AC099489.3 (novel transcript, antisense to a novel protein gene) - Rat Genome Database

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Gene: AC099489.3 (novel transcript, antisense to a novel protein gene) Homo sapiens
Analyze
Symbol: AC099489.3
Name: novel transcript, antisense to a novel protein gene
RGD ID: 16563660
Description: ASSOCIATED WITH Schizophrenia; schizophrenia
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: LOC101927131; uncharacterized LOC101927131
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38.p14 Ensembl - Human Genome Assembly GRCh38 Ensembl
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381611,465,260 - 11,473,175 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1611,465,260 - 11,473,174 (+)EnsemblGRCh38hg38GRCh38
GRCh371611,559,116 - 11,567,031 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map16p13.13NCBI
HuRef1611,477,402 - 11,485,662 (+)NCBIHuRef
CHM1_11611,559,069 - 11,566,981 (+)NCBICHM1_1
T2T-CHM13v2.01611,501,523 - 11,509,435 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
schizophrenia  (IAGP)

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
Schizophrenia  (IAGP)
References
Additional References at PubMed
PMID:12477932  


Genomics

Variants

.
Variants in AC099489.3
2 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
Single allele duplication Schizophrenia [RCV000754168] Chr16:11369400..13577493 [GRCh38]
Chr16:16p13.13-13.12		 likely pathogenic
GRCh38/hg38 16p13.3-11.2(chr16:4644892-29170820)x3 copy number gain See cases [RCV000133809] Chr16:4644892..29170820 [GRCh38]
Chr16:4694893..29182141 [GRCh37]
Chr16:4634894..29089642 [NCBI36]
Chr16:16p13.3-11.2		 pathogenic
GRCh38/hg38 16p13.3-13.11(chr16:666662-15743104)x3 copy number gain See cases [RCV000143710] Chr16:666662..15743104 [GRCh38]
Chr16:716662..15836961 [GRCh37]
Chr16:656663..15744462 [NCBI36]
Chr16:16p13.3-13.11		 pathogenic
GRCh38/hg38 16p13.3-13.12(chr16:43732-13326806)x3 copy number gain See cases [RCV000139166] Chr16:43732..13326806 [GRCh38]
Chr16:93732..13420663 [GRCh37]
Chr16:33732..13328164 [NCBI36]
Chr16:16p13.3-13.12		 pathogenic
GRCh38/hg38 16p13.3-13.13(chr16:46766-11525516)x3 copy number gain See cases [RCV000133780] Chr16:46766..11525516 [GRCh38]
Chr16:96766..11619372 [GRCh37]
Chr16:36766..11526873 [NCBI36]
Chr16:16p13.3-13.13		 pathogenic
NM_001370704.1(LOC400499):c.3177C>T (p.His1059=) single nucleotide variant not provided [RCV003411273] Chr16:11469226 [GRCh38]
Chr16:11563082 [GRCh37]
Chr16:16p13.13		 likely benign
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:29
Count of miRNA genes:28
Interacting mature miRNAs:29
Transcripts:ENST00000572950
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 adipose tissue appendage entire extraembryonic component
High
Medium 1
Low 6 182 8 1 249 1 14 8 11 11 358 27 6 1 1
Below cutoff 882 1675 641 218 1184 154 2335 816 1275 167 558 1057 75 645 1442 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000572950
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1611,465,260 - 11,473,174 (+)Ensembl
RefSeq Acc Id: NR_110907
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381611,465,260 - 11,473,175 (+)NCBI
T2T-CHM13v2.01611,501,523 - 11,509,435 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC AC099489.3 COSMIC
Ensembl Genes ENSG00000262999 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000572950 ENTREZGENE
GTEx ENSG00000262999 GTEx
Human Proteome Map AC099489.3 Human Proteome Map
NCBI Gene LOC101927131 ENTREZGENE
RNAcentral URS000075E693 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-06-25 AC099489.3  novel transcript, antisense to a novel protein gene  LOC101927131  uncharacterized LOC101927131  Symbol and/or name change 19259462 PROVISIONAL
2020-06-18 LOC101927131  uncharacterized LOC101927131  AC099489.3  novel transcript, antisense to a novel protein gene  Symbol and/or name change 5135510 APPROVED