AL162457.1 (novel transcript, antisense to CDH4) - Rat Genome Database

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Gene: AL162457.1 (novel transcript, antisense to CDH4) Homo sapiens
Analyze
Symbol: AL162457.1
Name: novel transcript, antisense to CDH4
RGD ID: 16550858
Description:
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: LOC100128310; uncharacterized LOC100128310
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38.p14 Ensembl - Human Genome Assembly GRCh38 Ensembl
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382061,717,506 - 61,719,748 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2061,717,506 - 61,719,748 (-)EnsemblGRCh38hg38GRCh38
GRCh372060,292,562 - 60,294,804 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map20q13.33NCBI
T2T-CHM13v2.02063,506,560 - 63,508,803 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:14702039  


Genomics

Variants

.
Variants in AL162457.1
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh37/hg19 20q13.2-13.33(chr20:51542616-62915555)x3 copy number gain See cases [RCV000511980] Chr20:51542616..62915555 [GRCh37]
Chr20:20q13.2-13.33		 likely pathogenic
GRCh37/hg19 20q13.33(chr20:60058100-60564395)x3 copy number gain not provided [RCV000845942] Chr20:60058100..60564395 [GRCh37]
Chr20:20q13.33		 uncertain significance
GRCh37/hg19 20p13-q13.33(chr20:63244-62948788)x3 copy number gain not provided [RCV000741058] Chr20:63244..62948788 [GRCh37]
Chr20:20p13-q13.33		 pathogenic
GRCh37/hg19 20p13-q13.33(chr20:63244-62961294)x3 copy number gain not provided [RCV000741059] Chr20:63244..62961294 [GRCh37]
Chr20:20p13-q13.33		 pathogenic
GRCh38/hg38 20q13.12-13.33(chr20:44787704-64277321)x3 copy number gain See cases [RCV000053035] Chr20:44787704..64277321 [GRCh38]
Chr20:43416345..62908674 [GRCh37]
Chr20:42849759..62379118 [NCBI36]
Chr20:20q13.12-13.33		 pathogenic
GRCh38/hg38 20p13-q13.33(chr20:99557-64277321)x3 copy number gain See cases [RCV000135859] Chr20:99557..64277321 [GRCh38]
Chr20:80198..62908674 [GRCh37]
Chr20:28198..62379118 [NCBI36]
Chr20:20p13-q13.33		 pathogenic
GRCh37/hg19 20p13-q13.33(chr20:61569-62915555) copy number gain See cases [RCV000512450] Chr20:61569..62915555 [GRCh37]
Chr20:20p13-q13.33		 pathogenic
GRCh37/hg19 20q13.2-13.33(chr20:54143747-62194881) copy number gain not provided [RCV000767669] Chr20:54143747..62194881 [GRCh37]
Chr20:20q13.2-13.33		 pathogenic
GRCh37/hg19 20q13.33(chr20:60053234-62961294)x3 copy number gain not provided [RCV000741328] Chr20:60053234..62961294 [GRCh37]
Chr20:20q13.33		 pathogenic
GRCh37/hg19 20q13.32-13.33(chr20:56788101-62762405)x3 copy number gain not provided [RCV001007098] Chr20:56788101..62762405 [GRCh37]
Chr20:20q13.32-13.33		 pathogenic
GRCh38/hg38 20q13.33(chr20:61262566-61742628)x1 copy number loss See cases [RCV000137811] Chr20:61262566..61742628 [GRCh38]
Chr20:59837622..60317684 [GRCh37]
Chr20:59271017..59751079 [NCBI36]
Chr20:20q13.33		 uncertain significance
GRCh38/hg38 20q13.33(chr20:61326548-61935972)x3 copy number gain See cases [RCV000138274] Chr20:61326548..61935972 [GRCh38]
Chr20:59901604..60511030 [GRCh37]
Chr20:59334999..59944425 [NCBI36]
Chr20:20q13.33		 uncertain significance
GRCh37/hg19 20p13-q13.33(chr20:63244-62912463)x3 copy number gain not provided [RCV000741057] Chr20:63244..62912463 [GRCh37]
Chr20:20p13-q13.33		 pathogenic
GRCh38/hg38 20q13.2-13.33(chr20:53236165-64284202)x3 copy number gain See cases [RCV000143584] Chr20:53236165..64284202 [GRCh38]
Chr20:51852704..62915555 [GRCh37]
Chr20:51286111..62385999 [NCBI36]
Chr20:20q13.2-13.33		 likely pathogenic
GRCh37/hg19 20q13.33(chr20:60063645-62961294)x3 copy number gain not provided [RCV000741329] Chr20:60063645..62961294 [GRCh37]
Chr20:20q13.33		 pathogenic
GRCh37/hg19 20q13.31-13.33(chr20:55743522-62032989)x3 copy number gain not provided [RCV001007097] Chr20:55743522..62032989 [GRCh37]
Chr20:20q13.31-13.33		 pathogenic
GRCh37/hg19 20q13.2-13.33(chr20:51799648-62916626)x3 copy number gain not provided [RCV001537917] Chr20:51799648..62916626 [GRCh37]
Chr20:20q13.2-13.33		 pathogenic
GRCh38/hg38 20q13.2-13.33(chr20:56198032-64277321)x3 copy number gain See cases [RCV000138035] Chr20:56198032..64277321 [GRCh38]
Chr20:54773088..62908674 [GRCh37]
Chr20:54206495..62379118 [NCBI36]
Chr20:20q13.2-13.33		 pathogenic
GRCh38/hg38 20q13.33(chr20:61326549-64277326)x3 copy number gain See cases [RCV000139100] Chr20:61326549..64277326 [GRCh38]
Chr20:59901605..62908679 [GRCh37]
Chr20:59335000..62379123 [NCBI36]
Chr20:20q13.33		 pathogenic
GRCh38/hg38 20q13.33(chr20:61588953-62241744)x3 copy number gain See cases [RCV000137839] Chr20:61588953..62241744 [GRCh38]
Chr20:60164009..60816800 [GRCh37]
Chr20:59597404..60250195 [NCBI36]
Chr20:20q13.33		 uncertain significance
GRCh38/hg38 20q13.31-13.33(chr20:57229415-64273089)x3 copy number gain See cases [RCV000141347] Chr20:57229415..64273089 [GRCh38]
Chr20:55804471..62904442 [GRCh37]
Chr20:55237878..62374886 [NCBI36]
Chr20:20q13.31-13.33		 pathogenic
GRCh38/hg38 20q13.32-13.33(chr20:59041966-64277321)x3 copy number gain See cases [RCV000135805] Chr20:59041966..64277321 [GRCh38]
Chr20:57617021..62908674 [GRCh37]
Chr20:57050416..62379118 [NCBI36]
Chr20:20q13.32-13.33		 pathogenic
GRCh37/hg19 20p13-q13.33(chr20:61569-62915555)x3 copy number gain See cases [RCV000510832] Chr20:61569..62915555 [GRCh37]
Chr20:20p13-q13.33		 pathogenic
GRCh37/hg19 20q13.32-13.33(chr20:56835739-62915555) copy number gain not specified [RCV002052713] Chr20:56835739..62915555 [GRCh37]
Chr20:20q13.32-13.33		 pathogenic
GRCh37/hg19 20q13.2-13.33(chr20:52773668-62965020)x3 copy number gain See cases [RCV003329549] Chr20:52773668..62965020 [GRCh37]
Chr20:20q13.2-13.33		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:682
Count of miRNA genes:500
Interacting mature miRNAs:553
Transcripts:ENST00000317652
Prediction methods:Miranda, Rnahybrid, Targetscan
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 5
Low 21 54 9 220 31 3 28 9 34 19 26 16
Below cutoff 944 1023 600 177 957 129 1421 501 1612 103 701 746 52 493 768 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000317652
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2061,717,506 - 61,719,748 (-)Ensembl
RefSeq Acc Id: NR_147702
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382061,717,506 - 61,719,748 (-)NCBI
T2T-CHM13v2.02063,506,560 - 63,508,803 (-)NCBI
Sequence:
Protein Sequences
GenBank Protein BAC05189 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences


Additional Information

Database Acc Id Source(s)
COSMIC AL162457.1 COSMIC
Ensembl Genes ENSG00000179253 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000317652 ENTREZGENE
GTEx ENSG00000179253 GTEx
Human Proteome Map AL162457.1 Human Proteome Map
NCBI Gene LOC100128310 ENTREZGENE
RNAcentral URS00007CB9E7 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-06-25 AL162457.1  novel transcript, antisense to CDH4  LOC100128310  uncharacterized LOC100128310  Symbol and/or name change 19259462 PROVISIONAL
2020-06-18 LOC100128310  uncharacterized LOC100128310  AL162457.1  novel transcript, antisense to CDH4  Symbol and/or name change 5135510 APPROVED