SLC14A2-AS1 (SLC14A2 antisense RNA 1) - Rat Genome Database

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Gene: SLC14A2-AS1 (SLC14A2 antisense RNA 1) Homo sapiens
Analyze
Symbol: SLC14A2-AS1
Name: SLC14A2 antisense RNA 1
RGD ID: 8695750
HGNC Page HGNC:51125
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
GRCh381845,364,887 - 45,507,063 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1845,423,764 - 45,483,218 (-)EnsemblGRCh38hg38GRCh38
GRCh371843,003,758 - 43,084,003 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map18q12.3NCBI
HuRef1839,861,346 - 39,941,599 (-)NCBIHuRef
CHM1_11842,930,786 - 43,011,580 (-)NCBICHM1_1
T2T-CHM13v2.01845,629,406 - 45,698,268 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations

Genomics

Variants

.
Variants in SLC14A2-AS1
12 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_001242692.1(SLC14A2):c.-124-3754T>C single nucleotide variant Lung cancer [RCV000100846] Chr18:45479479 [GRCh38]
Chr18:43059444 [GRCh37]
Chr18:18q12.3		 uncertain significance
GRCh38/hg38 18p11.32-q23(chr18:149089-80234391)x3 copy number gain See cases [RCV000134110] Chr18:149089..80234391 [GRCh38]
Chr18:149089..77992274 [GRCh37]
Chr18:139089..76093265 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18q12.2-22.1(chr18:38794728-65632804)x3 copy number gain See cases [RCV000136910] Chr18:38794728..65632804 [GRCh38]
Chr18:36374692..63300040 [GRCh37]
Chr18:34628690..61451020 [NCBI36]
Chr18:18q12.2-22.1		 pathogenic
GRCh38/hg38 18q12.1-23(chr18:32123105-80252149)x3 copy number gain See cases [RCV000136890] Chr18:32123105..80252149 [GRCh38]
Chr18:29703068..78010032 [GRCh37]
Chr18:27957066..76111023 [NCBI36]
Chr18:18q12.1-23		 pathogenic
GRCh38/hg38 18q12.3(chr18:44401938-45869924)x1 copy number loss See cases [RCV000136681] Chr18:44401938..45869924 [GRCh38]
Chr18:41981903..43449889 [GRCh37]
Chr18:40235901..41703887 [NCBI36]
Chr18:18q12.3		 uncertain significance
GRCh38/hg38 18q12.3-21.1(chr18:42335174-46726460)x1 copy number loss See cases [RCV000136771] Chr18:42335174..46726460 [GRCh38]
Chr18:39915139..44306423 [GRCh37]
Chr18:38169137..42560421 [NCBI36]
Chr18:18q12.3-21.1		 pathogenic
GRCh38/hg38 18q12.3-23(chr18:42651392-80254946)x3 copy number gain See cases [RCV000138034] Chr18:42651392..80254946 [GRCh38]
Chr18:40231357..78012829 [GRCh37]
Chr18:38485355..76113817 [NCBI36]
Chr18:18q12.3-23		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:118760-80254946)x3 copy number gain See cases [RCV000138656] Chr18:118760..80254946 [GRCh38]
Chr18:118760..78012829 [GRCh37]
Chr18:108760..76113817 [NCBI36]
Chr18:18p11.32-q23		 pathogenic|conflicting data from submitters
GRCh38/hg38 18p11.32-q23(chr18:149089-80254936)x3 copy number gain See cases [RCV000139397] Chr18:149089..80254936 [GRCh38]
Chr18:149089..78012819 [GRCh37]
Chr18:139089..76113807 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18q12.3-21.1(chr18:43833480-46144138)x1 copy number loss See cases [RCV000141093] Chr18:43833480..46144138 [GRCh38]
Chr18:41413445..43724104 [GRCh37]
Chr18:39667443..41978102 [NCBI36]
Chr18:18q12.3-21.1		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:136227-80256240)x3 copy number gain See cases [RCV000142244] Chr18:136227..80256240 [GRCh38]
Chr18:136227..78014123 [GRCh37]
Chr18:126227..76115097 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18q12.3-23(chr18:40367455-80256240)x3 copy number gain See cases [RCV000142227] Chr18:40367455..80256240 [GRCh38]
Chr18:37947419..78014123 [GRCh37]
Chr18:36201417..76115097 [NCBI36]
Chr18:18q12.3-23		 pathogenic
GRCh38/hg38 18q11.1-22.3(chr18:20962119-74691446)x3 copy number gain See cases [RCV000143057] Chr18:20962119..74691446 [GRCh38]
Chr18:18542080..72403402 [GRCh37]
Chr18:16796078..70532390 [NCBI36]
Chr18:18q11.1-22.3		 pathogenic
GRCh38/hg38 18q12.3-21.1(chr18:41722823-49043887)x1 copy number loss See cases [RCV000142696] Chr18:41722823..49043887 [GRCh38]
Chr18:39302787..46570257 [GRCh37]
Chr18:37556785..44824255 [NCBI36]
Chr18:18q12.3-21.1		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:136226-80256240)x3 copy number gain See cases [RCV000143218] Chr18:136226..80256240 [GRCh38]
Chr18:136226..78014123 [GRCh37]
Chr18:126226..76115097 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:148963-80252149)x3 copy number gain See cases [RCV000148072] Chr18:148963..80252149 [GRCh38]
Chr18:148963..78010032 [GRCh37]
Chr18:138963..76111023 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18q12.1-22.1(chr18:29249202-65448117)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052563]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052563]|See cases [RCV000052563] Chr18:29249202..65448117 [GRCh38]
Chr18:26829167..63115353 [GRCh37]
Chr18:25083165..61266333 [NCBI36]
Chr18:18q12.1-22.1		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:53345-80209986)x3 copy number gain See cases [RCV000052501] Chr18:53345..80209986 [GRCh38]
Chr18:53345..77967869 [GRCh37]
Chr18:43345..76068860 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:148763-80252290)x3 copy number gain See cases [RCV000052507] Chr18:148763..80252290 [GRCh38]
Chr18:148763..78010173 [GRCh37]
Chr18:138763..76111164 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:148963-80244381)x3 copy number gain See cases [RCV000052514] Chr18:148963..80244381 [GRCh38]
Chr18:148963..78002264 [GRCh37]
Chr18:138963..76103255 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18q11.1-23(chr18:20960320-80234429)x3 copy number gain See cases [RCV000052543] Chr18:20960320..80234429 [GRCh38]
Chr18:18540281..77992312 [GRCh37]
Chr18:16794279..76093303 [NCBI36]
Chr18:18q11.1-23		 pathogenic
GRCh38/hg38 18q12.2-21.1(chr18:36859191-47164436)x1 copy number loss See cases [RCV000053831] Chr18:36859191..47164436 [GRCh38]
Chr18:34439154..44690807 [GRCh37]
Chr18:32693152..42944805 [NCBI36]
Chr18:18q12.2-21.1		 pathogenic
GRCh38/hg38 18q12.3-21.1(chr18:40718750-47042515)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053832]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053832]|See cases [RCV000053832] Chr18:40718750..47042515 [GRCh38]
Chr18:38298714..44568886 [GRCh37]
Chr18:36552712..42822884 [NCBI36]
Chr18:18q12.3-21.1		 pathogenic
GRCh38/hg38 18q12.3-21.1(chr18:40718750-48354407)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053833]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053833]|See cases [RCV000053833] Chr18:40718750..48354407 [GRCh38]
Chr18:38298714..45880778 [GRCh37]
Chr18:36552712..44134776 [NCBI36]
Chr18:18q12.3-21.1		 pathogenic
GRCh38/hg38 18p11.32-q23(chr18:148963-80252149)x3 copy number gain See cases [RCV000051048] Chr18:148963..80252149 [GRCh38]
Chr18:148963..78010032 [GRCh37]
Chr18:138963..76111023 [NCBI36]
Chr18:18p11.32-q23		 pathogenic
GRCh38/hg38 18q11.1-23(chr18:20989762-80209986)x3 copy number gain See cases [RCV000052549] Chr18:20989762..80209986 [GRCh38]
Chr18:18569723..77967869 [GRCh37]
Chr18:16823721..76068860 [NCBI36]
Chr18:18q11.1-23		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:475
Count of miRNA genes:336
Interacting mature miRNAs:346
Transcripts:ENST00000585759, ENST00000586330, ENST00000592286, ENST00000592899
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 213
Low 13 51 83 3 18 3 247 11 110 69 206 85 260 58
Below cutoff 1105 1669 939 141 486 76 2279 884 1713 216 572 972 67 883 1583 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NR_110899 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_002958204 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_002958205 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_002958206 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_007066350 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_007066351 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_007066352 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AA868102 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC021517 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC021810 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC091151 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK126075 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX109976 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CD357906 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068260 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HY036726 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KF456392 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  OA986905 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000585759
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1845,424,110 - 45,483,218 (-)Ensembl
RefSeq Acc Id: ENST00000586330
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1845,423,764 - 45,435,297 (-)Ensembl
RefSeq Acc Id: ENST00000592286
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1845,438,186 - 45,447,623 (-)Ensembl
RefSeq Acc Id: ENST00000592899
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1845,438,174 - 45,447,346 (-)Ensembl
RefSeq Acc Id: NR_110899
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01845,629,406 - 45,698,268 (-)NCBI
Sequence:
RefSeq Acc Id: XR_007066350
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381845,423,764 - 45,507,063 (-)NCBI
RefSeq Acc Id: XR_007066351
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381845,423,764 - 45,503,825 (-)NCBI
RefSeq Acc Id: XR_007066352
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381845,364,887 - 45,504,147 (-)NCBI
Promoters
RGD ID:15097164
Promoter ID:EPDNEWNC_H1984
Type:initiation region
Name:SLC14A2-AS1_2
Description:SLC14A2 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:51125]
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
GRCh381845,447,643 - 45,447,703EPDNEWNC
RGD ID:15097155
Promoter ID:EPDNEWNC_H1985
Type:initiation region
Name:SLC14A2-AS1_1
Description:SLC14A2 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:51125]
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
GRCh381845,483,260 - 45,483,320EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC SLC14A2-AS1 COSMIC
Ensembl Genes ENSG00000267097 Ensembl
GTEx ENSG00000267097 GTEx
HGNC ID HGNC:51125 ENTREZGENE
Human Proteome Map SLC14A2-AS1 Human Proteome Map
NCBI Gene SLC14A2-AS1 ENTREZGENE
RNAcentral URS0000A76725 RNACentral