AC087392.1 (novel transcript, antisense to NXN) - Rat Genome Database

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Gene: AC087392.1 (novel transcript, antisense to NXN) Homo sapiens
Analyze
Symbol: AC087392.1
Name: novel transcript, antisense to NXN
RGD ID: 16563496
Description: ASSOCIATED WITH Autosomal Recessive Robinow Syndrome 2
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: LOC101927727; uncharacterized LOC101927727
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38.p14 Ensembl - Human Genome Assembly GRCh38 Ensembl
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3817909,632 - 911,212 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl17909,632 - 911,212 (+)EnsemblGRCh38hg38GRCh38
GRCh3717812,872 - 814,452 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map17p13.3NCBI
HuRef17721,385 - 722,983 (+)NCBIHuRef
CHM1_117820,648 - 822,246 (+)NCBICHM1_1
T2T-CHM13v2.017795,275 - 796,855 (+)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 17p13.3(chr17:193307-1376276)x1 copy number loss See cases [RCV000053385] Chr17:193307..1376276 [GRCh38]
Chr17:45835..1279570 [GRCh37]
Chr17:43098..1226320 [NCBI36]
Chr17:17p13.3		 pathogenic
GRCh38/hg38 17p13.3(chr17:855404-1345517)x1 copy number loss See cases [RCV000053402] Chr17:855404..1345517 [GRCh38]
Chr17:758644..1248811 [GRCh37]
Chr17:705394..1195561 [NCBI36]
Chr17:17p13.3		 pathogenic
GRCh38/hg38 17p13.3(chr17:234496-2385512)x3 copy number gain See cases [RCV000052429] Chr17:234496..2385512 [GRCh38]
Chr17:396627..2288806 [GRCh37]
Chr17:84287..2235556 [NCBI36]
Chr17:17p13.3		 pathogenic
GRCh38/hg38 17p13.3(chr17:445331-2385512)x3 copy number gain See cases [RCV000052434] Chr17:445331..2385512 [GRCh38]
Chr17:396627..2288806 [GRCh37]
Chr17:295350..2235556 [NCBI36]
Chr17:17p13.3		 pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:237248-4735533)x1 copy number loss See cases [RCV000141559] Chr17:237248..4735533 [GRCh38]
Chr17:396627..4638828 [GRCh37]
Chr17:87039..4585577 [NCBI36]
Chr17:17p13.3-13.2		 pathogenic
GRCh38/hg38 17p13.3(chr17:198748-2685361)x1 copy number loss See cases [RCV000134971] Chr17:198748..2685361 [GRCh38]
Chr17:50690..2588655 [GRCh37]
Chr17:48539..2535405 [NCBI36]
Chr17:17p13.3		 pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:198748-4265640)x1 copy number loss See cases [RCV000142440] Chr17:198748..4265640 [GRCh38]
Chr17:50690..4168935 [GRCh37]
Chr17:48539..4115684 [NCBI36]
Chr17:17p13.3-13.2		 pathogenic
GRCh38/hg38 17p13.3(chr17:198748-1920952)x1 copy number loss See cases [RCV000133787] Chr17:198748..1920952 [GRCh38]
Chr17:50690..1824246 [GRCh37]
Chr17:48539..1770996 [NCBI36]
Chr17:17p13.3		 pathogenic
GRCh38/hg38 17p13.3(chr17:523549-1311896)x1 copy number loss See cases [RCV000137793] Chr17:523549..1311896 [GRCh38]
Chr17:426789..1215190 [GRCh37]
Chr17:373539..1161940 [NCBI36]
Chr17:17p13.3		 likely benign
GRCh38/hg38 17p13.3-13.2(chr17:150732-5935377)x1 copy number loss See cases [RCV000141658] Chr17:150732..5935377 [GRCh38]
Chr17:525..5838697 [GRCh37]
Chr17:525..5779421 [NCBI36]
Chr17:17p13.3-13.2		 pathogenic
GRCh38/hg38 17p13.3-12(chr17:162016-12343901)x3 copy number gain See cases [RCV000138531] Chr17:162016..12343901 [GRCh38]
Chr17:45835..12247218 [GRCh37]
Chr17:11807..12187943 [NCBI36]
Chr17:17p13.3-12		 pathogenic
NM_022463.5(NXN):c.-6172_361-75725del deletion Robinow syndrome, autosomal recessive 2 [RCV000791462] Chr17:901803..985850 [GRCh38]
Chr17:805043..889090 [GRCh37]
Chr17:17p13.3		 pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:226472-3655099)x1 copy number loss See cases [RCV000135857] Chr17:226472..3655099 [GRCh38]
Chr17:396627..3558393 [GRCh37]
Chr17:76263..3505142 [NCBI36]
Chr17:17p13.3-13.2		 pathogenic
GRCh38/hg38 17p13.3(chr17:847955-1589181)x3 copy number gain See cases [RCV000051045] Chr17:847955..1589181 [GRCh38]
Chr17:751195..1492475 [GRCh37]
Chr17:697945..1439225 [NCBI36]
Chr17:17p13.3		 pathogenic
GRCh38/hg38 17p13.3(chr17:759449-999134)x3 copy number gain See cases [RCV000136986] Chr17:759449..999134 [GRCh38]
Chr17:662689..902374 [GRCh37]
Chr17:609439..849124 [NCBI36]
Chr17:17p13.3		 uncertain significance
GRCh38/hg38 17p13.3-13.1(chr17:162088-6959050)x1 copy number loss See cases [RCV000134135] Chr17:162088..6959050 [GRCh38]
Chr17:45835..6862369 [GRCh37]
Chr17:11879..6803093 [NCBI36]
Chr17:17p13.3-13.1		 pathogenic
GRCh38/hg38 17p13.3-12(chr17:150732-14764202)x3 copy number gain See cases [RCV000142236] Chr17:150732..14764202 [GRCh38]
Chr17:525..14667519 [GRCh37]
Chr17:525..14608244 [NCBI36]
Chr17:17p13.3-12		 pathogenic
GRCh38/hg38 17p13.3-13.2(chr17:193307-5652222)x1 copy number loss See cases [RCV000053384] Chr17:193307..5652222 [GRCh38]
Chr17:45835..5555542 [GRCh37]
Chr17:43098..5496266 [NCBI36]
Chr17:17p13.3-13.2		 pathogenic
GRCh38/hg38 17p13.3(chr17:644280-2193615)x3 copy number gain See cases [RCV000051125] Chr17:644280..2193615 [GRCh38]
Chr17:547520..2096909 [GRCh37]
Chr17:494270..2043659 [NCBI36]
Chr17:17p13.3		 pathogenic
GRCh38/hg38 17p13.3(chr17:436763-2527511)x3 copy number gain See cases [RCV000052432] Chr17:436763..2527511 [GRCh38]
Chr17:396627..2430805 [GRCh37]
Chr17:286785..2377555 [NCBI36]
Chr17:17p13.3		 pathogenic
GRCh38/hg38 17p13.3(chr17:226272-1065849)x1 copy number loss See cases [RCV000052025] Chr17:226272..1065849 [GRCh38]
Chr17:396627..969089 [GRCh37]
Chr17:76063..915839 [NCBI36]
Chr17:17p13.3		 uncertain significance
GRCh38/hg38 17p13.3-13.1(chr17:162016-7697012)x1 copy number loss See cases [RCV000138214] Chr17:162016..7697012 [GRCh38]
Chr17:45835..7600330 [GRCh37]
Chr17:11807..7541055 [NCBI36]
Chr17:17p13.3-13.1		 pathogenic
GRCh38/hg38 17p13.3(chr17:162016-2099130)x1 copy number loss See cases [RCV000138246] Chr17:162016..2099130 [GRCh38]
Chr17:45835..2002424 [GRCh37]
Chr17:11807..1949174 [NCBI36]
Chr17:17p13.3		 likely pathogenic
GRCh38/hg38 17p13.3(chr17:150732-3242868)x1 copy number loss See cases [RCV000142323] Chr17:150732..3242868 [GRCh38]
Chr17:525..3146162 [GRCh37]
Chr17:525..3092912 [NCBI36]
Chr17:17p13.3		 pathogenic
GRCh38/hg38 17p13.3(chr17:847955-984405)x3 copy number gain See cases [RCV000140223] Chr17:847955..984405 [GRCh38]
Chr17:751195..887645 [GRCh37]
Chr17:697945..834395 [NCBI36]
Chr17:17p13.3		 benign
GRCh38/hg38 17p13.3(chr17:186959-969740)x1 copy number loss See cases [RCV000142477] Chr17:186959..969740 [GRCh38]
Chr17:45835..872980 [GRCh37]
Chr17:36750..819730 [NCBI36]
Chr17:17p13.3		 uncertain significance
GRCh38/hg38 17p13.3(chr17:847955-1641601)x3 copy number gain See cases [RCV000135574] Chr17:847955..1641601 [GRCh38]
Chr17:751195..1544895 [GRCh37]
Chr17:697945..1491645 [NCBI36]
Chr17:17p13.3		 pathogenic
GRCh38/hg38 17p13.3(chr17:198748-3102332)x1 copy number loss See cases [RCV000050936] Chr17:198748..3102332 [GRCh38]
Chr17:50690..3005626 [GRCh37]
Chr17:48539..2952376 [NCBI36]
Chr17:17p13.3		 pathogenic
GRCh38/hg38 17p13.3(chr17:198748-2261786)x1 copy number loss See cases [RCV000051148] Chr17:198748..2261786 [GRCh38]
Chr17:50690..2165080 [GRCh37]
Chr17:48539..2111830 [NCBI36]
Chr17:17p13.3		 pathogenic
GRCh38/hg38 17p13.3-13.1(chr17:198748-7491129)x3 copy number gain See cases [RCV000134970] Chr17:198748..7491129 [GRCh38]
Chr17:50690..7394448 [GRCh37]
Chr17:48539..7335172 [NCBI36]
Chr17:17p13.3-13.1		 pathogenic
GRCh38/hg38 17p13.3(chr17:162016-1904358)x1 copy number loss See cases [RCV000137940] Chr17:162016..1904358 [GRCh38]
Chr17:45835..1807652 [GRCh37]
Chr17:11807..1754402 [NCBI36]
Chr17:17p13.3		 likely pathogenic
GRCh38/hg38 17p13.3(chr17:162016-1682817)x3 copy number gain See cases [RCV000138202] Chr17:162016..1682817 [GRCh38]
Chr17:45835..1586111 [GRCh37]
Chr17:11807..1532861 [NCBI36]
Chr17:17p13.3		 likely pathogenic
GRCh38/hg38 17p13.3-12(chr17:165730-11404096)x3 copy number gain Chromosome 17p13.3 duplication syndrome [RCV003327726] Chr17:165730..11404096 [GRCh38]
Chr17:17p13.3-12		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:442
Count of miRNA genes:382
Interacting mature miRNAs:400
Transcripts:ENST00000358446, ENST00000576252
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 1 20 18 10 18 21 6 2 1 11 12 4 13
Low 299 230 484 436 129 316 2308 220 172 82 924 424 122 717 1057 1
Below cutoff 1608 1595 910 128 664 90 1499 1440 2262 201 395 889 44 396 1340 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000576252
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl17909,632 - 911,212 (+)Ensembl
RefSeq Acc Id: NR_135633
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh3817909,632 - 911,212 (+)NCBI
T2T-CHM13v2.017795,275 - 796,855 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC AC087392.1 COSMIC
Ensembl Genes ENSG00000262003 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000576252 ENTREZGENE
GTEx ENSG00000262003 GTEx
Human Proteome Map AC087392.1 Human Proteome Map
NCBI Gene LOC101927727 ENTREZGENE
RNAcentral URS0000A77218 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-06-25 AC087392.1  novel transcript, antisense to NXN  LOC101927727  uncharacterized LOC101927727  Symbol and/or name change 19259462 PROVISIONAL
2020-06-18 LOC101927727  uncharacterized LOC101927727  AC087392.1  novel transcript, antisense to NXN  Symbol and/or name change 5135510 APPROVED