CASC11 (cancer susceptibility 11) - Rat Genome Database

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Gene: CASC11 (cancer susceptibility 11) Homo sapiens
Analyze
Symbol: CASC11
Name: cancer susceptibility 11
RGD ID: 8553151
HGNC Page HGNC
Description: INTERACTS WITH butanal
Type: ncrna
RefSeq Status: VALIDATED
Also known as: cancer susceptibility 11 (non-protein coding); cancer susceptibility candidate 11 (non-protein coding); CARLo-7; CARLO7; LINC00990; MYMLR; TCONS_00014535
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl8127,686,343 - 127,738,987 (-)EnsemblGRCh38hg38GRCh38
GRCh388127,700,608 - 127,733,967 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh378128,712,853 - 128,746,213 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map8q24.21NCBI
HuRef8124,019,209 - 124,067,723 (-)NCBIHuRef
CHM1_18128,753,091 - 128,786,449 (-)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

References

References - curated
1. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:18794855   PMID:24594601   PMID:27012187   PMID:27729273   PMID:30503497   PMID:30910841   PMID:30914434   PMID:30915898   PMID:30916832   PMID:30965130   PMID:31121483   PMID:31181314  
PMID:31361039   PMID:31378894   PMID:31537383   PMID:31571846   PMID:31645055   PMID:31696474   PMID:32223575  


Genomics

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:486
Count of miRNA genes:425
Interacting mature miRNAs:462
Transcripts:ENST00000502463, ENST00000518376, ENST00000519071
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 adipose tissue appendage entire extraembryonic component
High
Medium 1 10 3
Low 15 28 1 4 3 2 38 31 1
Below cutoff 1934 1553 992 267 1109 120 3571 1315 1952 199 1128 1031 159 1085 2195 3

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000502463
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8127,686,343 - 127,733,967 (-)Ensembl
RefSeq Acc Id: ENST00000518376
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8127,730,157 - 127,733,965 (-)Ensembl
RefSeq Acc Id: ENST00000519071
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8127,700,608 - 127,733,956 (-)Ensembl
RefSeq Acc Id: ENST00000672637
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8127,699,370 - 127,716,217 (-)Ensembl
RefSeq Acc Id: ENST00000672942
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl8127,730,157 - 127,738,987 (-)Ensembl
RefSeq Acc Id: NR_117101
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh388127,730,194 - 127,733,967 (-)NCBI
CHM1_18128,782,676 - 128,786,449 (-)NCBI
Sequence:
RefSeq Acc Id: NR_117102
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh388127,700,608 - 127,733,967 (-)NCBI
CHM1_18128,753,091 - 128,786,449 (-)NCBI
Sequence:
Promoters
RGD ID:15096263
Promoter ID:EPDNEWNC_H1103
Type:initiation region
Name:CASC11_1
Description:cancer susceptibility 11 [Source:HGNC Symbol;Acc:HGNC:48939]
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
GRCh388127,733,969 - 127,734,029EPDNEWNC

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 8q24.13-24.21(chr8:122454392-128513076)x3 copy number gain See cases [RCV000133620] Chr8:122454392..128513076 [GRCh38]
Chr8:123466631..129525322 [GRCh37]
Chr8:123535812..129594504 [NCBI36]
Chr8:8q24.13-24.21
pathogenic
GRCh38/hg38 8q22.1-24.3(chr8:94682154-145068656)x3 copy number gain See cases [RCV000134353] Chr8:94682154..145068656 [GRCh38]
Chr8:95694382..146294042 [GRCh37]
Chr8:95763558..146264846 [NCBI36]
Chr8:8q22.1-24.3
pathogenic
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 8q24.13-24.3(chr8:124498498-145068712)x3 copy number gain See cases [RCV000137346] Chr8:124498498..145068712 [GRCh38]
Chr8:125510739..146294098 [GRCh37]
Chr8:125579920..146264902 [NCBI36]
Chr8:8q24.13-24.3
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 8q22.1-24.3(chr8:97382873-145070385)x3 copy number gain See cases [RCV000140447] Chr8:97382873..145070385 [GRCh38]
Chr8:98395101..146295771 [GRCh37]
Chr8:98464277..146266575 [NCBI36]
Chr8:8q22.1-24.3
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 8q22.3-24.3(chr8:100867343-145070385)x3 copy number gain See cases [RCV000141694] Chr8:100867343..145070385 [GRCh38]
Chr8:101879571..146295771 [GRCh37]
Chr8:101948747..146266575 [NCBI36]
Chr8:8q22.3-24.3
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 8q22.3-24.3(chr8:103306336-145068712)x3 copy number gain See cases [RCV000142810] Chr8:103306336..145068712 [GRCh38]
Chr8:104318564..146294098 [GRCh37]
Chr8:104387740..146264902 [NCBI36]
Chr8:8q22.3-24.3
pathogenic|likely 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 8q24.13-24.3(chr8:124514090-145054634)x3 copy number gain See cases [RCV000148117] Chr8:124514090..145054634 [GRCh38]
Chr8:125526331..146280020 [GRCh37]
Chr8:125595512..146250824 [NCBI36]
Chr8:8q24.13-24.3
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 8q23.3-24.3(chr8:113580402-145054634)x3 copy number gain See cases [RCV000050638] Chr8:113580402..145054634 [GRCh38]
Chr8:114592631..146280020 [GRCh37]
Chr8:114661807..146250824 [NCBI36]
Chr8:8q23.3-24.3
pathogenic
GRCh38/hg38 8q24.21(chr8:127118340-127858575)x3 copy number gain See cases [RCV000050763] Chr8:127118340..127858575 [GRCh38]
Chr8:128130585..128870821 [GRCh37]
Chr8:128199767..128940003 [NCBI36]
Chr8:8q24.21
pathogenic
GRCh38/hg38 8q22.1-24.3(chr8:95606052-145054775)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053677]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053677]|See cases [RCV000053677] Chr8:95606052..145054775 [GRCh38]
Chr8:96618280..146280161 [GRCh37]
Chr8:96687456..146250965 [NCBI36]
Chr8:8q22.1-24.3
pathogenic
GRCh38/hg38 8q24.13-24.3(chr8:124514090-145054634)x3 copy number gain See cases [RCV000053678] Chr8:124514090..145054634 [GRCh38]
Chr8:125526331..146280020 [GRCh37]
Chr8:125595512..146250824 [NCBI36]
Chr8:8q24.13-24.3
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 8q24.21-24.23(chr8:126626164-137169427)x1 copy number loss See cases [RCV000054306] Chr8:126626164..137169427 [GRCh38]
Chr8:127638409..138181670 [GRCh37]
Chr8:127707591..138250852 [NCBI36]
Chr8:8q24.21-24.23
pathogenic

Additional Information

Database Acc Id Source(s)
COSMIC CASC11 COSMIC
Ensembl Genes ENSG00000249375 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000518376 ENTREZGENE
  ENST00000519071 ENTREZGENE
GTEx ENSG00000249375 GTEx
HGNC ID HGNC:48939 ENTREZGENE
Human Proteome Map CASC11 Human Proteome Map
NCBI Gene CASC11 ENTREZGENE
OMIM 617704 OMIM
RNAcentral URS000021F429 RNACentral
  URS0000392533 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-05-22 CASC11  cancer susceptibility 11    cancer susceptibility 11 (non-protein coding)  Symbol and/or name change 5135510 APPROVED
2017-01-31 CASC11  cancer susceptibility 11 (non-protein coding)    cancer susceptibility candidate 11 (non-protein coding)  Symbol and/or name change 5135510 APPROVED