PLCB1-IT1 (PLCB1 intronic transcript 1) - Rat Genome Database

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Gene: PLCB1-IT1 (PLCB1 intronic transcript 1) Homo sapiens
Analyze
Symbol: PLCB1-IT1
Name: PLCB1 intronic transcript 1
RGD ID: 6481050
HGNC Page HGNC:41414
Description: INTERACTS WITH propofol
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38208,248,704 - 8,249,742 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl208,248,704 - 8,256,918 (+)EnsemblGRCh38hg38GRCh38
GRCh37208,229,351 - 8,230,389 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map20p12.3NCBI
CHM1_1208,229,432 - 8,233,680 (+)NCBICHM1_1
T2T-CHM13v2.0208,290,671 - 8,291,709 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
propofol  (EXP)

References
Additional References at PubMed
PMID:7566098  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 20p13-12.1(chr20:80106-13029401)x3 copy number gain See cases [RCV000138677] Chr20:80106..13029401 [GRCh38]
Chr20:60747..13010049 [GRCh37]
Chr20:8747..12958049 [NCBI36]
Chr20:20p13-12.1		 pathogenic
GRCh38/hg38 20p12.3(chr20:8215937-8276043)x1 copy number loss See cases [RCV000141044] Chr20:8215937..8276043 [GRCh38]
Chr20:8196584..8256690 [GRCh37]
Chr20:8144584..8204690 [NCBI36]
Chr20:20p12.3		 benign
GRCh38/hg38 20p12.3(chr20:7125410-8606171)x3 copy number gain See cases [RCV000142356] Chr20:7125410..8606171 [GRCh38]
Chr20:7106057..8586818 [GRCh37]
Chr20:7054057..8534818 [NCBI36]
Chr20:20p12.3		 uncertain significance
GRCh38/hg38 20p13-12.3(chr20:1269303-8626911)x3 copy number gain See cases [RCV000142917] Chr20:1269303..8626911 [GRCh38]
Chr20:1249947..8607558 [GRCh37]
Chr20:1197947..8555558 [NCBI36]
Chr20:20p13-12.3		 pathogenic
GRCh38/hg38 20p13-11.23(chr20:80928-18688031)x3 copy number gain See cases [RCV000143426] Chr20:80928..18688031 [GRCh38]
Chr20:61569..18668675 [GRCh37]
Chr20:9569..18616675 [NCBI36]
Chr20:20p13-11.23		 pathogenic
GRCh38/hg38 20p12.3(chr20:7123110-8577546)x3 copy number gain See cases [RCV000148075] Chr20:7123110..8577546 [GRCh38]
Chr20:7103757..8558193 [GRCh37]
Chr20:7051757..8506193 [NCBI36]
Chr20:20p12.3		 uncertain significance
GRCh38/hg38 20p12.3(chr20:7123110-8577546)x3 copy number gain See cases [RCV000050394] Chr20:7123110..8577546 [GRCh38]
Chr20:7103757..8558193 [GRCh37]
Chr20:7051757..8506193 [NCBI36]
Chr20:20p12.3		 pathogenic|uncertain significance|conflicting data from submitters
GRCh38/hg38 20p12.3(chr20:7123110-8577546)x1 copy number loss See cases [RCV000050395] Chr20:7123110..8577546 [GRCh38]
Chr20:7103757..8558193 [GRCh37]
Chr20:7051757..8506193 [NCBI36]
Chr20:20p12.3		 pathogenic
GRCh38/hg38 20p12.3(chr20:6336607-8577546)x1 copy number loss See cases [RCV000050903] Chr20:6336607..8577546 [GRCh38]
Chr20:6317254..8558193 [GRCh37]
Chr20:6265254..8506193 [NCBI36]
Chr20:20p12.3		 pathogenic
GRCh38/hg38 20p13-11.23(chr20:89939-19146279)x3 copy number gain See cases [RCV000051041] Chr20:89939..19146279 [GRCh38]
Chr20:70580..19126923 [GRCh37]
Chr20:18580..19074923 [NCBI36]
Chr20:20p13-11.23		 pathogenic
GRCh38/hg38 20p13-11.21(chr20:89939-25697564)x3 copy number gain See cases [RCV000051227] Chr20:89939..25697564 [GRCh38]
Chr20:70580..25678200 [GRCh37]
Chr20:18580..25626200 [NCBI36]
Chr20:20p13-11.21		 pathogenic
GRCh38/hg38 20p13-11.22(chr20:89939-21787252)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052996]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052996]|See cases [RCV000052996] Chr20:89939..21787252 [GRCh38]
Chr20:70580..21767890 [GRCh37]
Chr20:18580..21715890 [NCBI36]
Chr20:20p13-11.22		 pathogenic
GRCh38/hg38 20p13-q11.1(chr20:80106-30227427)x3 copy number gain See cases [RCV000133996] Chr20:80106..30227427 [GRCh38]
Chr20:60747..29462103 [GRCh37]
Chr20:8747..28075764 [NCBI36]
Chr20:20p13-q11.1		 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
GRCh38/hg38 20p12.3-12.2(chr20:7566644-11028694)x1 copy number loss See cases [RCV000052739] Chr20:7566644..11028694 [GRCh38]
Chr20:7547291..11009342 [GRCh37]
Chr20:7495291..10957342 [NCBI36]
Chr20:20p12.3-12.2		 pathogenic
GRCh38/hg38 20p13-11.23(chr20:89939-19071495)x3 copy number gain See cases [RCV000052995] Chr20:89939..19071495 [GRCh38]
Chr20:70580..19052139 [GRCh37]
Chr20:18580..19000139 [NCBI36]
Chr20:20p13-11.23		 pathogenic
GRCh38/hg38 20p13-12.1(chr20:89939-14818511)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052997]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052997]|See cases [RCV000052997] Chr20:89939..14818511 [GRCh38]
Chr20:70580..14799157 [GRCh37]
Chr20:18580..14747157 [NCBI36]
Chr20:20p13-12.1		 pathogenic
GRCh38/hg38 20p13-11.1(chr20:80927-26324843)x3 copy number gain See cases [RCV000142017] Chr20:80927..26324843 [GRCh38]
Chr20:61568..26305479 [GRCh37]
Chr20:9568..26253479 [NCBI36]
Chr20:20p13-11.1		 pathogenic
GRCh38/hg38 20p12.3-12.1(chr20:6617695-13392559)x1 copy number loss See cases [RCV000135292] Chr20:6617695..13392559 [GRCh38]
Chr20:6598342..13373206 [GRCh37]
Chr20:6546342..13321206 [NCBI36]
Chr20:20p12.3-12.1		 pathogenic
GRCh38/hg38 20p12.3(chr20:6186076-8804328)x3 copy number gain See cases [RCV000138041] Chr20:6186076..8804328 [GRCh38]
Chr20:6166723..8784975 [GRCh37]
Chr20:6114723..8732975 [NCBI36]
Chr20:20p12.3		 uncertain significance
GRCh38/hg38 20p13-11.21(chr20:87153-23635465)x3 copy number gain Renal agenesis [RCV003327640] Chr20:87153..23635465 [GRCh38]
Chr20:20p13-11.21		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:243
Count of miRNA genes:224
Interacting mature miRNAs:236
Transcripts:ENST00000441231, ENST00000451443
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 2 4 3
Low 4 6 2 1 20 1 6 4 14 1 352 3 1 3 1
Below cutoff 287 124 114 47 86 33 246 178 479 26 134 97 14 89 136 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000441231
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl208,248,704 - 8,249,742 (+)Ensembl
RefSeq Acc Id: ENST00000451443
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl208,248,725 - 8,256,918 (+)Ensembl
RefSeq Acc Id: NR_046809
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38208,248,704 - 8,249,742 (+)NCBI
T2T-CHM13v2.0208,290,671 - 8,291,709 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC PLCB1-IT1 COSMIC
Ensembl Genes ENSG00000225479 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000441231 ENTREZGENE
GTEx ENSG00000225479 GTEx
HGNC ID HGNC:41414 ENTREZGENE
Human Proteome Map PLCB1-IT1 Human Proteome Map
NCBI Gene PLCB1-IT1 ENTREZGENE
RNAcentral URS000048F109 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-03-03 PLCB1-IT1  PLCB1 intronic transcript 1    PLCB1 intronic transcript 1 (non-protein coding)  Symbol and/or name change 5135510 APPROVED