CCAT2 (colon cancer associated transcript 2) - Rat Genome Database

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Gene: CCAT2 (colon cancer associated transcript 2) Homo sapiens
Analyze
Symbol: CCAT2
Name: colon cancer associated transcript 2
RGD ID: 7247298
HGNC Page HGNC:47044
Description: This gene produces a long non-coding RNA that is upregulated in colon cancer and other cancers. This transcript promotes cell proliferation and suppresses apoptosis. It negatively regulates the biogenesis of microRNA 145. [provided by RefSeq, Dec 2017]
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: REVIEWED
Previously known as: colon cancer associated transcript 2 (non-protein coding); LINC00873; NCCP1
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh388127,400,399 - 127,402,150 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl8127,400,399 - 127,402,150 (+)EnsemblGRCh38hg38GRCh38
GRCh378128,412,644 - 128,414,395 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map8q24.21NCBI
HuRef8123,730,840 - 123,732,589 (+)NCBIHuRef
CHM1_18128,452,890 - 128,454,641 (+)NCBICHM1_1
T2T-CHM13v2.08128,527,937 - 128,529,688 (+)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:17401363   PMID:17618284   PMID:18264096   PMID:18264097   PMID:18372905   PMID:21242260   PMID:21743057   PMID:23266556   PMID:23796952   PMID:24077681   PMID:24504682   PMID:24740154  
PMID:24753544   PMID:24836286   PMID:25677908   PMID:25755774   PMID:25919911   PMID:26442763   PMID:26722527   PMID:26853146   PMID:26983975   PMID:27015551   PMID:27283598   PMID:27347113  
PMID:27470400   PMID:27558961   PMID:27830684   PMID:27833083   PMID:27875818   PMID:27904778   PMID:27938499   PMID:28088736   PMID:28089750   PMID:28244168   PMID:28248065   PMID:28263738  
PMID:28272713   PMID:28280353   PMID:28480695   PMID:28531944   PMID:28550684   PMID:28623646   PMID:28638466   PMID:28656228   PMID:28671055   PMID:28718366   PMID:28838211   PMID:28934601  
PMID:28964256   PMID:29088900   PMID:29176650   PMID:29181105   PMID:29298720   PMID:29329034   PMID:29393466   PMID:29502343   PMID:29525942   PMID:29567676   PMID:30877883   PMID:30922920  
PMID:30982978   PMID:31398859   PMID:31626095   PMID:31789385   PMID:31904506   PMID:32037568   PMID:32236863   PMID:32591878   PMID:32633397   PMID:32805281   PMID:32908615   PMID:33099922  
PMID:33125134   PMID:33336741   PMID:33432117   PMID:33475889   PMID:34515990   PMID:34830370   PMID:35115025   PMID:35968984   PMID:36103972   PMID:36375570   PMID:36482069   PMID:37347737  
PMID:37354353   PMID:37874495   PMID:38556336  


Genomics

Variants

.
Variants in CCAT2
2 total Variants

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 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 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 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
GRCh38/hg38 8q23.3-24.23(chr8:115586904-135607135)x3 copy number gain Neurodevelopmental disorder [RCV003327615] Chr8:115586904..135607135 [GRCh38]
Chr8:8q23.3-24.23		 pathogenic

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
High
Medium 1 1
Low 32 2 6 2 7 1 7 2 1 4 8 11 1 1
Below cutoff 861 571 668 169 350 42 2002 564 587 76 612 737 132 820 1050

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000630920
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl8127,400,399 - 127,402,150 (+)Ensembl
RefSeq Acc Id: NR_109834
RefSeq Status: REVIEWED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh388127,400,399 - 127,402,150 (+)NCBI
HuRef8123,730,840 - 123,732,589 (+)NCBI
CHM1_18128,452,890 - 128,454,641 (+)NCBI
T2T-CHM13v2.08128,527,937 - 128,529,688 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC CCAT2 COSMIC
Ensembl Genes ENSG00000280997 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000630920 ENTREZGENE
GTEx ENSG00000280997 GTEx
HGNC ID HGNC:47044 ENTREZGENE
Human Proteome Map CCAT2 Human Proteome Map
NCBI Gene CCAT2 ENTREZGENE
OMIM 619403 OMIM
RNAcentral URS000010576B RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-05-22 CCAT2  colon cancer associated transcript 2    colon cancer associated transcript 2 (non-protein coding)  Symbol and/or name change 5135510 APPROVED