902)x4 copy number gain See cases [RCV000142149] Chr12:64620..34682902 [GRCh38]
Chr12:173786..34835837 [GRCh37]
Chr12:44047..34727104 [NCBI36]
Chr12:12p13.33-11.1		 pathogenic
GRCh38/hg38 12p13.33-11.22(chr12:121055-28415184)x1 copy number loss See cases [RCV000052776] Chr12:121055..28415184 [GRCh38]
Chr12:282465..28568117 [GRCh37]
Chr12:100482..28459384 [NCBI36]
Chr12:12p13.33-11.22		 pathogenic
GRCh38/hg38 12p13.31(chr12:6728665-7705620)x1 copy number loss See cases [RCV000052779] Chr12:6728665..7705620 [GRCh38]
Chr12:6837831..7858216 [GRCh37]
Chr12:6708092..7749483 [NCBI36]
Chr12:12p13.31		 pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:77187-34380176)x3 copy number gain See cases [RCV000053660] Chr12:77187..34380176 [GRCh38]
Chr12:282465..34533111 [GRCh37]
Chr12:56614..34424378 [NCBI36]
Chr12:12p13.33-11.1		 pathogenic
GRCh38/hg38 12p13.33-12.1(chr12:80412-25470329)x3 copy number gain See cases [RCV000053662] Chr12:80412..25470329 [GRCh38]
Chr12:282465..25623263 [GRCh37]
Chr12:59839..25514530 [NCBI36]
Chr12:12p13.33-12.1		 pathogenic
GRCh38/hg38 12p13.33-13.31(chr12:121055-7272606)x3 copy number gain See cases [RCV000053663] Chr12:121055..7272606 [GRCh38]
Chr12:282465..7425202 [GRCh37]
Chr12:100482..7316469 [NCBI36]
Chr12:12p13.33-13.31		 pathogenic
GRCh38/hg38 12p13.33-13.31(chr12:121255-8361746)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053664]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053664]|See cases [RCV000053664] Chr12:121255..8361746 [GRCh38]
Chr12:282465..8514342 [GRCh37]
Chr12:100682..8405609 [NCBI36]
Chr12:12p13.33-13.31		 pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:212976-33926913)x4 copy number gain See cases [RCV000053666] Chr12:212976..33926913 [GRCh38]
Chr12:322142..34079848 [GRCh37]
Chr12:192403..33971115 [NCBI36]
Chr12:12p13.33-11.1		 pathogenic
NC_000012.12:g.(1_3750000)_(5250000_9000000)del deletion Tumoral calcinosis, hyperphosphatemic, familial, 1 [RCV000758697] Chr12:3750000..5250000 [GRCh38]
Chr12:12p13.33-13.31		 pathogenic|not provided
NM_016546.4(C1RL):c.79C>G (p.Leu27Val) single nucleotide variant not specified [RCV004170386] Chr12:7108472 [GRCh38]
Chr12:7261068 [GRCh37]
Chr12:12p13.31		 uncertain significance
NM_016546.4(C1RL):c.85C>A (p.Leu29Ile) single nucleotide variant not specified [RCV004116669] Chr12:7108466 [GRCh38]
Chr12:7261062 [GRCh37]
Chr12:12p13.31		 uncertain significance
NM_016546.4(C1RL):c.217G>C (p.Ala73Pro) single nucleotide variant not specified [RCV004128231] Chr12:7108334 [GRCh38]
Chr12:7260930 [GRCh37]
Chr12:12p13.31		 uncertain significance
NM_016546.4(C1RL):c.150G>C (p.Gln50His) single nucleotide variant not specified [RCV004181296] Chr12:7108401 [GRCh38]
Chr12:7260997 [GRCh37]
Chr12:12p13.31		 uncertain significance
NM_016546.4(C1RL):c.92G>T (p.Gly31Val) single nucleotide variant not specified [RCV004429626] Chr12:7108459 [GRCh38]
Chr12:7261055 [GRCh37]
Chr12:12p13.31		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1438
Count of miRNA genes:663
Interacting mature miRNAs:786
Transcripts:ENST00000382215, ENST00000435921, ENST00000535078, ENST00000536679, ENST00000541775, ENST00000545775
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
D12S1953  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37127,268,368 - 7,268,711UniSTSGRCh37
Build 36127,159,644 - 7,159,987RGDNCBI36
Celera128,844,581 - 8,844,924RGD
Cytogenetic Map12p13.31UniSTS
HuRef127,081,155 - 7,081,498UniSTS
GeneMap99-GB4 RH Map1245.78UniSTS
Whitehead-RH Map1280.6UniSTS
NCBI RH Map12117.6UniSTS
G42647  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37127,268,879 - 7,269,069UniSTSGRCh37
Build 36127,160,155 - 7,160,345RGDNCBI36
Celera128,845,092 - 8,845,282RGD
Cytogenetic Map12p13.31UniSTS
HuRef127,081,666 - 7,081,856UniSTS


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 visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 102 22 135 82 426 79 154 28 149 94 212 123 7 19 136
Low 2322 2666 1583 539 1432 384 3749 1571 1604 299 1225 1464 166 1185 2244 2 1
Below cutoff 9 302 8 2 90 2 439 591 1972 26 17 22 2 1 408 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000382215
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl127,108,571 - 7,121,027 (+)Ensembl
RefSeq Acc Id: ENST00000435921
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl127,108,052 - 7,111,606 (+)Ensembl
RefSeq Acc Id: ENST00000535078
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl127,108,323 - 7,122,524 (+)Ensembl
RefSeq Acc Id: ENST00000536679
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl127,108,571 - 7,110,470 (+)Ensembl
RefSeq Acc Id: ENST00000541775
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl127,108,308 - 7,121,851 (+)Ensembl
RefSeq Acc Id: NR_026947
RefSeq Status: PREDICTED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38127,108,308 - 7,121,851 (+)NCBI
GRCh37127,260,904 - 7,274,447 (+)NCBI
HuRef127,073,787 - 7,087,232 (+)NCBI
CHM1_1127,259,941 - 7,273,471 (+)NCBI
T2T-CHM13v2.0127,121,492 - 7,135,036 (+)NCBI
Sequence:
Protein Sequences
GenBank Protein AAQ89092 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences

Promoters
RGD ID:15096559
Promoter ID:EPDNEWNC_H1402
Type:initiation region
Name:C1RL-AS1_2
Description:C1RL antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:27461]
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
GRCh38127,108,282 - 7,108,342EPDNEWNC
RGD ID:15096560
Promoter ID:EPDNEWNC_H1403
Type:initiation region
Name:C1RL-AS1_1
Description:C1RL antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:27461]
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
GRCh38127,108,593 - 7,108,653EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC C1RL-AS1 COSMIC
Ensembl Genes ENSG00000205885 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000541775 ENTREZGENE
GTEx ENSG00000205885 GTEx
HGNC ID HGNC:27461 ENTREZGENE
Human Proteome Map C1RL-AS1 Human Proteome Map
NCBI Gene C1RL-AS1 ENTREZGENE
RNAcentral URS000075A17C RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-08-21 C1RL-AS1  C1RL antisense RNA 1  C1RL-AS1  C1RL antisense RNA 1 (non-protein coding)  Symbol and/or name change 5135510 APPROVED