CIBAR1-DT (CIBAR1 divergent transcript) - Rat Genome Database

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Gene: CIBAR1-DT (CIBAR1 divergent transcript) Homo sapiens
Analyze
Symbol: CIBAR1-DT
Name: CIBAR1 divergent transcript
RGD ID: 6480356
HGNC Page HGNC
Description: INTERACTS WITH aflatoxin B1; antirheumatic drug; rotenone
Type: ncrna
RefSeq Status: VALIDATED
Also known as: LINC00535; long intergenic non-protein coding RNA 535; RP11-163D8.1
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl893,213,302 - 93,700,433 (-)EnsemblGRCh38hg38GRCh38
GRCh38893,346,467 - 93,700,433 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37894,358,695 - 94,712,661 (-)ENTREZGENEGRCh37GRCh37hg19GRCh37
Celera890,545,434 - 90,898,770 (-)NCBI
Cytogenetic Map8q22.1ENTREZGENE
HuRef889,565,999 - 89,920,186 (-)ENTREZGENEHuRef
CHM1_1894,398,901 - 94,752,948 (-)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

References - curated
1. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
Additional References at PubMed
PMID:12477932  


Genomics

Position Markers
D8S2097  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37894,701,569 - 94,701,694UniSTSGRCh37
Build 36894,770,745 - 94,770,870RGDNCBI36
Celera890,887,659 - 90,887,784RGD
Cytogenetic Map8q22.1UniSTS
HuRef889,909,114 - 89,909,239UniSTS
RH102558  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37894,712,070 - 94,712,151UniSTSGRCh37
Build 36894,781,246 - 94,781,327RGDNCBI36
Celera890,898,179 - 90,898,260RGD
Cytogenetic Map8q22.1UniSTS
HuRef889,919,595 - 89,919,676UniSTS
GeneMap99-GB4 RH Map8432.88UniSTS
SHGC-79712  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37894,457,915 - 94,458,197UniSTSGRCh37
Build 36894,527,091 - 94,527,373RGDNCBI36
Celera890,644,547 - 90,644,829RGD
Cytogenetic Map8q22.1UniSTS
HuRef889,665,304 - 89,665,586UniSTS
TNG Radiation Hybrid Map845193.0UniSTS
SHGC-106116  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37894,660,566 - 94,660,881UniSTSGRCh37
Build 36894,729,742 - 94,730,057RGDNCBI36
Celera890,846,618 - 90,846,933RGD
Cytogenetic Map8q22.1UniSTS
HuRef889,867,451 - 89,867,766UniSTS
TNG Radiation Hybrid Map845354.0UniSTS
D8S1455  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37894,444,383 - 94,444,586UniSTSGRCh37
Build 36894,513,559 - 94,513,762RGDNCBI36
Celera890,631,018 - 90,631,221RGD
Cytogenetic Map8q22.1UniSTS
HuRef889,651,773 - 89,651,976UniSTS
Whitehead-YAC Contig Map8 UniSTS
GDB:1317564  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37894,458,152 - 94,458,229UniSTSGRCh37
Build 36894,527,328 - 94,527,405RGDNCBI36
Celera890,644,784 - 90,644,861RGD
Cytogenetic Map8q22.1UniSTS
HuRef889,665,541 - 89,665,618UniSTS
D8S1637  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37894,493,782 - 94,493,908UniSTSGRCh37
Build 36894,562,958 - 94,563,084RGDNCBI36
Celera890,680,415 - 90,680,541RGD
Cytogenetic Map8q22.1UniSTS
HuRef889,700,997 - 89,701,123UniSTS
Whitehead-RH Map8541.0UniSTS
Whitehead-YAC Contig Map8 UniSTS
NCBI RH Map8949.6UniSTS
SHGC-156129  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37894,402,864 - 94,403,163UniSTSGRCh37
Build 36894,472,040 - 94,472,339RGDNCBI36
Celera890,589,629 - 90,589,928RGD
Cytogenetic Map8q22.1UniSTS
HuRef889,610,211 - 89,610,510UniSTS
TNG Radiation Hybrid Map845172.0UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:394
Count of miRNA genes:206
Interacting mature miRNAs:214
Transcripts:ENST00000501400, ENST00000517785, ENST00000520096, ENST00000520513
Prediction methods:Microtar, 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 visual system adipose tissue appendage entire extraembryonic component
High
Medium 1 1 1 176
Low 381 190 350 77 70 79 702 159 1135 74 403 464 5 1 63 625 1
Below cutoff 1969 2198 1291 486 736 351 3242 1853 2575 290 812 1032 143 1119 1896 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000501400
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl893,346,467 - 93,700,433 (-)Ensembl
RefSeq Acc Id: ENST00000517785
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl893,213,327 - 93,250,723 (-)Ensembl
RefSeq Acc Id: ENST00000520096
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl893,213,310 - 93,420,880 (-)Ensembl
RefSeq Acc Id: ENST00000520513
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl893,213,302 - 93,292,686 (-)Ensembl
RefSeq Acc Id: NR_033858
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38893,346,467 - 93,700,433 (-)NCBI
GRCh37894,358,695 - 94,712,661 (-)ENTREZGENE
HuRef889,565,999 - 89,920,186 (-)ENTREZGENE
CHM1_1894,398,901 - 94,752,948 (-)NCBI
Sequence:
Promoters
RGD ID:15096231
Promoter ID:EPDNEWNC_H1074
Type:initiation region
Name:LINC00535_1
Description:long intergenic non-protein coding RNA 535 [Source:HGNCSymbol;Acc:HGNC:43644]
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
GRCh38893,700,433 - 93,700,493EPDNEWNC

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NR_033858.1(LINC00535):n.1133+14179C>G single nucleotide variant Lung cancer [RCV000107896] Chr8:93517039 [GRCh38]
Chr8:94529267 [GRCh37]
Chr8:8q22.1
uncertain significance
NR_033858.1(LINC00535):n.1046-4159C>A single nucleotide variant Lung cancer [RCV000107897] Chr8:93535464 [GRCh38]
Chr8:94547692 [GRCh37]
Chr8:8q22.1
uncertain significance
NR_033858.1(LINC00535):n.948+3332A>G single nucleotide variant Lung cancer [RCV000107898] Chr8:93656095 [GRCh38]
Chr8:94668323 [GRCh37]
Chr8:8q22.1
uncertain significance
GRCh38/hg38 8q21.3-24.23(chr8:86300584-137022587)x3 copy number gain See cases [RCV000135621] Chr8:86300584..137022587 [GRCh38]
Chr8:87312813..138034830 [GRCh37]
Chr8:87381929..138104012 [NCBI36]
Chr8:8q21.3-24.23
pathogenic|likely pathogenic
GRCh38/hg38 8q22.1(chr8:93038175-95667782)x1 copy number loss See cases [RCV000136519] Chr8:93038175..95667782 [GRCh38]
Chr8:94050403..96680010 [GRCh37]
Chr8:94119579..96749186 [NCBI36]
Chr8:8q22.1
pathogenic
GRCh38/hg38 8q13.1-22.1(chr8:66171669-93505509)x3 copy number gain See cases [RCV000137050] Chr8:66171669..93505509 [GRCh38]
Chr8:67083904..94517737 [GRCh37]
Chr8:67246458..94586913 [NCBI36]
Chr8:8q13.1-22.1
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241605-145054781)x3 copy number gain See cases [RCV000138643] Chr8:241605..145054781 [GRCh38]
Chr8:191605..146280167 [GRCh37]
Chr8:181605..146250971 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q21.3-24.3(chr8:87931152-145068712)x3 copy number gain See cases [RCV000138551] Chr8:87931152..145068712 [GRCh38]
Chr8:88943380..146294098 [GRCh37]
Chr8:89012496..146264902 [NCBI36]
Chr8:8q21.3-24.3
pathogenic
GRCh38/hg38 8q21.13-24.3(chr8:77480050-145068712)x3 copy number gain See cases [RCV000139036] Chr8:77480050..145068712 [GRCh38]
Chr8:78392286..146294098 [GRCh37]
Chr8:78554841..146264902 [NCBI36]
Chr8:8q21.13-24.3
pathogenic
GRCh38/hg38 8q11.1-24.3(chr8:46031340-139285494)x3 copy number gain See cases [RCV000139539] Chr8:46031340..139285494 [GRCh38]
Chr8:46942962..140297737 [GRCh37]
Chr8:47062127..140366919 [NCBI36]
Chr8:8q11.1-24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:208048-145070385)x3 copy number gain See cases [RCV000141808] Chr8:208048..145070385 [GRCh38]
Chr8:158048..146295771 [GRCh37]
Chr8:148048..146266575 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8p21.3-q24.3(chr8:21291522-145070385)x3 copy number gain See cases [RCV000142021] Chr8:21291522..145070385 [GRCh38]
Chr8:21149033..146295771 [GRCh37]
Chr8:21193313..146266575 [NCBI36]
Chr8:8p21.3-q24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:226452-145068712)x3 copy number gain See cases [RCV000142858] Chr8:226452..145068712 [GRCh38]
Chr8:176452..146294098 [GRCh37]
Chr8:166452..146264902 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q21.13-24.3(chr8:78614077-145054634)x3 copy number gain See cases [RCV000142597] Chr8:78614077..145054634 [GRCh38]
Chr8:79526312..146280020 [GRCh37]
Chr8:79688867..146250824 [NCBI36]
Chr8:8q21.13-24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145054634)x3 copy number gain See cases [RCV000148092] Chr8:241530..145054634 [GRCh38]
Chr8:191530..146280020 [GRCh37]
Chr8:181530..146250824 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q21.2-24.3(chr8:85765999-145070385)x3 copy number gain See cases [RCV000143659] Chr8:85765999..145070385 [GRCh38]
Chr8:86778228..146295771 [GRCh37]
Chr8:86863079..146266575 [NCBI36]
Chr8:8q21.2-24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145049449)x3 copy number gain See cases [RCV000051206] Chr8:241530..145049449 [GRCh38]
Chr8:191530..146274835 [GRCh37]
Chr8:181530..146245639 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q21.2-22.1(chr8:85835757-93610142)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053676]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053676]|See cases [RCV000053676] Chr8:85835757..93610142 [GRCh38]
Chr8:86847986..94622370 [GRCh37]
Chr8:86917086..94691546 [NCBI36]
Chr8:8q21.2-22.1
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145054634)x3 copy number gain See cases [RCV000053602] Chr8:241530..145054634 [GRCh38]
Chr8:191530..146280020 [GRCh37]
Chr8:181530..146250824 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:244417-145054775)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053604]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053604]|See cases [RCV000053604] Chr8:244417..145054775 [GRCh38]
Chr8:194417..146280161 [GRCh37]
Chr8:184417..146250965 [NCBI36]
Chr8:8p23.3-q24.3
pathogenic
GRCh38/hg38 8q21.13-22.1(chr8:78672463-95366868)x1 copy number loss See cases [RCV000054262] Chr8:78672463..95366868 [GRCh38]
Chr8:79584698..96379096 [GRCh37]
Chr8:79747253..96448272 [NCBI36]
Chr8:8q21.13-22.1
pathogenic
GRCh38/hg38 8q21.3-22.1(chr8:90940996-94538343)x1 copy number loss See cases [RCV000054263] Chr8:90940996..94538343 [GRCh38]
Chr8:91953224..95550571 [GRCh37]
Chr8:92022400..95619747 [NCBI36]
Chr8:8q21.3-22.1
pathogenic
GRCh38/hg38 8q21.3-22.1(chr8:92283179-95786443)x1 copy number loss See cases [RCV000054265] Chr8:92283179..95786443 [GRCh38]
Chr8:93295407..96798671 [GRCh37]
Chr8:93364583..96867847 [NCBI36]
Chr8:8q21.3-22.1
pathogenic
GRCh38/hg38 8q21.3-22.1(chr8:92287062-95786443)x1 copy number loss See cases [RCV000054277] Chr8:92287062..95786443 [GRCh38]
Chr8:93299290..96798671 [GRCh37]
Chr8:93368466..96867847 [NCBI36]
Chr8:8q21.3-22.1
pathogenic
GRCh38/hg38 8q22.1(chr8:92755532-97792132)x1 copy number loss See cases [RCV000054278] Chr8:92755532..97792132 [GRCh38]
Chr8:93767760..98804360 [GRCh37]
Chr8:93836936..98873536 [NCBI36]
Chr8:8q22.1
pathogenic

Additional Information

Database Acc Id Source(s)
COSMIC CIBAR1-DT COSMIC
Ensembl Genes ENSG00000246662 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000501400 ENTREZGENE
GTEx ENSG00000246662 GTEx
HGNC ID HGNC:43644 ENTREZGENE
Human Proteome Map CIBAR1-DT Human Proteome Map
NCBI Gene LINC00535 ENTREZGENE
RNAcentral URS000075B4CF RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-05-03 CIBAR1-DT  CIBAR1 divergent transcript  LINC00535  long intergenic non-protein coding RNA 535  Symbol and/or name change 19259463 PROVISIONAL