CFAP20DC-AS1 (CFAP20DC antisense RNA 1) - Rat Genome Database

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Gene: CFAP20DC-AS1 (CFAP20DC antisense RNA 1) Homo sapiens
Analyze
Symbol: CFAP20DC-AS1
Name: CFAP20DC antisense RNA 1
RGD ID: 8552149
HGNC Page HGNC:41063
Description:
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: C3orf67 antisense RNA 1; C3orf67-AS1
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38358,824,471 - 59,019,093 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl358,824,437 - 59,019,093 (+)EnsemblGRCh38hg38GRCh38
GRCh37358,810,197 - 59,004,819 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map3p14.2NCBI
HuRef358,907,421 - 59,101,707 (+)NCBIHuRef
CHM1_1358,760,349 - 58,955,002 (+)NCBICHM1_1
T2T-CHM13v2.0358,864,882 - 59,059,508 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
Additional References at PubMed
PMID:14702039  


Genomics

Variants

.
Variants in CFAP20DC-AS1
11 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_198463.2(C3orf67):c.1314G>A (p.Glu438=) single nucleotide variant Malignant melanoma [RCV000066171] Chr3:58831794 [GRCh38]
Chr3:58817520 [GRCh37]
Chr3:58792560 [NCBI36]
Chr3:3p14.2		 not provided
NM_198463.2(C3orf67):c.1218+14417C>T single nucleotide variant Malignant melanoma [RCV000066172] Chr3:58849141 [GRCh38]
Chr3:58834867 [GRCh37]
Chr3:58809907 [NCBI36]
Chr3:3p14.2		 not provided
NM_198463.2(C3orf67):c.1127C>T (p.Ser376Leu) single nucleotide variant Malignant melanoma [RCV000066173] Chr3:58863649 [GRCh38]
Chr3:58849375 [GRCh37]
Chr3:58824415 [NCBI36]
Chr3:3p14.2		 not provided
GRCh38/hg38 3p14.3-14.1(chr3:57430538-64884522)x1 copy number loss See cases [RCV000139570] Chr3:57430538..64884522 [GRCh38]
Chr3:57416265..64870197 [GRCh37]
Chr3:57391305..64845237 [NCBI36]
Chr3:3p14.3-14.1		 pathogenic
GRCh38/hg38 3p14.3-11.1(chr3:57140424-90259960)x1 copy number loss See cases [RCV000139626] Chr3:57140424..90259960 [GRCh38]
Chr3:57174452..90309110 [GRCh37]
Chr3:57149492..90391800 [NCBI36]
Chr3:3p14.3-11.1		 pathogenic
GRCh38/hg38 3p14.3-14.2(chr3:58498793-60217173)x3 copy number gain See cases [RCV000142126] Chr3:58498793..60217173 [GRCh38]
Chr3:58484520..60202901 [GRCh37]
Chr3:58459560..60177941 [NCBI36]
Chr3:3p14.3-14.2		 uncertain significance
GRCh38/hg38 3p14.3-14.2(chr3:58534847-60199939)x3 copy number gain See cases [RCV000142665] Chr3:58534847..60199939 [GRCh38]
Chr3:58520574..60185667 [GRCh37]
Chr3:58495614..60160707 [NCBI36]
Chr3:3p14.3-14.2		 uncertain significance
GRCh38/hg38 3p14.2(chr3:58870233-59620738)x3 copy number gain See cases [RCV000142700] Chr3:58870233..59620738 [GRCh38]
Chr3:58855959..59606464 [GRCh37]
Chr3:58830999..59581504 [NCBI36]
Chr3:3p14.2		 uncertain significance
GRCh38/hg38 3p14.3-14.2(chr3:58532827-60193441)x3 copy number gain See cases [RCV000051469] Chr3:58532827..60193441 [GRCh38]
Chr3:58518554..60179169 [GRCh37]
Chr3:58493594..60154209 [NCBI36]
Chr3:3p14.3-14.2		 uncertain significance
GRCh38/hg38 3p21.1-14.1(chr3:54045018-66060461)x1 copy number loss See cases [RCV000051081] Chr3:54045018..66060461 [GRCh38]
Chr3:54079045..66046136 [GRCh37]
Chr3:54054085..66021176 [NCBI36]
Chr3:3p21.1-14.1		 pathogenic
NM_001394063.1(CFAP20DC):c.1252C>G (p.Gln418Glu) single nucleotide variant not provided [RCV000950390] Chr3:58866572 [GRCh38]
Chr3:58852298 [GRCh37]
Chr3:3p14.2		 benign|likely benign
NM_001394063.1(CFAP20DC):c.665G>A (p.Arg222His) single nucleotide variant not provided [RCV000954248] Chr3:58884595 [GRCh38]
Chr3:58870321 [GRCh37]
Chr3:3p14.2		 benign
NM_001394063.1(CFAP20DC):c.780C>T (p.Ile260=) single nucleotide variant not provided [RCV000949699] Chr3:58870245 [GRCh38]
Chr3:58855971 [GRCh37]
Chr3:3p14.2		 benign
NM_001394063.1(CFAP20DC):c.1534G>A (p.Val512Met) single nucleotide variant not provided [RCV003433098] Chr3:58863617 [GRCh38]
Chr3:58849343 [GRCh37]
Chr3:3p14.2		 likely benign
NM_001394063.1(CFAP20DC):c.1135+4T>G single nucleotide variant not provided [RCV003437885] Chr3:58867813 [GRCh38]
Chr3:58853539 [GRCh37]
Chr3:3p14.2		 likely benign
NM_001394063.1(CFAP20DC):c.799C>T (p.Leu267Phe) single nucleotide variant not specified [RCV004428734] Chr3:58870226 [GRCh38]
Chr3:58855952 [GRCh37]
Chr3:3p14.2		 uncertain significance
NM_001394063.1(CFAP20DC):c.1384G>C (p.Glu462Gln) single nucleotide variant not specified [RCV004428732] Chr3:58863767 [GRCh38]
Chr3:58849493 [GRCh37]
Chr3:3p14.2		 uncertain significance
NM_001394063.1(CFAP20DC):c.407G>T (p.Cys136Phe) single nucleotide variant not specified [RCV004428733] Chr3:58913851 [GRCh38]
Chr3:58899577 [GRCh37]
Chr3:3p14.2		 uncertain significance
NM_001394063.1(CFAP20DC):c.866T>C (p.Val289Ala) single nucleotide variant not specified [RCV004428735] Chr3:58869477 [GRCh38]
Chr3:58855203 [GRCh37]
Chr3:3p14.2		 uncertain significance
NM_001394063.1(CFAP20DC):c.1100A>G (p.Lys367Arg) single nucleotide variant not specified [RCV004428737] Chr3:58867852 [GRCh38]
Chr3:58853578 [GRCh37]
Chr3:3p14.2		 uncertain significance
NM_001394063.1(CFAP20DC):c.1037A>C (p.His346Pro) single nucleotide variant not specified [RCV004428736] Chr3:58867915 [GRCh38]
Chr3:58853641 [GRCh37]
Chr3:3p14.2		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:320
Count of miRNA genes:247
Interacting mature miRNAs:254
Transcripts:ENST00000463703, ENST00000482372, ENST00000492031, ENST00000493123
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 visual system adipose tissue appendage
High
Medium
Low 1 114 2 2 2 1 975 2 95 1 3 1
Below cutoff 491 165 341 138 148 81 620 128 1830 59 437 135 57 114 449

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000463703
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl358,824,471 - 58,971,880 (+)Ensembl
RefSeq Acc Id: ENST00000482372
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl358,824,471 - 59,019,093 (+)Ensembl
RefSeq Acc Id: ENST00000492031
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl358,824,441 - 58,972,057 (+)Ensembl
RefSeq Acc Id: ENST00000493123
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl358,824,437 - 59,017,637 (+)Ensembl
RefSeq Acc Id: ENST00000662588
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl358,824,465 - 59,018,933 (+)Ensembl
RefSeq Acc Id: ENST00000666146
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl358,824,465 - 58,971,882 (+)Ensembl
RefSeq Acc Id: NR_110820
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38358,824,471 - 59,019,093 (+)NCBI
CHM1_1358,760,355 - 58,955,002 (+)NCBI
T2T-CHM13v2.0358,864,882 - 59,059,508 (+)NCBI
Sequence:
Promoters
RGD ID:15095606
Promoter ID:EPDNEWNC_H449
Type:initiation region
Name:C3orf67-AS1_1
Description:C3orf67 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:41063]
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
GRCh38358,824,441 - 58,824,501EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC CFAP20DC-AS1 COSMIC
Ensembl Genes ENSG00000242428 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000482372 ENTREZGENE
GTEx ENSG00000242428 GTEx
HGNC ID HGNC:41063 ENTREZGENE
Human Proteome Map CFAP20DC-AS1 Human Proteome Map
NCBI Gene C3orf67-AS1 ENTREZGENE
RNAcentral URS00002BB309 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-02-11 CFAP20DC-AS1  CFAP20DC antisense RNA 1  C3orf67-AS1  C3orf67 antisense RNA 1  Symbol and/or name change 5135510 APPROVED