REL-DT (REL divergent transcript) - Rat Genome Database

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Gene: REL-DT (REL divergent transcript) Homo sapiens
Analyze
Symbol: REL-DT
Name: REL divergent transcript
RGD ID: 8177884
HGNC Page HGNC:49572
Description:
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: AC010733.4; LINC01185; long intergenic non-protein coding RNA 1185
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38260,847,760 - 60,881,314 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl260,823,069 - 60,881,393 (-)EnsemblGRCh38hg38GRCh38
GRCh37261,074,895 - 61,108,449 (-)NCBIGRCh37GRCh37hg19GRCh37
Celera260,918,486 - 60,952,044 (-)NCBICelera
Cytogenetic Map2p16.1NCBI
HuRef260,817,064 - 60,850,351 (-)NCBIHuRef
CHM1_1261,005,335 - 61,038,850 (-)NCBICHM1_1
T2T-CHM13v2.0260,853,584 - 60,887,160 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:20953189   PMID:20953190   PMID:22170493  


Genomics

Variants

.
Variants in REL-DT
4 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2p16.1-11.2(chr2:58279519-83586962)x3 copy number gain See cases [RCV000136053] Chr2:58279519..83586962 [GRCh38]
Chr2:58506654..83814086 [GRCh37]
Chr2:58360158..83667597 [NCBI36]
Chr2:2p16.1-11.2		 pathogenic
GRCh38/hg38 2p16.1-15(chr2:60359313-61775405)x3 copy number gain See cases [RCV000137542] Chr2:60359313..61775405 [GRCh38]
Chr2:60586448..62002540 [GRCh37]
Chr2:60439952..61856044 [NCBI36]
Chr2:2p16.1-15		 uncertain significance
GRCh38/hg38 2p16.3-11.2(chr2:47620388-86702722)x3 copy number gain See cases [RCV000137586] Chr2:47620388..86702722 [GRCh38]
Chr2:47847527..86929845 [GRCh37]
Chr2:47701031..86783356 [NCBI36]
Chr2:2p16.3-11.2		 uncertain significance
GRCh38/hg38 2p16.1-15(chr2:60359313-61704436)x3 copy number gain See cases [RCV000139201] Chr2:60359313..61704436 [GRCh38]
Chr2:60586448..61931571 [GRCh37]
Chr2:60439952..61785075 [NCBI36]
Chr2:2p16.1-15		 likely pathogenic|likely benign
GRCh38/hg38 2p25.1-11.2(chr2:7495123-87705899)x3 copy number gain See cases [RCV000141494] Chr2:7495123..87705899 [GRCh38]
Chr2:7635254..88005418 [GRCh37]
Chr2:7552705..87786533 [NCBI36]
Chr2:2p25.1-11.2		 benign
GRCh38/hg38 2p16.1-15(chr2:58031916-63611810)x1 copy number loss See cases [RCV000143007] Chr2:58031916..63611810 [GRCh38]
Chr2:58259051..63838944 [GRCh37]
Chr2:58112555..63692448 [NCBI36]
Chr2:2p16.1-15		 pathogenic
GRCh38/hg38 2p16.1-15(chr2:59658846-62336083)x1 copy number loss See cases [RCV000050796] Chr2:59658846..62336083 [GRCh38]
Chr2:59885981..62563218 [GRCh37]
Chr2:59739485..62416722 [NCBI36]
Chr2:2p16.1-15		 pathogenic
GRCh38/hg38 2p16.1-15(chr2:60803569-61070455)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052124]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052124]|See cases [RCV000052124] Chr2:60803569..61070455 [GRCh38]
Chr2:61030704..61297590 [GRCh37]
Chr2:60884208..61151094 [NCBI36]
Chr2:2p16.1-15		 uncertain significance
GRCh38/hg38 2p16.1-15(chr2:60009106-62006709)x3 copy number gain See cases [RCV000052660] Chr2:60009106..62006709 [GRCh38]
Chr2:60236241..62233844 [GRCh37]
Chr2:60089745..62087348 [NCBI36]
Chr2:2p16.1-15		 uncertain significance
GRCh38/hg38 2p16.1-15(chr2:56738054-62473668)x1 copy number loss See cases [RCV000054020] Chr2:56738054..62473668 [GRCh38]
Chr2:56965189..62700803 [GRCh37]
Chr2:56818693..62554307 [NCBI36]
Chr2:2p16.1-15		 pathogenic
GRCh38/hg38 2p16.1-15(chr2:57249378-61842734)x1 copy number loss See cases [RCV000054021] Chr2:57249378..61842734 [GRCh38]
Chr2:57476513..62069869 [GRCh37]
Chr2:57330017..61923373 [NCBI36]
Chr2:2p16.1-15		 pathogenic
GRCh38/hg38 2p16.1-14(chr2:58873039-64190332)x1 copy number loss See cases [RCV000054022] Chr2:58873039..64190332 [GRCh38]
Chr2:59100174..64417466 [GRCh37]
Chr2:58953678..64270970 [NCBI36]
Chr2:2p16.1-14		 pathogenic
GRCh38/hg38 2p16.1-15(chr2:59224998-61621710)x1 copy number loss See cases [RCV000054052] Chr2:59224998..61621710 [GRCh38]
Chr2:59452133..61848845 [GRCh37]
Chr2:59305637..61702349 [NCBI36]
Chr2:2p16.1-15		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:302
Count of miRNA genes:267
Interacting mature miRNAs:280
Transcripts:ENST00000439412, ENST00000452343
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 visual system adipose tissue appendage entire extraembryonic component
High
Medium 2
Low 2 2 1 65 1 1 4 58 3 384 9 1
Below cutoff 685 823 822 153 876 63 1534 615 3121 117 625 798 94 1 361 1025 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000439412
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl260,823,069 - 60,881,317 (-)Ensembl
RefSeq Acc Id: ENST00000452343
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl260,847,760 - 60,881,314 (-)Ensembl
RefSeq Acc Id: ENST00000701510
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl260,880,979 - 60,881,393 (-)Ensembl
RefSeq Acc Id: NR_033980
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38260,847,760 - 60,881,314 (-)NCBI
HuRef260,817,064 - 60,850,351 (-)NCBI
CHM1_1261,005,335 - 61,038,850 (-)NCBI
T2T-CHM13v2.0260,853,584 - 60,887,160 (-)NCBI
Sequence:
Promoters
RGD ID:15095420
Promoter ID:EPDNEWNC_H257
Type:initiation region
Name:LINC01185_1
Description:long intergenic non-protein coding RNA 1185 [Source:HGNCSymbol;Acc:HGNC:49572]
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
GRCh38260,881,329 - 60,881,389EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC REL-DT COSMIC
Ensembl Genes ENSG00000228414 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000452343 ENTREZGENE
GTEx ENSG00000228414 GTEx
HGNC ID HGNC:49572 ENTREZGENE
Human Proteome Map REL-DT Human Proteome Map
NCBI Gene LINC01185 ENTREZGENE
RNAcentral URS00005C12D0 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-08-02 REL-DT  REL divergent transcript  LINC01185  long intergenic non-protein coding RNA 1185  Symbol and/or name change 19259463 PROVISIONAL