AC079385.2 (novel transcript, antisense to RFX4) - Rat Genome Database

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Gene: AC079385.2 (novel transcript, antisense to RFX4) Homo sapiens
Analyze
Symbol: AC079385.2
Name: novel transcript, antisense to RFX4
RGD ID: 16561405
Description:
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: LOC100505978; uncharacterized LOC100505978
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38.p14 Ensembl - Human Genome Assembly GRCh38 Ensembl
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3812106,680,758 - 106,684,700 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl12106,678,583 - 106,684,707 (-)EnsemblGRCh38hg38GRCh38
GRCh3712107,074,536 - 107,078,478 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map12q23.3NCBI
HuRef12104,134,944 - 104,138,883 (-)NCBIHuRef
CHM1_112107,040,348 - 107,044,290 (-)NCBICHM1_1
T2T-CHM13v2.012106,644,421 - 106,648,366 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:12477932  


Genomics

Variants

.
Variants in AC079385.2
2 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
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 12q23.3-24.11(chr12:105644967-108994840)x1 copy number loss See cases [RCV000138537] Chr12:105644967..108994840 [GRCh38]
Chr12:106038745..109432645 [GRCh37]
Chr12:104562875..107917026 [NCBI36]
Chr12:12q23.3-24.11		 uncertain significance
GRCh38/hg38 12q21.33-24.11(chr12:91044318-109133210)x3 copy number gain See cases [RCV000142447] Chr12:91044318..109133210 [GRCh38]
Chr12:91438095..109571015 [GRCh37]
Chr12:89962226..108055398 [NCBI36]
Chr12:12q21.33-24.11		 pathogenic
GRCh38/hg38 12q23.1-23.3(chr12:100670616-108583607)x1 copy number loss See cases [RCV000051320] Chr12:100670616..108583607 [GRCh38]
Chr12:101064394..108977383 [GRCh37]
Chr12:99588525..107501512 [NCBI36]
Chr12:12q23.1-23.3		 pathogenic
GRCh38/hg38 12q23.3-24.13(chr12:105234677-112194686)x1 copy number loss See cases [RCV000050807] Chr12:105234677..112194686 [GRCh38]
Chr12:105628455..112632490 [GRCh37]
Chr12:104152585..111116873 [NCBI36]
Chr12:12q23.3-24.13		 pathogenic
NM_213594.3(RFX4):c.364C>T (p.Arg122Ter) single nucleotide variant not provided [RCV001752514] Chr12:106682041 [GRCh38]
Chr12:107075819 [GRCh37]
Chr12:12q23.3		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:180
Count of miRNA genes:167
Interacting mature miRNAs:177
Transcripts:ENST00000547531
Prediction methods:Miranda, Rnahybrid, Targetscan
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 347
Low 4 1 263 6 84 6 79 16 682 28 81 185 1 4
Below cutoff 588 624 778 116 531 93 937 412 2449 217 439 734 25 326 549 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000547531
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl12106,680,757 - 106,684,707 (-)Ensembl
RefSeq Acc Id: ENST00000655603
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl12106,678,583 - 106,683,494 (-)Ensembl
RefSeq Acc Id: ENST00000656627
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl12106,680,758 - 106,684,707 (-)Ensembl
RefSeq Acc Id: NR_038912
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh3812106,680,758 - 106,684,700 (-)NCBI
T2T-CHM13v2.012106,644,421 - 106,648,366 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC AC079385.2 COSMIC
Ensembl Genes ENSG00000257711 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000547531 ENTREZGENE
GTEx ENSG00000257711 GTEx
Human Proteome Map AC079385.2 Human Proteome Map
NCBI Gene LOC100505978 ENTREZGENE
RNAcentral URS0000759FD4 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-06-25 AC079385.2  novel transcript, antisense to RFX4  LOC100505978  uncharacterized LOC100505978  Symbol and/or name change 19259462 PROVISIONAL
2020-06-18 LOC100505978  uncharacterized LOC100505978  AC079385.2  novel transcript, antisense to RFX4  Symbol and/or name change 5135510 APPROVED