HDAC11-AS1 (HDAC11 antisense RNA 1) - Rat Genome Database

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Gene: HDAC11-AS1 (HDAC11 antisense RNA 1) Homo sapiens
Analyze
Symbol: HDAC11-AS1
Name: HDAC11 antisense RNA 1
RGD ID: 6481308
HGNC Page HGNC:40868
Description: ASSOCIATED WITH 3p deletion syndrome
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
GRCh38313,476,987 - 13,480,053 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl313,476,982 - 13,480,053 (-)EnsemblGRCh38hg38GRCh38
GRCh37313,518,487 - 13,521,553 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map3p25.1NCBI
HuRef313,451,753 - 13,454,816 (-)NCBIHuRef
CHM1_1313,468,520 - 13,471,586 (-)NCBICHM1_1
T2T-CHM13v2.0313,477,446 - 13,480,512 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3p25.1(chr3:13325295-13882924)x4 copy number gain See cases [RCV000137624] Chr3:13325295..13882924 [GRCh38]
Chr3:13366795..13924421 [GRCh37]
Chr3:13341795..13899422 [NCBI36]
Chr3:3p25.1		 uncertain significance
GRCh38/hg38 3p26.3-24.1(chr3:32241-30064208)x3 copy number gain See cases [RCV000138004] Chr3:32241..30064208 [GRCh38]
Chr3:73914..30105699 [GRCh37]
Chr3:48914..30080703 [NCBI36]
Chr3:3p26.3-24.1		 pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:32241-20334387)x3 copy number gain See cases [RCV000137941] Chr3:32241..20334387 [GRCh38]
Chr3:73914..20375879 [GRCh37]
Chr3:48914..20350883 [NCBI36]
Chr3:3p26.3-24.3		 pathogenic
GRCh38/hg38 3p26.3-25.1(chr3:32241-13613818)x3 copy number gain See cases [RCV000138946] Chr3:32241..13613818 [GRCh38]
Chr3:73914..13655318 [GRCh37]
Chr3:48914..13630319 [NCBI36]
Chr3:3p26.3-25.1		 pathogenic
GRCh38/hg38 3p26.3-22.1(chr3:53308-41381521)x3 copy number gain See cases [RCV000141810] Chr3:53308..41381521 [GRCh38]
Chr3:94991..41423012 [GRCh37]
Chr3:69991..41398016 [NCBI36]
Chr3:3p26.3-22.1		 pathogenic
GRCh38/hg38 3p26.1-25.1(chr3:7356110-14360442)x3 copy number gain See cases [RCV000143766] Chr3:7356110..14360442 [GRCh38]
Chr3:7397797..14401942 [GRCh37]
Chr3:7372797..14376946 [NCBI36]
Chr3:3p26.1-25.1		 pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:52066-20280127)x3 copy number gain See cases [RCV000051690] Chr3:52066..20280127 [GRCh38]
Chr3:93749..20321619 [GRCh37]
Chr3:68749..20296623 [NCBI36]
Chr3:3p26.3-24.3		 pathogenic
GRCh38/hg38 3p26.3-24.1(chr3:52266-29248782)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051718]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051718]|See cases [RCV000051718] Chr3:52266..29248782 [GRCh38]
Chr3:93949..29290273 [GRCh37]
Chr3:68949..29265277 [NCBI36]
Chr3:3p26.3-24.1		 pathogenic
GRCh38/hg38 3p25.3-22.2(chr3:11463328-38919543)x3 copy number gain See cases [RCV000051720] Chr3:11463328..38919543 [GRCh38]
Chr3:11504802..38961034 [GRCh37]
Chr3:11479802..38936038 [NCBI36]
Chr3:3p25.3-22.2		 pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:63843-19510600)x3 copy number gain See cases [RCV000051719] Chr3:63843..19510600 [GRCh38]
Chr3:105526..19552092 [GRCh37]
Chr3:80526..19527096 [NCBI36]
Chr3:3p26.3-24.3		 pathogenic
Single allele deletion 3p- syndrome [RCV002280352] Chr3:13371737..20095506 [GRCh38]
Chr3:3p25.1-24.3		 pathogenic
GRCh38/hg38 3p26.3-22.2(chr3:52266-37148076)x3 copy number gain See cases [RCV000051097] Chr3:52266..37148076 [GRCh38]
Chr3:93949..37189567 [GRCh37]
Chr3:68949..37164571 [NCBI36]
Chr3:3p26.3-22.2		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:213
Count of miRNA genes:201
Interacting mature miRNAs:213
Transcripts:ENST00000424112
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 entire extraembryonic component
High
Medium 23
Low 62 11 42 17 83 18 42 16 41 66 455 97 1 4 6 2
Below cutoff 212 125 243 91 237 90 365 154 356 163 175 280 9 1 65 156 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000424112
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl313,476,982 - 13,480,053 (-)Ensembl
RefSeq Acc Id: NR_046690
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38313,476,987 - 13,480,053 (-)NCBI
CHM1_1313,468,520 - 13,471,586 (-)NCBI
T2T-CHM13v2.0313,477,446 - 13,480,512 (-)NCBI
Sequence:
Promoters
RGD ID:15095572
Promoter ID:EPDNEWNC_H408
Type:initiation region
Name:HDAC11-AS1_1
Description:HDAC11 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:40868]
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
GRCh38313,480,042 - 13,480,102EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC HDAC11-AS1 COSMIC
Ensembl Genes ENSG00000244502 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000424112 ENTREZGENE
GTEx ENSG00000244502 GTEx
HGNC ID HGNC:40868 ENTREZGENE
Human Proteome Map HDAC11-AS1 Human Proteome Map
NCBI Gene HDAC11-AS1 ENTREZGENE
RNAcentral URS000075E905 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-08-21 HDAC11-AS1  HDAC11 antisense RNA 1  HDAC11-AS1  HDAC11 antisense RNA 1 (non-protein coding)  Symbol and/or name change 5135510 APPROVED