TMEM108-AS1 (TMEM108 antisense RNA 1) - Rat Genome Database

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Gene: TMEM108-AS1 (TMEM108 antisense RNA 1) Homo sapiens
Analyze
Symbol: TMEM108-AS1
Name: TMEM108 antisense RNA 1
RGD ID: 8552051
HGNC Page HGNC:50307
Description:
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
GRCh383133,246,448 - 133,257,121 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3133,245,603 - 133,257,207 (-)EnsemblGRCh38hg38GRCh38
GRCh373132,965,292 - 132,975,965 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map3q22.1NCBI
HuRef3130,345,674 - 130,356,415 (-)NCBIHuRef
CHM1_13132,928,671 - 132,939,412 (-)NCBICHM1_1
T2T-CHM13v2.03135,991,203 - 136,001,877 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:12477932  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3q13.11-29(chr3:103426882-198110178)x3 copy number gain See cases [RCV000134948] Chr3:103426882..198110178 [GRCh38]
Chr3:103145726..197837049 [GRCh37]
Chr3:104628416..199321446 [NCBI36]
Chr3:3q13.11-29		 pathogenic
GRCh38/hg38 3q22.1-24(chr3:129817243-143381624)x1 copy number loss See cases [RCV000136558] Chr3:129817243..143381624 [GRCh38]
Chr3:129536086..143100466 [GRCh37]
Chr3:131018776..144583156 [NCBI36]
Chr3:3q22.1-24		 pathogenic
GRCh38/hg38 3q22.1-23(chr3:130401265-139005019)x1 copy number loss See cases [RCV000139240] Chr3:130401265..139005019 [GRCh38]
Chr3:130120109..138723861 [GRCh37]
Chr3:131602799..140206551 [NCBI36]
Chr3:3q22.1-23		 pathogenic
GRCh38/hg38 3q22.1-23(chr3:129817243-141425155)x1 copy number loss See cases [RCV000140995] Chr3:129817243..141425155 [GRCh38]
Chr3:129536086..141143997 [GRCh37]
Chr3:131018776..142626687 [NCBI36]
Chr3:3q22.1-23		 pathogenic
GRCh38/hg38 3q21.3-23(chr3:126106779-140918089)x3 copy number gain See cases [RCV000142010] Chr3:126106779..140918089 [GRCh38]
Chr3:125825622..140636931 [GRCh37]
Chr3:127308312..142119621 [NCBI36]
Chr3:3q21.3-23		 uncertain significance
GRCh38/hg38 3q11.1-24(chr3:93800620-145695381)x3 copy number gain See cases [RCV000142340] Chr3:93800620..145695381 [GRCh38]
Chr3:93519464..145413168 [GRCh37]
Chr3:95002154..146895858 [NCBI36]
Chr3:3q11.1-24		 pathogenic
GRCh38/hg38 3q21.3-22.1(chr3:127607945-133566661)x1 copy number loss See cases [RCV000142787] Chr3:127607945..133566661 [GRCh38]
Chr3:127326788..133285505 [GRCh37]
Chr3:128809478..134768195 [NCBI36]
Chr3:3q21.3-22.1		 likely pathogenic
GRCh38/hg38 3q22.1-24(chr3:132716978-144784743)x1 copy number loss See cases [RCV000143634] Chr3:132716978..144784743 [GRCh38]
Chr3:132435822..144503585 [GRCh37]
Chr3:133918512..145986275 [NCBI36]
Chr3:3q22.1-24		 pathogenic
GRCh38/hg38 3q22.1(chr3:132662034-133263499)x3 copy number gain See cases [RCV000051533] Chr3:132662034..133263499 [GRCh38]
Chr3:132380878..132982343 [GRCh37]
Chr3:133863568..134465033 [NCBI36]
Chr3:3q22.1		 uncertain significance
GRCh38/hg38 3q22.1-23(chr3:132690641-141064444)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051570]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051570]|See cases [RCV000051570] Chr3:132690641..141064444 [GRCh38]
Chr3:132409485..140783286 [GRCh37]
Chr3:133892175..142265976 [NCBI36]
Chr3:3q22.1-23		 pathogenic
GRCh38/hg38 3q22.1-22.3(chr3:132972567-136894498)x1 copy number loss See cases [RCV000051571] Chr3:132972567..136894498 [GRCh38]
Chr3:132691411..136613340 [GRCh37]
Chr3:134174101..138096030 [NCBI36]
Chr3:3q22.1-22.3		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:228
Count of miRNA genes:221
Interacting mature miRNAs:225
Transcripts:ENST00000504993, ENST00000505721
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 2 2
Low 2 2 7 2 4 2 10 9 151 1 12 19 2 1
Below cutoff 598 372 541 61 203 32 714 531 1619 28 394 666 30 146 412

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000504993
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3133,246,106 - 133,257,048 (-)Ensembl
RefSeq Acc Id: ENST00000505721
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3133,245,603 - 133,257,207 (-)Ensembl
RefSeq Acc Id: NR_110812
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh383133,246,448 - 133,257,121 (-)NCBI
CHM1_13132,928,671 - 132,939,345 (-)NCBI
T2T-CHM13v2.03135,991,203 - 136,001,877 (-)NCBI
Sequence:
Promoters
RGD ID:15095724
Promoter ID:EPDNEWNC_H504
Type:initiation region
Name:TMEM108-AS1_1
Description:TMEM108 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:50307]
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
GRCh383133,257,148 - 133,257,208EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC TMEM108-AS1 COSMIC
Ensembl Genes ENSG00000251011 Ensembl
GTEx ENSG00000251011 GTEx
HGNC ID HGNC:50307 ENTREZGENE
Human Proteome Map TMEM108-AS1 Human Proteome Map
NCBI Gene TMEM108-AS1 ENTREZGENE
RNAcentral URS000075AC5F RNACentral