AL138799.3 (novel transcript) - Rat Genome Database

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Gene: AL138799.3 (novel transcript) Homo sapiens
Analyze
Symbol: AL138799.3
Name: novel transcript
RGD ID: 16556066
Description:
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: AL138799.4; LOC101927434; uncharacterized LOC101927434
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38.p14 Ensembl - Human Genome Assembly GRCh38 Ensembl
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38181,513,880 - 81,557,702 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl181,513,880 - 81,557,702 (-)EnsemblGRCh38hg38GRCh38
GRCh37181,979,565 - 82,023,387 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map1p31.1NCBI
HuRef180,110,839 - 80,112,152 (-)NCBIHuRef
CHM1_1182,094,596 - 82,095,909 (-)NCBICHM1_1
T2T-CHM13v2.0181,351,439 - 81,395,272 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Genomics

Variants

.
Variants in AL138799.3
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1p32.1-22.3(chr1:58819605-86098611)x1 copy number loss See cases [RCV000136913] Chr1:58819605..86098611 [GRCh38]
Chr1:59285277..86564294 [GRCh37]
Chr1:59057865..86336882 [NCBI36]
Chr1:1p32.1-22.3		 pathogenic
Single allele deletion not provided [RCV000844927] Chr1:66085524..88429789 [GRCh37]
Chr1:1p31.3-22.2		 not provided
GRCh37/hg19 1p31.1-22.1(chr1:72044544-92505091)x1 copy number loss See cases [RCV000510161] Chr1:72044544..92505091 [GRCh37]
Chr1:1p31.1-22.1		 pathogenic
GRCh37/hg19 1p31.3-22.3(chr1:64321264-88153669)x1 copy number loss See cases [RCV000511392] Chr1:64321264..88153669 [GRCh37]
Chr1:1p31.3-22.3		 pathogenic|uncertain significance
GRCh37/hg19 1p36.12-12(chr1:20608823-120546301)x3 copy number loss not provided [RCV000762767] Chr1:20608823..120546301 [GRCh37]
Chr1:1p36.12-12		 likely benign
GRCh37/hg19 1p36.22-21.1(chr1:103343285-103455144)x3 copy number gain Global developmental delay [RCV000787285] Chr1:103343285..103455144 [GRCh37]
Chr1:1p36.22-21.1		 uncertain significance
GRCh37/hg19 1p36.33-q44(chr1:82154-249218992)x3 copy number gain not provided [RCV000736305] Chr1:82154..249218992 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh38/hg38 1p31.1-22.2(chr1:76419302-88628464)x1 copy number loss See cases [RCV000138957] Chr1:76419302..88628464 [GRCh38]
Chr1:76884987..89094147 [GRCh37]
Chr1:76657575..88866735 [NCBI36]
Chr1:1p31.1-22.2		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684)x3 copy number gain See cases [RCV000510383] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:47851-249228449)x3 copy number gain not provided [RCV000736295] Chr1:47851..249228449 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh38/hg38 1p31.1(chr1:80621564-82040802)x1 copy number loss See cases [RCV000136991] Chr1:80621564..82040802 [GRCh38]
Chr1:81087249..82506486 [GRCh37]
Chr1:80859837..82279074 [NCBI36]
Chr1:1p31.1		 benign
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684) copy number gain See cases [RCV000510926] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p31.3-22.3(chr1:67851233-86101340)x1 copy number loss not provided [RCV000846441] Chr1:67851233..86101340 [GRCh37]
Chr1:1p31.3-22.3		 pathogenic
GRCh37/hg19 1p31.1-22.2(chr1:80804502-89490384)x3 copy number gain not provided [RCV001259073] Chr1:80804502..89490384 [GRCh37]
Chr1:1p31.1-22.2		 likely pathogenic
GRCh37/hg19 1p31.3-22.1(chr1:68180293-92731957) copy number loss not specified [RCV002053392] Chr1:68180293..92731957 [GRCh37]
Chr1:1p31.3-22.1		 pathogenic
GRCh37/hg19 1p31.1(chr1:79960197-82532594) copy number gain not specified [RCV002053469] Chr1:79960197..82532594 [GRCh37]
Chr1:1p31.1		 uncertain significance
GRCh37/hg19 1p31.1-22.3(chr1:73616197-87012961)x1 copy number loss not provided [RCV003885448] Chr1:73616197..87012961 [GRCh37]
Chr1:1p31.1-22.3		 likely pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:77
Count of miRNA genes:62
Interacting mature miRNAs:63
Transcripts:ENST00000443939
Prediction methods:Microtar, 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
Low 3 2 1 3 1 2 1 2 1 89 7 1
Below cutoff 65 213 292 50 55 49 43 58 163 12 270 266 1 5 19

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000443939
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl181,513,880 - 81,557,702 (-)Ensembl
RefSeq Acc Id: NR_125943
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38181,513,880 - 81,557,702 (-)NCBI
T2T-CHM13v2.0181,351,439 - 81,395,272 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC AL138799.3 COSMIC
Ensembl Genes ENSG00000234953 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000443939 ENTREZGENE
GTEx ENSG00000234953 GTEx
Human Proteome Map AL138799.3 Human Proteome Map
NCBI Gene LOC101927434 ENTREZGENE
RNAcentral URS00007E4C59 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-06-25 AL138799.3  novel transcript  LOC101927434  uncharacterized LOC101927434  Symbol and/or name change 19259462 PROVISIONAL
2020-06-18 LOC101927434  uncharacterized LOC101927434  AL138799.3  novel transcript  Symbol and/or name change 5135510 APPROVED
2020-04-30 AL138799.3  novel transcript  AL138799.4  novel transcript  Symbol and/or name change 19259462 PROVISIONAL