CLIP1-AS1 (CLIP1 antisense RNA 1) - Rat Genome Database

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Gene: CLIP1-AS1 (CLIP1 antisense RNA 1) Homo sapiens
Analyze
Symbol: CLIP1-AS1
Name: CLIP1 antisense RNA 1
RGD ID: 8551557
HGNC Page HGNC:48586
Description: INTERACTS WITH 2-hydroxypropanoic acid; cisplatin; rac-lactic acid
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3812122,395,542 - 122,399,944 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl12122,395,542 - 122,400,857 (+)EnsemblGRCh38hg38GRCh38
GRCh3712122,880,089 - 122,884,491 (+)NCBIGRCh37GRCh37hg19GRCh37
Celera12122,470,602 - 122,475,007 (+)NCBICelera
Cytogenetic Map12q24.31NCBI
HuRef12119,841,101 - 119,845,505 (+)NCBIHuRef
CHM1_112122,848,376 - 122,852,778 (+)NCBICHM1_1
T2T-CHM13v2.012122,391,332 - 122,395,736 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 12q24.31-24.33(chr12:120697672-133202490)x3 copy number gain See cases [RCV000137651] Chr12:120697672..133202490 [GRCh38]
Chr12:121135475..133779076 [GRCh37]
Chr12:119619858..132289149 [NCBI36]
Chr12:12q24.31-24.33		 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 12q24.31-24.32(chr12:120718786-127500215)x1 copy number loss See cases [RCV000142454] Chr12:120718786..127500215 [GRCh38]
Chr12:121156589..127984760 [GRCh37]
Chr12:119640972..126550713 [NCBI36]
Chr12:12q24.31-24.32		 pathogenic
GRCh38/hg38 12q24.31-24.32(chr12:121917758-127802717)x1 copy number loss See cases [RCV000143250] Chr12:121917758..127802717 [GRCh38]
Chr12:122355664..128287262 [GRCh37]
Chr12:120840047..126853215 [NCBI36]
Chr12:12q24.31-24.32		 pathogenic
GRCh38/hg38 12q24.21-24.33(chr12:114268403-133201316)x3 copy number gain See cases [RCV000143656] Chr12:114268403..133201316 [GRCh38]
Chr12:114706208..133777902 [GRCh37]
Chr12:113190591..132287975 [NCBI36]
Chr12:12q24.21-24.33		 pathogenic
GRCh38/hg38 12q24.31(chr12:120504068-122459718)x1 copy number loss See cases [RCV000051342] Chr12:120504068..122459718 [GRCh38]
Chr12:120941871..122944265 [GRCh37]
Chr12:119426254..121510218 [NCBI36]
Chr12:12q24.31		 pathogenic
GRCh38/hg38 12q24.31(chr12:121325874-122505529)x1 copy number loss See cases [RCV000051343] Chr12:121325874..122505529 [GRCh38]
Chr12:121956483..122990076 [GRCh37]
Chr12:120248060..121556029 [NCBI36]
Chr12:12q24.31		 pathogenic
GRCh38/hg38 12q24.31(chr12:121471000-122459718)x1 copy number loss See cases [RCV000051344] Chr12:121471000..122459718 [GRCh38]
Chr12:121956483..122944265 [GRCh37]
Chr12:120393186..121510218 [NCBI36]
Chr12:12q24.31		 pathogenic
GRCh38/hg38 12q24.23-24.33(chr12:118165459-133182322)x3 copy number gain See cases [RCV000050866] Chr12:118165459..133182322 [GRCh38]
Chr12:118603264..133758908 [GRCh37]
Chr12:117087647..132268981 [NCBI36]
Chr12:12q24.23-24.33		 pathogenic
GRCh38/hg38 12q24.23-24.31(chr12:119286893-122638552)x3 copy number gain See cases [RCV000051981] Chr12:119286893..122638552 [GRCh38]
Chr12:119724698..123123099 [GRCh37]
Chr12:118209081..121689052 [NCBI36]
Chr12:12q24.23-24.31		 uncertain significance
GRCh38/hg38 12q24.21-24.33(chr12:115131583-133166920)x3 copy number gain See cases [RCV000053689] Chr12:115131583..133166920 [GRCh38]
Chr12:115569388..133743506 [GRCh37]
Chr12:114053771..132253579 [NCBI36]
Chr12:12q24.21-24.33		 pathogenic
GRCh38/hg38 12q24.23-24.33(chr12:119417382-133191400)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053691]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053691]|See cases [RCV000053691] Chr12:119417382..133191400 [GRCh38]
Chr12:119855187..133767986 [GRCh37]
Chr12:118339570..132278059 [NCBI36]
Chr12:12q24.23-24.33		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:377
Count of miRNA genes:321
Interacting mature miRNAs:340
Transcripts:ENST00000535976, ENST00000539034
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 1
Low 39 14 29 11 35 11 73 31 36 19 385 85 2 6 37 1
Below cutoff 1473 1536 1216 317 731 209 2849 1509 1949 206 679 1077 113 618 1917

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000535976
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl12122,395,606 - 122,400,857 (+)Ensembl
RefSeq Acc Id: ENST00000539034
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl12122,395,542 - 122,399,618 (+)Ensembl
RefSeq Acc Id: NR_045382
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh3812122,395,542 - 122,399,944 (+)NCBI
HuRef12119,841,101 - 119,845,505 (+)NCBI
CHM1_112122,848,376 - 122,852,778 (+)NCBI
T2T-CHM13v2.012122,391,332 - 122,395,736 (+)NCBI
Sequence:
Promoters
RGD ID:15096687
Promoter ID:EPDNEWNC_H1507
Type:initiation region
Name:CLIP1-AS1_1
Description:CLIP1 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:48586]
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
GRCh3812122,395,537 - 122,395,597EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC CLIP1-AS1 COSMIC
Ensembl Genes ENSG00000257097 Ensembl
GTEx ENSG00000257097 GTEx
HGNC ID HGNC:48586 ENTREZGENE
Human Proteome Map CLIP1-AS1 Human Proteome Map
NCBI Gene CLIP1-AS1 ENTREZGENE
RNAcentral URS000075B10A RNACentral