NTRAS (non-coding transcript regulating alternative splicing) - Rat Genome Database

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Gene: NTRAS (non-coding transcript regulating alternative splicing) Homo sapiens
Analyze
Symbol: NTRAS
Name: non-coding transcript regulating alternative splicing
RGD ID: 11563479
HGNC Page HGNC:52478
Description: INTERACTS WITH aristolochic acid A
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: LINC01693; long intergenic non-protein coding RNA 1693
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381211,639,808 - 211,654,622 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1211,639,440 - 211,654,627 (+)EnsemblGRCh38hg38GRCh38
GRCh371211,813,150 - 211,827,964 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map1q32.3NCBI
CHM1_11213,085,539 - 213,100,368 (+)NCBICHM1_1
T2T-CHM13v2.01210,885,902 - 210,900,728 (+)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:30937967   PMID:35527520  


Genomics

Variants

.
Variants in NTRAS
3 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1q32.2-44(chr1:207346642-248930485)x3 copy number gain See cases [RCV000143727] Chr1:207346642..248930485 [GRCh38]
Chr1:207519987..249224684 [GRCh37]
Chr1:205586610..247191307 [NCBI36]
Chr1:1q32.2-44		 pathogenic
GRCh38/hg38 1q32.1-42.12(chr1:204764914-225408698)x3 copy number gain See cases [RCV000142054] Chr1:204764914..225408698 [GRCh38]
Chr1:204734042..225596400 [GRCh37]
Chr1:203000665..223663023 [NCBI36]
Chr1:1q32.1-42.12		 pathogenic
GRCh38/hg38 1q32.2-44(chr1:209646207-248931113)x3 copy number gain See cases [RCV000051861] Chr1:209646207..248931113 [GRCh38]
Chr1:209819552..249225312 [GRCh37]
Chr1:207886175..247191935 [NCBI36]
Chr1:1q32.2-44		 pathogenic
GRCh38/hg38 1q32.2-44(chr1:209963625-248918469)x3 copy number gain See cases [RCV000134979] Chr1:209963625..248918469 [GRCh38]
Chr1:210136970..249212668 [GRCh37]
Chr1:208203593..247179291 [NCBI36]
Chr1:1q32.2-44		 pathogenic
GRCh38/hg38 1q31.1-42.11(chr1:187143981-224299417)x3 copy number gain See cases [RCV000051857] Chr1:187143981..224299417 [GRCh38]
Chr1:187113113..224487119 [GRCh37]
Chr1:185379736..222553742 [NCBI36]
Chr1:1q31.1-42.11		 pathogenic
GRCh38/hg38 1q32.2-42.13(chr1:228006998-228061271)x2 copy number loss Orofacial cleft 2 [RCV002481175] Chr1:228006998..228061271 [GRCh38]
Chr1:1q32.2-42.13		 association
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:415
Count of miRNA genes:369
Interacting mature miRNAs:388
Transcripts:ENST00000412871, ENST00000430123
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
High
Medium 1 3 5 1
Low 6 4 13 6 3 7 74 7 296 71 57 37 1 71
Below cutoff 81 153 103 56 56 45 411 46 1560 106 313 133 14 73 332

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000412871
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1211,639,695 - 211,654,581 (+)Ensembl
RefSeq Acc Id: ENST00000430123
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1211,639,682 - 211,654,624 (+)Ensembl
RefSeq Acc Id: ENST00000653761
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1211,652,147 - 211,654,622 (+)Ensembl
RefSeq Acc Id: ENST00000653827
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1211,639,644 - 211,654,625 (+)Ensembl
RefSeq Acc Id: ENST00000654864
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1211,639,804 - 211,654,622 (+)Ensembl
RefSeq Acc Id: ENST00000660041
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1211,639,633 - 211,654,624 (+)Ensembl
RefSeq Acc Id: ENST00000661623
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1211,639,804 - 211,640,703 (+)Ensembl
RefSeq Acc Id: ENST00000661855
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1211,639,814 - 211,654,622 (+)Ensembl
RefSeq Acc Id: ENST00000664125
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1211,639,669 - 211,654,625 (+)Ensembl
RefSeq Acc Id: ENST00000666922
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1211,639,693 - 211,654,603 (+)Ensembl
RefSeq Acc Id: ENST00000667263
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1211,639,684 - 211,654,621 (+)Ensembl
RefSeq Acc Id: ENST00000667986
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1211,639,693 - 211,654,622 (+)Ensembl
RefSeq Acc Id: ENST00000670044
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1211,639,440 - 211,654,627 (+)Ensembl
RefSeq Acc Id: NR_131925
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381211,639,808 - 211,654,622 (+)NCBI
CHM1_11213,085,539 - 213,100,368 (+)NCBI
T2T-CHM13v2.01210,885,902 - 210,900,728 (+)NCBI
Sequence:
Promoters
RGD ID:15095337
Promoter ID:EPDNEWNC_H177
Type:initiation region
Name:LINC01693_1
Description:long intergenic non-protein coding RNA 1693 [Source:HGNCSymbol;Acc:HGNC:52478]
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
GRCh381211,639,693 - 211,639,753EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC NTRAS COSMIC
Ensembl Genes ENSG00000227764 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000430123 ENTREZGENE
GTEx ENSG00000227764 GTEx
HGNC ID HGNC:52478 ENTREZGENE
Human Proteome Map NTRAS Human Proteome Map
NCBI Gene LINC01693 ENTREZGENE
RNAcentral URS00008E39CF RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-08-22 NTRAS  non-coding transcript regulating alternative splicing  LINC01693  long intergenic non-protein coding RNA 1693  Symbol and/or name change 19259463 PROVISIONAL