VTRNA1-2 (vault RNA 1-2) - Rat Genome Database

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Gene: VTRNA1-2 (vault RNA 1-2) Homo sapiens
Analyze
Symbol: VTRNA1-2
Name: vault RNA 1-2
RGD ID: 1347664
HGNC Page HGNC:12655
Description: ASSOCIATED WITH autosomal dominant intellectual developmental disorder 31; familial adenomatous polyposis 1; Hereditary Neoplastic Syndromes; INTERACTS WITH benzo[a]pyrene; methylisothiazolinone
Type: ncrna (Ensembl: vault_RNA)
RefSeq Status: PROVISIONAL
Previously known as: hvg-2; HVG2; VAULTRC2; VR2
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385140,718,926 - 140,719,013 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5140,718,925 - 140,719,013 (+)EnsemblGRCh38hg38GRCh38
GRCh375140,098,511 - 140,098,598 (+)NCBIGRCh37GRCh37hg19GRCh37
Celera5136,175,259 - 136,175,346 (+)NCBICelera
Cytogenetic Map5q31.3NCBI
HuRef5135,243,760 - 135,243,847 (+)NCBIHuRef
CHM1_15139,531,783 - 139,531,870 (+)NCBICHM1_1
T2T-CHM13v2.05141,244,309 - 141,244,396 (+)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:9535882   PMID:10551828   PMID:19298825   PMID:19491402   PMID:21555518   PMID:29507755  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 5q23.3-33.2(chr5:130860928-155321811)x3 copy number gain See cases [RCV000051193] Chr5:130860928..155321811 [GRCh38]
Chr5:130196621..154701371 [GRCh37]
Chr5:130224520..154681564 [NCBI36]
Chr5:5q23.3-33.2
pathogenic
GRCh38/hg38 5q31.2-32(chr5:138871137-145812309)x1 copy number loss See cases [RCV000052142] Chr5:138871137..145812309 [GRCh38]
Chr5:138206826..145191872 [GRCh37]
Chr5:138234725..145172065 [NCBI36]
Chr5:5q31.2-32
pathogenic
GRCh38/hg38 5q21.3-33.2(chr5:106619588-156124387)x1 copy number loss See cases [RCV000053524] Chr5:106619588..156124387 [GRCh38]
Chr5:105955289..155551397 [GRCh37]
Chr5:105983188..155483975 [NCBI36]
Chr5:5q21.3-33.2
pathogenic
GRCh38/hg38 5q23.3-33.2(chr5:129847794-153353546)x3 copy number gain See cases [RCV000138808] Chr5:129847794..153353546 [GRCh38]
Chr5:129183487..152733106 [GRCh37]
Chr5:129211386..152713299 [NCBI36]
Chr5:5q23.3-33.2
pathogenic
GRCh38/hg38 5q31.2-31.3(chr5:138942857-144605017)x3 copy number gain See cases [RCV000142806] Chr5:138942857..144605017 [GRCh38]
Chr5:138278546..143984580 [GRCh37]
Chr5:138306445..143964773 [NCBI36]
Chr5:5q31.2-31.3
uncertain significance
GRCh37/hg19 5q15-35.3(chr5:94844077-178830410)x3 copy number gain not provided [RCV000487658] Chr5:94844077..178830410 [GRCh37]
Chr5:5q15-35.3
likely benign
GRCh37/hg19 5q23.3-33.3(chr5:130125085-157574910)x3 copy number gain See cases [RCV000449349] Chr5:130125085..157574910 [GRCh37]
Chr5:5q23.3-33.3
pathogenic
GRCh37/hg19 5q21.3-35.3(chr5:106716357-180687338)x3 copy number gain See cases [RCV000448245] Chr5:106716357..180687338 [GRCh37]
Chr5:5q21.3-35.3
pathogenic
GRCh37/hg19 5p15.1-q35.2(chr5:17628741-176575720)x1 copy number loss See cases [RCV000511978] Chr5:17628741..176575720 [GRCh37]
Chr5:5p15.1-q35.2
pathogenic
GRCh37/hg19 5p15.33-q35.3(chr5:113577-180719789)x3 copy number gain See cases [RCV000512039] Chr5:113577..180719789 [GRCh37]
Chr5:5p15.33-q35.3
pathogenic
GRCh37/hg19 5p15.33-q35.3(chr5:113577-180719789) copy number gain See cases [RCV000510723] Chr5:113577..180719789 [GRCh37]
Chr5:5p15.33-q35.3
pathogenic
NC_000005.9:g.(?_86400000)_(154000000_?)del deletion Familial adenomatous polyposis 1 [RCV002231249]|Hereditary cancer-predisposing syndrome [RCV000554476] Chr5:86400000..154000000 [GRCh37]
Chr5:5q14.3-33.2
pathogenic
GRCh37/hg19 5q31.2-31.3(chr5:139147238-141540491)x1 copy number loss not provided [RCV000682600] Chr5:139147238..141540491 [GRCh37]
Chr5:5q31.2-31.3
pathogenic
GRCh37/hg19 5p15.33-q35.3(chr5:25328-180693344)x3 copy number gain not provided [RCV000744323] Chr5:25328..180693344 [GRCh37]
Chr5:5p15.33-q35.3
pathogenic
GRCh37/hg19 5p15.33-q35.3(chr5:13648-180905029)x3 copy number gain not provided [RCV000744317] Chr5:13648..180905029 [GRCh37]
Chr5:5p15.33-q35.3
pathogenic
Single allele deletion Neurodevelopmental disorder [RCV000787436] Chr5:14685137..149511942 [GRCh37]
Chr5:5p15.2-q32
uncertain significance
NC_000005.9:g.(?_136633338)_(140998481_?)dup duplication PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome [RCV001339088] Chr5:136633338..140998481 [GRCh37]
Chr5:5q31.2-31.3
uncertain significance
GRCh37/hg19 5q31.2-31.3(chr5:139493717-140517454)x1 copy number loss PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome [RCV001801202] Chr5:139493717..140517454 [GRCh37]
Chr5:5q31.2-31.3
pathogenic
GRCh37/hg19 5q23.3-33.3(chr5:130125085-157574910) copy number gain not specified [RCV002053526] Chr5:130125085..157574910 [GRCh37]
Chr5:5q23.3-33.3
pathogenic
GRCh37/hg19 5q31.3(chr5:140082762-140773954)x3 copy number gain not provided [RCV002474614] Chr5:140082762..140773954 [GRCh37]
Chr5:5q31.3
uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:147
Count of miRNA genes:143
Interacting mature miRNAs:147
Transcripts:ENST00000365241
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 14 8 6 20 9 9 9 26 11 42 32 2
Low 136 90 96 33 115 32 91 20 69 66 159 118 2 28 29 1
Below cutoff 100 54 45 11 29 8 56 26 53 9 51 25 4 45 19 1

Sequence


RefSeq Acc Id: ENST00000365241
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5140,718,925 - 140,719,013 (+)Ensembl
RefSeq Acc Id: NR_026704
RefSeq Status: PROVISIONAL
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385140,718,926 - 140,719,013 (+)NCBI
GRCh375140,098,511 - 140,098,598 (+)RGD
Celera5136,175,259 - 136,175,346 (+)RGD
HuRef5135,243,760 - 135,243,847 (+)ENTREZGENE
CHM1_15139,531,783 - 139,531,870 (+)NCBI
T2T-CHM13v2.05141,244,309 - 141,244,396 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC VTRNA1-2 COSMIC
Ensembl Genes ENSG00000202111 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000365241 ENTREZGENE
GTEx ENSG00000202111 GTEx
HGNC ID HGNC:12655 ENTREZGENE
Human Proteome Map VTRNA1-2 Human Proteome Map
NCBI Gene 56663 ENTREZGENE
OMIM 612696 OMIM
PharmGKB PA37278 PharmGKB
RNAcentral URS0000000A8C RNACentral