ODC1-DT (ODC1 divergent transcript) - Rat Genome Database

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Gene: ODC1-DT (ODC1 divergent transcript) Homo sapiens
Analyze
Symbol: ODC1-DT
Name: ODC1 divergent transcript
RGD ID: 13801140
HGNC Page HGNC:54070
Description: INTERACTS WITH sodium arsenite
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: lncRNA-MIF
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38210,449,728 - 10,455,552 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl210,448,654 - 10,457,693 (+)EnsemblGRCh38hg38GRCh38
GRCh37210,589,854 - 10,595,678 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map2p25.1NCBI
HuRef210,441,084 - 10,443,151 (+)NCBIHuRef
CHM1_1210,518,233 - 10,520,301 (+)NCBICHM1_1
T2T-CHM13v2.0210,479,337 - 10,485,162 (+)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:12477932   PMID:27317567  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2p25.1-24.3(chr2:10216779-13474790)x3 copy number gain See cases [RCV000052627] Chr2:10216779..13474790 [GRCh38]
Chr2:10356905..13614915 [GRCh37]
Chr2:10274356..13532366 [NCBI36]
Chr2:2p25.1-24.3		 uncertain significance
GRCh38/hg38 2p25.1(chr2:10216979-10515005)x1 copy number loss See cases [RCV000052118] Chr2:10216979..10515005 [GRCh38]
Chr2:10357105..10655131 [GRCh37]
Chr2:10274556..10572582 [NCBI36]
Chr2:2p25.1		 uncertain significance
GRCh38/hg38 2p25.3-23.3(chr2:17019-26318846)x3 copy number gain See cases [RCV000137344] Chr2:17019..26318846 [GRCh38]
Chr2:17019..26541714 [GRCh37]
Chr2:7019..26395218 [NCBI36]
Chr2:2p25.3-23.3		 pathogenic
GRCh38/hg38 2p25.3-21(chr2:236816-45983232)x3 copy number gain See cases [RCV000143682] Chr2:236816..45983232 [GRCh38]
Chr2:236816..46210371 [GRCh37]
Chr2:226816..46063875 [NCBI36]
Chr2:2p25.3-21		 pathogenic
GRCh38/hg38 2p25.3-24.1(chr2:17019-20001056)x3 copy number gain See cases [RCV000141226] Chr2:17019..20001056 [GRCh38]
Chr2:17019..20200817 [GRCh37]
Chr2:7019..20064298 [NCBI36]
Chr2:2p25.3-24.1		 pathogenic
GRCh38/hg38 2p25.3-23.1(chr2:30141-31766749)x3 copy number gain See cases [RCV000052929] Chr2:30141..31766749 [GRCh38]
Chr2:30141..31991818 [GRCh37]
Chr2:20141..31845322 [NCBI36]
Chr2:2p25.3-23.1		 pathogenic
GRCh38/hg38 2p25.3-23.3(chr2:12770-25039694)x3 copy number gain See cases [RCV000141877] Chr2:12770..25039694 [GRCh38]
Chr2:12770..25262563 [GRCh37]
Chr2:2770..25116067 [NCBI36]
Chr2:2p25.3-23.3		 pathogenic
GRCh38/hg38 2p25.3-16.1(chr2:66097-55570637)x3 copy number gain See cases [RCV000052933] Chr2:66097..55570637 [GRCh38]
Chr2:66097..55797773 [GRCh37]
Chr2:56097..55651277 [NCBI36]
Chr2:2p25.3-16.1		 pathogenic
GRCh38/hg38 2p25.3-24.1(chr2:1664615-23664142)x3 copy number gain See cases [RCV000137913] Chr2:1664615..23664142 [GRCh38]
Chr2:1668387..23887012 [GRCh37]
Chr2:1647394..23740517 [NCBI36]
Chr2:2p25.3-24.1		 pathogenic|likely pathogenic
GRCh38/hg38 2p25.3-22.3(chr2:12770-33711509)x3 copy number gain See cases [RCV000141829] Chr2:12770..33711509 [GRCh38]
Chr2:12770..33936576 [GRCh37]
Chr2:2770..33790080 [NCBI36]
Chr2:2p25.3-22.3		 pathogenic
GRCh38/hg38 2p25.3-24.3(chr2:30342-14866951)x3 copy number gain See cases [RCV000052931] Chr2:30342..14866951 [GRCh38]
Chr2:30342..15007075 [GRCh37]
Chr2:20342..14924526 [NCBI36]
Chr2:2p25.3-24.3		 pathogenic
GRCh38/hg38 2p25.2-24.3(chr2:6531172-16103799)x1 copy number loss See cases [RCV000053978] Chr2:6531172..16103799 [GRCh38]
Chr2:6671304..16243921 [GRCh37]
Chr2:6588755..16161372 [NCBI36]
Chr2:2p25.2-24.3		 pathogenic
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 2p25.3-24.3(chr2:30141-14494040)x3 copy number gain See cases [RCV000052928] Chr2:30141..14494040 [GRCh38]
Chr2:30141..14634164 [GRCh37]
Chr2:20141..14551615 [NCBI36]
Chr2:2p25.3-24.3		 pathogenic
GRCh38/hg38 2p25.3-23.2(chr2:30341-28419664)x3 copy number gain See cases [RCV000135398] Chr2:30341..28419664 [GRCh38]
Chr2:30341..28642531 [GRCh37]
Chr2:20341..28496035 [NCBI36]
Chr2:2p25.3-23.2		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:261
Count of miRNA genes:238
Interacting mature miRNAs:247
Transcripts:ENST00000547349, ENST00000553181
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 visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 2 1 2 1 2 1 128 6
Low 1967 1744 1518 474 1330 410 2804 1017 2538 316 1193 1431 73 1 975 1702 3 1
Below cutoff 467 1228 207 149 606 55 1538 1165 1187 99 136 175 100 229 1078 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000404616
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl210,452,319 - 10,455,552 (+)Ensembl
RefSeq Acc Id: ENST00000547349
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl210,448,689 - 10,450,794 (+)Ensembl
RefSeq Acc Id: ENST00000553181
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl210,448,689 - 10,457,692 (+)Ensembl
RefSeq Acc Id: ENST00000667698
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl210,450,181 - 10,457,543 (+)Ensembl
RefSeq Acc Id: ENST00000670859
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl210,453,798 - 10,457,693 (+)Ensembl
RefSeq Acc Id: ENST00000684804
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl210,448,654 - 10,449,235 (+)Ensembl
RefSeq Acc Id: ENST00000684902
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl210,448,785 - 10,450,739 (+)Ensembl
RefSeq Acc Id: ENST00000690575
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl210,448,654 - 10,449,235 (+)Ensembl
RefSeq Acc Id: ENST00000702529
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl210,448,682 - 10,450,742 (+)Ensembl
RefSeq Acc Id: NR_110597
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38210,449,728 - 10,455,552 (+)NCBI
T2T-CHM13v2.0210,479,337 - 10,485,162 (+)NCBI
Sequence:
Promoters
RGD ID:15095389
Promoter ID:EPDNEWNC_H215
Type:initiation region
Name:ODC1-DT_1
Description:novel transcript
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
GRCh38210,448,716 - 10,448,776EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC ODC1-DT COSMIC
Ensembl Genes ENSG00000257135 Ensembl
GTEx ENSG00000257135 GTEx
HGNC ID HGNC:54070 ENTREZGENE
Human Proteome Map ODC1-DT Human Proteome Map
NCBI Gene ODC1-DT ENTREZGENE
RNAcentral URS000075CD89 RNACentral