ENST00000607033.1
Revision as of 13:33, 29 June 2016 by Chunlei Yu (talk | contribs)
TARID,shorted for TCF21 antisense RNA inducing promoter demethylation, spanning 3002 bp in 6q23.2, may function together with GADD45A, TDG, and TET proteins as part of a surveillance mechanism that protects TCF21 from hypermethylation and transcriptional silencing.
Contents
Annotated Information
Name
TARID: TCF21 antisense RNA inducing promoter demethylation(HGNC nomenclature)
Function
,_a_regulator_of_DNA_demethylation.jpg)
TARID interacts with both the TCF21 promoter and GADD45A (growth arrest and DNA-damage-inducible, alpha), a regulator of DNA demethylation. [1]
Model Depicting the Role of TARID in Regulation of TCF21[1]
TARID interacts with both the TCF21 promoter and GADD45A (growth arrest and DNA-damage-inducible, alpha), a regulator of DNA demethylation. GADD45A in turn recruits thymine-DNA glycosylase for base excision repair-mediated demethylation involving oxidation of 5-methylcytosine to 5-hydroxymethylcytosine in the TCF21 promoter by ten-eleven translocation methylcytosine dioxygenase proteins, which reveals a function of TARID, serving as a genomic address label for GADD45A-mediated demethylation of specific target genes[1].
Expression
| RT-PCR | Forward | Reverse |
|---|---|---|
| TARID | CGGTCACCACTTCTTTCAGG | CGTATGTGAAGACAAAGGCAAC |
| RT-qPCR | Forward | Reverse |
|---|---|---|
| TCF21 | CATTCACCCGGTCAACCT | TCAGGTCACTCTCGGGTTTC[1] |
| TARID | AAATGAAGACAAGTGCTTCCTAGAAT | TTAGGGTGGATGTGGTCATTTA[1] |
| HPRT1 | TGACACTGGCAAAACAATGCA | GGTCCTTTTCACCAGCAAGCT[1] |
| SDHA | TGGGAACAAGAGGGCATCTG | CCACCACTGCATCAAATTCATG[1] |
| rRNA | AGTCGGGTTGCTTGGGAATGC | CCCTTACGGTACTTGTTGACT[1] |
| GADD45A | GAGAGCAGAAGACCGAAAGG | TGACTCAGGGCTTTGCTGA[1] |
| GADD45B | AGTCGGCCAAGTTGATGAAT | CCTCCTCCTCCTCGTCAAT[1] |
| XPA | GACACAGGAGGAGGCTTCATT | GCTTGTGTTTATCATCAGCATCTC[1] |
| XPC | TAAAGGGGTCCATGAGGACA | TGGCTGCAGATGTTATTTCG[1] |
| XPF | CCACTGACACTCGGAAAGC | CACGCATATCCACAACTATGC[1] |
| XPG | TGAATCTCTGTTTCCTGTATTAAAGC | AAGGAATCAATTCGGAGCTG[1] |
| TDG | ATGCAGCAGTGAACCTTGTG | GGAATTTGGTCTGTAAATGACTGG[1] |
| TET1 | TGTTGTGCCTCTGGAGGTTA | TCTGACTTGGGGCCATTTAC[1] |
| TET2 | TAGAAAGGAGACCCGACTGC | AGGGTGTGCTGCTGAATGTT[1] |
| TET3 | AAGTAGGGCAACTGGGCTTT | GGACAATCCACCCTTCAGAG[1] |
Labs working on this lncRNA
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany[1].
References
- ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 1.15 1.16 1.17 1.18 Arab K, Park YJ, Lindroth AM, Schafer A, Oakes C, Weichenhan D, et al. Long noncoding RNA TARID directs demethylation and activation of the tumor suppressor TCF21 via GADD45A[J]. Molecular cell. 2014,55(4):604-14.
Basic Information
| Transcript ID |
ENST00000607033.1 |
| Source |
Gencode19 |
| Same with |
' |
| Classification |
antisense |
| Length |
2960 nt |
| Genomic location |
chr6-:133823390..134210120 |
| Exon number |
9 |
| Exons |
133823390..133823818,133827217..133827408,133828382..133828459,133856918..133858496,133889328..133889386,134081323..134081398,134089969..134090061,134167015..134167089,134209742..134210120 |
| Genome context |
|
| Sequence |
000001 CAGACCCTGA TTTGCAACTT GTAATGTAAA TCAACTCAAC TGCATCATGT ACTTACCAGC CACCTTCTCC CAACTGTGGC 000080
000081 CGGGGCCGAG AAGCAGCATG TTCTGTCCAT CTGTAAAAGG CCTTCTTTCT CTCTTAAGAC GTCACAACTG GTTGTTACTG 000160 000161 AGAACTTTAG AAAAACGACT AGATCGTTTG GCTCTTTCTG GGCCTTCCAC CTACACTCCA TGCCCTCTCT CCTCCCAAGA 000240 000241 AAACACGAAT TAAAATACAG GGAGTATCAA CCGCATCCTG CCAACACCTC ATAAGACTCC AAGGCTTTAC CGAGATCTTC 000320 000321 CACCTTCCCC GGGATAAATG AAGACAAGTG CTTCCTAGAA TCTTTATGGT GATGGAAAAG ATATACTAAA AGAAGACAGA 000400 000401 TCAGTCTCTC TCCTGATAAG AAGAGTCACC AAGAGGAACA TCTGCAACAA CTAGATGCTG CTACAAAGAG ACCAATCAAC 000480 000481 AACTGCTCAG CAGAGATACA GATCTGAAGC ACAGAAGTGC AATAGACCTT CCTGATGCCT TCGCCAGGAG CATGGAATTC 000560 000561 TTCCCAGAGT CACAGAAGAT GGCACAGCCT GGGGACAATT GGGAATCACC TGGAGGATGG CAGACAACAC GAACCTGCAA 000640 000641 GTAATCATCC GACCAACTTC CTCTACTGCT TGGGAATTGC AGGTTGTATA ATCTTGGGAG GTCACTTCAA CTATACAATT 000720 000721 GGACTAAGAA CACTGACTCT CGTGGGTGTT ATAATTAAAT CAGGTAATAT ATGGTAAGGT AAGCATTGAT TAGTCTCTTC 000800 000801 ATTAGTTGAT TAGCCTCTTC AAATGTTAGT TTGATTAGTC TCTTCAAACG TTAGTTTCCT TCCTCTTTTC AGTATGCTCG 000880 000881 CTGAAAAGCT GGCTACAGAG CGAGTGACTG AATCAAAGCA TCACATCCTA CATGCTCCCA TTCCCCATCT TGCTACAGTG 000960 000961 GTACCAGCTT CTGTGCCCAG AAGATGGTGC TGTGGTTGGA TGAATAAAAC AATTACAGGG CCTTCAAGGA TAAGAAGAAG 001040 001041 GAACATGGAT AAATATCCCC ATTCTGCCTA GACAGAAATA AGAAAAACAT TCCCTTTTCT CTTCTTTAAA ACGAATTCTT 001120 001121 GAGTCATGCA TGGCAACAAT ATGTGTTGCC AAAAGTGGCC AGTTTGTGGT AGTAGGTTTT ATTCAGAAAA TCAGTGGGTG 001200 001201 ATGAAAATTT AGAAGATGCA CTCATCATTT GTAAAACTGT AGATGAAAGT TTAAAAGATG ATGTTATACC ACTTTTTCTT 001280 001281 CACTGCCCTC ATCAGTGGCT CCATCCCACC CTCCTGCTGT TCTCATAACT GATGTAGAAA TAATTTCATG AGCCAAACAG 001360 001361 GATGGTTTTA TACGTGTGTG TTTGGCATTA ACTTTATTTC CTATTCACGT ACCAGATATT ACTGCCCGCT CTTATGAAAT 001440 001441 AGTTTATTCC ACCATAAATG TATGTTTTAA TGATCACCAC ATTTTTTTGG AATACATTAA TCTGTCTAAA AATAGGTGAT 001520 001521 TAAATCATCT GTCATTCTGC TGTGAAGCTC TTTAATGTTT TCTTTGGGAA ATAAATTAGA ATGCCATATT GGTTTCCAAG 001600 001601 CAGACATAAG CTGGCGATGA CTTTTTTGTA CAAAAGTTAC TGATGAAAAG CTCATAGAGG CATTTGGATT TCTTCAGGGT 001680 001681 TGTAAATCCA GGTATGTTAC TACTTTATCT ACTGGAAATT GGGGTAATGC AGGAGATGGG AAAGCATGAT GTTAAATCAA 001760 001761 CTGGTGACCC CAAATAATTT TCCATGGTGT TCATCAGCCA TGCACACACT GTATTACTGT CATCATTCCT AGCTTTTCCA 001840 001841 CTATGCTGTC TCAAGTTTGC ACAAATTGTA AGTGATTTTA AATCATTAAC TGATGTGACA TAATCAAATT ACTTAGGGTT 001920 001921 TTATTTACTG TGCTCCGAGT AATTCAGTTA TGACTTGGCA AGGTATTTAA CAGACAATAG TGAAGTTACT ACAAATTCAA 002000 002001 CTTTGCATTG GACAACTCCA TTTGAGGATA CCACCACCTT CAAATTAACA ATTCCAGAAA CTGGTCTCAG TATCTCGTTC 002080 002081 CAACAACAAG CATCACCCAC TACAATAAAA ACAGCAAGTA GAATCTTTTT ACTTCTTTTG TGTTTCTCAT CTCGGCAAAC 002160 002161 TGCACTACAA TCTACCAAAC TGCCCGAGCC AGAAACCTAG AGGTCAGGCT GGATTTTCCT GAGGACATGA GGTGAAGAAG 002240 002241 CAACCACTGC GAAGTACTAA GCAAAGGATG GGTCAGAAGT ATGTGCTCTG GAGCCACGCA AATCTGCTTC AAATTCCAGT 002320 002321 TCTGCCATTT AGATAGCAGG TTATCTACAG ATACAGAAAC CATCTAGGAG GTCTGGTGTT GGATACAACT ATTTGTACCT 002400 002401 TGTAAAATTC TTACCTCTAA ATCATTAAAA AACAAATGAG TATCAGCAAG ATTAAAAATC ATTTCTTCCA TGCGGAGTCC 002480 002481 AAGGGTTACA GCCATGGGGG GATCCTGTAA AGAAAATGTA CACATAATGA GCTTACTAAG TCACTGGGAC AGCTAATTCT 002560 002561 AAGTGAGCAG ATTACAGCAC TGCATTTTTC CAGCTAAAGG ACTCACAGAT CCAAGAATCC CAGAAAGATG ACTGGACATT 002640 002641 TGGTGGGTGT AGCCTTAGCA ATGCTGGGCA CCCTCCATCT TGCCAAACTG CTGTGAGGGA GCTGCCAGCA CCTGCAATTC 002720 002721 CACTGTTTTA TCAGGCATGT GAGAATGAAA CATACTTCTG GATTGAACCC AAGTTTTATA CAGAGATGTT TGCTCATTTT 002800 002801 CATTAGATGT TTGTAGAATT ATGGGCACCT TATGAATCAA GAGTTGCTTT TTTTTAATTT GCATTTAAGT GTAGTGAATG 002880 002881 TTGAGTTTAG GGTCTAAAAT GAGGTGATAG CAAAATCTTG GATAGAGGAA AAAAGTGGGA TAATAAAGGC ACTAACAGGG 002960 |
