CCAT1 (colon cancer associated transcript 1) - Rat Genome Database

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Gene: CCAT1 (colon cancer associated transcript 1) Homo sapiens
Analyze
Symbol: CCAT1
Name: colon cancer associated transcript 1
RGD ID: 7241106
HGNC Page HGNC
Description: This gene produces a long non-coding RNA that promotes tumor formation and is upregulated in colon cancer and other cancer cell types. This transcript may regulate long range chromosomal interactions, including at the Myc oncoprotein locus. This RNA may also function as a molecular sponge for microRNAs. [provided by RefSeq, Dec 2017]
Type: ncrna
RefSeq Status: REVIEWED
Also known as: CARLo-5; CARLO5; colon cancer associated transcript 1 (non-protein coding); onco-lncRNA-40
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh388127,207,382 - 127,219,268 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh378128,219,627 - 128,231,513 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map8q24.21NCBI
HuRef8123,537,365 - 123,549,068 (-)NCBIHuRef
CHM1_18128,259,773 - 128,271,659 (-)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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

References - curated
1. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:14702039   PMID:21547902   PMID:23143645   PMID:23416875   PMID:23594791   PMID:24594601   PMID:24662484   PMID:25129441   PMID:25185650   PMID:25569100   PMID:25674211   PMID:25864709  
PMID:25884472   PMID:26191246   PMID:26225650   PMID:26433964   PMID:26464701   PMID:26752646   PMID:26823726   PMID:26825578   PMID:26923190   PMID:27134049   PMID:27212446   PMID:27432114  
PMID:27566568   PMID:27638771   PMID:27765628   PMID:27830017   PMID:27956498   PMID:28078015   PMID:28088735   PMID:28184029   PMID:28239816   PMID:28358263   PMID:28381168   PMID:28387907  
PMID:28409554   PMID:28413645   PMID:28470345   PMID:28475287   PMID:28549102   PMID:28594897   PMID:28631575   PMID:28719351   PMID:28724210   PMID:28754469   PMID:28777430   PMID:28838211  
PMID:28849215   PMID:28921383   PMID:28978096   PMID:29020498   PMID:29024383   PMID:29050269   PMID:29163801   PMID:29190961   PMID:29228867   PMID:29231252   PMID:29424889   PMID:29565477  
PMID:29666003   PMID:29863242   PMID:29940756   PMID:30190462   PMID:30221381   PMID:30222365   PMID:30519593   PMID:30535444   PMID:30615124   PMID:30633886   PMID:30773676   PMID:30943439  
PMID:31039730   PMID:31093977   PMID:31114981   PMID:31218739   PMID:31310241   PMID:31387890   PMID:31478245   PMID:31544294   PMID:31599709   PMID:31661565   PMID:31695775   PMID:31790145  
PMID:31935379   PMID:32009633   PMID:32089062   PMID:32124583   PMID:32173521   PMID:32227563   PMID:32243922   PMID:32323859   PMID:32380476   PMID:32413192   PMID:33023331  


Genomics

Position Markers
SHGC-34702  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh378128,220,115 - 128,220,253UniSTSGRCh37
Build 368128,289,297 - 128,289,435RGDNCBI36
Celera8124,400,061 - 124,400,199RGD
HuRef8123,537,851 - 123,537,989UniSTS
TNG Radiation Hybrid Map862994.0UniSTS
Stanford-G3 RH Map27569.0UniSTS
NCBI RH Map21448.5UniSTS
GeneMap99-G3 RH Map28424.0UniSTS


Expression


Sequence


Reference Sequences
RefSeq Acc Id: NR_108049
RefSeq Status: REVIEWED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh388127,207,382 - 127,219,268 (-)NCBI
HuRef8123,537,363 - 123,549,248 (-)NCBI
CHM1_18128,259,773 - 128,271,659 (-)NCBI
Sequence:

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

Additional Information

Database Acc Id Source(s)
COSMIC CCAT1 COSMIC
GTEx CCAT1 GTEx
HGNC ID HGNC:45128 ENTREZGENE
Human Proteome Map CCAT1 Human Proteome Map
NCBI Gene CCAT1 ENTREZGENE
OMIM 617705 OMIM
RNAcentral URS000075ADFF RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-05-22 CCAT1  colon cancer associated transcript 1    colon cancer associated transcript 1 (non-protein coding)  Symbol and/or name change 5135510 APPROVED