ENST00000604200.1

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Please cite: Chunlei Yu (2015) lncRNA: "ENST00000604200.1" in LncRNAWiki, available at http://lncrna.big.ac.cn/index.php?title=ENST00000604200.1&oldid=1270706 (Last update: Apr 10, 2015). [See details]

CAHM(Colorectal Adenocarcinoma HyperMethylated), which is located about 730bp upstream of the adjacent gene, QKI, shows specially hypermethylated in colorectal neoplasia.

Contents

Annotated Information

Name

CAHM: colon adenocarcinoma hypermethylated(non-protein coding)(HGNC nomenclature)

LINC00468, "long intergenic non-protein coding RNA 468"[1]

Characteristics

CAHM is located adjacent to the gene QKI.[1]

Function

Level of hypermethylated CAHM DNA in blood plasma. [1].

CAHM shows specially hypermethylated in colorectal neoplasia compared with lung, prostate and breast cancer[1].

The levels of hypermethylated CAHM of CRC patients are increased in blood than normals. Moreover, the increaseing levels of mythylated CAHM is correlated with advancing disease stage. According to these results, CAHM may act as a potential marker for CRC substypes.


Expression

Expression of CAHM RNA in colorectal tissue. [1]

It has been found that CAHM and its neighboring gene QKI are both downregulated in colorectal neoplasia because of hypermethylation, which suggests their high positive correlation.

Input Material Gene targets Oligonucleotides
Deep Sequencing
BisDNA CAHM Region A

A1:5’-ATt TGT AAA AAT GTT GAt TTt TGt TTT TtA Gat-3’ A2:5’-TCT TaT TaC ACC TTC CCR TTA TTC Ta-3’[1]

CAHM Region B

B1:5’-GtY GTG tTG tTT Ttt AGt tTt TtA GtA AAT t-3' B2:5’-CAC RaT aCR aAa aaC Taa Taa aCT TTC CTT a-3’[1]

Bisulphite conversion dependent quantitative PCR
BisDNA CAHM (within Region A)

1:5’-GAA GGA AGt AAT TCG AGt ACG AtT GAC-3’ 2:5’-CCC gaA CGC AaC GaC TTA a-3’[1]

RNA expression
cDNA CAHM 2.1:5’-AGG GGA GCG TCA GTC GTG CT-3 ’

2.2:5’-TGC GGC TTC ATT CCC TCA CGG-3’[1]

Diseases

  • colorectal adenocarcinoma[1]


Labs working on this lncRNA

  • Clinical Genomics Pty Ltd; North Ryde, NSW Australia.[1].

References

  1. 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 Pedersen SK, Mitchell SM, Graham LD, McEvoy A, Thomas ML, Baker RT, et al. CAHM, a long non-coding RNA gene hypermethylated in colorectal neoplasia[J]. Epigenetics : official journal of the DNA Methylation Society. 2014,9(8):1071-82.


Basic Information

Transcript ID

ENST00000604200.1

Source

Gencode19

Same with

CAHM ,LINC00468

Classification

intergenic

Length

896 nt

Genomic location

chr6-:163834097..163834992

Exon number

1

Exons

163834097..163834992

Genome context

Sequence
000001 CCCCGGAGCG CGCCTGCGTG GGGCGGGGGC GGCAGCCGAC TAGGGGCTGG GTCTGGCCGT TTAGGGCCGG GTCTTGGCCC 000080
000081 GTCGCCCACG GTGCGGAGGG CTGGTGGGCT TTCCTTGGCC GTCGGGCCCG CCACGGCGCG GGTCTTGGCT GCGGGGCGGA 000160
000161 GGTGGGGCGG GAGAGCCGAG GATAAGAGTT TGAGGCTTTT CGAGGCGCGT GCCGCGGCGT CCGCCTCTGC GGGACTCTGC 000240
000241 GCCGGGCGCC CTCGGCCGGC GCGCCCGGCT CCCGCTTTGT CGCCGAGGGA AGCACGCGCG ACGCCCCTCC CGTCGCCGCC 000320
000321 GTGGCTTCTT TCGGTGTTCG TGATTTGCTG AGAGGCTGGA AAGCAGCACG GCGGAGAGGA GCCTTGCACT CGCCAGGCGG 000400
000401 GAAGCCTGCG CGGACACGCG TGCGCACCCA CGGGGCGGCG GGCGGGCGTG GGGGGTCCGG GCCACGCGGG CGACGCGCCT 000480
000481 CTAGGGAAGC GATCTTGTTG CACCTTCCCG TTATTCTGAA AGCAAATCGT AGCCAGACCC GAGCGCAGCG GCTTAGCAAA 000560
000561 TAATAAGGGG AGCGTCAGTC GTGCTCGAAA TGCTTCCTTC GCGATGGCGT CAGTGTTCCG TGAGGGAATG AAGCCGCAGT 000640
000641 AGGAAATAAA GAGGCTGTGC GCGTAGTCTG AAAAGCAGAA GTCAACATTT TTACAGATGA AGAAAGAATA CGGAGGCAAG 000720
000721 AGGTCTTTCT CTGCAGTTTG GTGGATTTCC AACATTTAGA CTTGTTTGGA AGAATTTCCT CAGCTGCACC AATGAAGTCC 000800
000801 TTGATCTATA GAAGTCGGCA GTCCCTAAAT CTACGTCTGC ATTTTGTTGC AAATCCTTTA TAACATTCCA TTAAAATAAT 000880
000881 GCAGAGTTAT TTAATA
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Please cite: Chunlei Yu (2015) lncRNA: "ENST00000604200.1" in LncRNAWiki, available at http://lncrna.big.ac.cn/index.php?title=ENST00000604200.1&oldid=1270706 (Last update: Apr 10, 2015).
ContributorContribution Score*Edit Count#Summed Edit QuantityΛAveraged Edit QualityLatest Edit TimeEdit Details
Chunlei Yu2.135122910.9322015-04-08 22:01:01[show]
Contributors with score < 1 are excluded from the authorship.
ContributorContribution Score*Edit Count#Summed Edit QuantityΛAveraged Edit QualityLatest Edit TimeEdit Details
Lina Ma0.159115912015-04-10 15:49:58[show]
Note: For each edit version that is contributed by a specific person, his/her contribution is quantified as its edit quality multiplied by its edit quantity; the edit quantity amounts to the edit distance in comparsion with its previous version (that is, the minimum number of edit operations required to transform one string into the other), and the edit quality corresponds to whether the edit persists in comparison with the last version, ranging from -1, when the edit is entirely reverted (short-lived), to 1, indicating that the edit is totally preserved in the last version (long-lived). Please also note that contribution quantification may take time to reflect recent edits.
*Since one person may perform many discontinuous edits for a wiki page, contribution score is the sum of quantified contributions over all participated edits.
#Multiple successive edits provided by a researcher are counted as one edit.
ΛSummed edit quantity is the sum of edit quantities over all participated edits.
Averaged edit quality is the edit quality normalized over all participated edits.
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