HOXB-AS4 (HOXB cluster antisense RNA 4) - Rat Genome Database

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Gene: HOXB-AS4 (HOXB cluster antisense RNA 4) Homo sapiens
Analyze
Symbol: HOXB-AS4
Name: HOXB cluster antisense RNA 4
RGD ID: 6480825
HGNC Page HGNC:40285
Description: INTERACTS WITH dimethylselenide; hydroxyl
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
GRCh381748,628,698 - 48,634,932 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1748,628,675 - 48,634,932 (+)EnsemblGRCh38hg38GRCh38
GRCh371746,706,060 - 46,712,294 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map17q21.32NCBI
T2T-CHM13v2.01749,492,294 - 49,498,528 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:16344560  


Genomics

Variants

.
Variants in HOXB-AS4
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 17q21.32-21.33(chr17:47986886-49329397)x1 copy number loss See cases [RCV000142900] Chr17:47986886..49329397 [GRCh38]
Chr17:46064252..47406759 [GRCh37]
Chr17:43419251..44761758 [NCBI36]
Chr17:17q21.32-21.33		 pathogenic
GRCh38/hg38 17q21.32-21.33(chr17:48520885-49511208)x1 copy number loss See cases [RCV000053431] Chr17:48520885..49511208 [GRCh38]
Chr17:46598247..47588570 [GRCh37]
Chr17:43953246..44943569 [NCBI36]
Chr17:17q21.32-21.33		 pathogenic
GRCh38/hg38 17q23.1-25.1(chr17:36449220-75053130)x3 copy number gain See cases [RCV000137437] Chr17:36449220..75053130 [GRCh38]
Chr17:57595736..73049225 [GRCh37]
Chr17:54950518..70560820 [NCBI36]
Chr17:17q23.1-25.1		 pathogenic
GRCh38/hg38 17q21.33-24.2(chr17:36449220-68170214)x3 copy number gain See cases [RCV000050957] Chr17:36449220..68170214 [GRCh38]
Chr17:48563237..65936105 [GRCh37]
Chr17:45918236..63677950 [NCBI36]
Chr17:17q21.33-24.2		 pathogenic
GRCh38/hg38 17q21.32-21.33(chr17:48450628-49552921)x3 copy number gain See cases [RCV000143451] Chr17:48450628..49552921 [GRCh38]
Chr17:46527990..47630283 [GRCh37]
Chr17:43882989..44985282 [NCBI36]
Chr17:17q21.32-21.33		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:545
Count of miRNA genes:424
Interacting mature miRNAs:455
Transcripts:ENST00000462131, ENST00000480386
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 123 2 2 1 2 1 2 3 17 17 15
Low 513 2 13 8 216 8 14 5 10 192 396 75 6 1 2
Below cutoff 395 362 269 59 370 43 513 213 315 151 496 254 19 184 331 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000462131
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1748,629,549 - 48,634,661 (+)Ensembl
RefSeq Acc Id: ENST00000480386
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1748,628,675 - 48,634,932 (+)Ensembl
RefSeq Acc Id: NR_046611
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381748,628,698 - 48,634,932 (+)NCBI
T2T-CHM13v2.01749,492,294 - 49,498,528 (+)NCBI
Sequence:
RefSeq Acc Id: NR_170224
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381748,629,521 - 48,634,932 (+)NCBI
T2T-CHM13v2.01749,493,117 - 49,498,528 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC HOXB-AS4 COSMIC
Ensembl Genes ENSG00000242207 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000480386 ENTREZGENE
GTEx ENSG00000242207 GTEx
HGNC ID HGNC:40285 ENTREZGENE
Human Proteome Map HOXB-AS4 Human Proteome Map
NCBI Gene HOXB-AS4 ENTREZGENE
RNAcentral URS0002123147 RNACentral
  URS00021231AE RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-08-21 HOXB-AS4  HOXB cluster antisense RNA 4  HOXB-AS4  HOXB cluster antisense RNA 4 (non-protein coding)  Symbol and/or name change 5135510 APPROVED