Difference between revisions of "DDX11-AS1"
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DDX11-AS1 (DDX11 antisense RNA 1) | DDX11-AS1 (DDX11 antisense RNA 1) | ||
===Synonyms=== | ===Synonyms=== | ||
| − | CONCR | + | CONCR, SCAT4 |
| − | [[File:CONCR Is a Nuclear lncRNA Negatively Regulated by p53 and Activated by MYC.jpg|right|thumb|400px|''' | + | [[File:CONCR Is a Nuclear lncRNA Negatively Regulated by p53 and Activated by MYC.jpg|right|thumb|400px|'''DDX11-AS1 is a nuclear lncRNA negatively regulated by p53 and activated by MYC'''<ref name="ref1" />]] |
| − | [[File:CONCR Is Upregulated in Multiple Cancer Types.jpg|right|thumb|400px|''' | + | [[File:CONCR Is Upregulated in Multiple Cancer Types.jpg|right|thumb|400px|'''DDX11-AS1 is upregulated in multiple cancer types'''<ref name="ref1" />]] |
===Chromosome=== | ===Chromosome=== | ||
12p11.21 | 12p11.21 | ||
===RefSeq(supplied by NCBI)=== | ===RefSeq(supplied by NCBI)=== | ||
NR_038927 | NR_038927 | ||
| − | === | + | ===LncBook transcript ID=== |
| − | + | HSALNT0288928 | |
===Characteristics=== | ===Characteristics=== | ||
DDX11-AS1 is a divergent non-overlapping transcript of the protein-coding gene DDX11, which is a predominant nuclear lncRNA. ChIP-seq data from ENCODE shows that MYC is bound to DDX11-AS1 promoter region in multiple cell types. | DDX11-AS1 is a divergent non-overlapping transcript of the protein-coding gene DDX11, which is a predominant nuclear lncRNA. ChIP-seq data from ENCODE shows that MYC is bound to DDX11-AS1 promoter region in multiple cell types. | ||
===Expression=== | ===Expression=== | ||
DDX11-AS1 is expressed in a panel of different human cell lines and upregulated in multiple cancer types. <ref name="ref1" /> | DDX11-AS1 is expressed in a panel of different human cell lines and upregulated in multiple cancer types. <ref name="ref1" /> | ||
| − | === | + | |
| + | The temporal expression of SCAT4, SCAT5, SCAT7, and SCAT8 elevated during S-phase in serum-starved Caki-2 cells<ref name="ref2" />. | ||
| + | |||
| + | ===Regulation=== | ||
DDX11-AS1 is negatively regulated by p53 and activated by MYC. <ref name="ref1" /> | DDX11-AS1 is negatively regulated by p53 and activated by MYC. <ref name="ref1" /> | ||
| + | |||
| + | ===Sequence=== | ||
| + | >NR_038927.2 Homo sapiens DDX11 antisense RNA 1 (DDX11-AS1), long non-coding RNA | ||
| + | <dnaseq>GCATGCGCACTCCGGGACGCGCGCGAACACGCAGCAGCGAGAATCTACAGGGGCGTGGTTTGCGCACGCG | ||
| + | GGAACTGGGATCTCAACCCCAGGGCTAGGTGCCTCCTCCCGCTGCTTTCCGCCAGCTGCGGGGTGTGAGA | ||
| + | TTAATCCCCGCCGATTAGCGCCAGGTGTACTAAGCGCTGGATGGTTCCCTGACCAGATGAAACATCAGCC | ||
| + | GATGTTCTAATGCCGGTCCCCTGGGCGCTGTCCCCGAGAGGGAAAACCTGTTTTCTGACCCCGGCTCTAG | ||
| + | TCGGCCTCTGGAGGTCTGCAGCTGGGTTATTTTACCTTTGAAACGGACGACACCTGCCCCGTGCACCCCA | ||
| + | GCGGCTCCTCCACACGGAGAGATGGTGTCAGTCAAAGGCCGTCTAGATGACGAGTTTATGAAATTGTTCC | ||
| + | TGGCCCGTGCCGGGCACGACCTTGCAGAGAGCCCAGAAGATGAAACCCCAGCCCTGCCAGGAGCTCACCT | ||
| + | GCTAATTAGGAGGACAACGAATCACCTCACCTCCCTAGACTTTGCTTCTCCTTTATTCAGTGAGGGATTG | ||
| + | GACTAGCTGGTCCTTGAGGACTTTTCAGAAAGTCTGGTTCTGGGAGATGACCAATGGGATCATCTTATGC | ||
| + | TATGAGCTTTCCTGGAATGACAGGTAATGGAGAGTGAGGAGATTTTACCTGATATGGTCCTGTTTGCACC | ||
| + | ATCAGCCAGCAACCTTTCTGGGAAGCGTGCTTATTATGTACCAACATAAAAGCTTGAATATAAGGAATCT | ||
| + | CACATCTTCTGCCAGCATCCTGAAACTATGGCAGACTCACTTGTTAACTTTGCAAATAAGGTCAAATTTC | ||
| + | AGAACCTTCACAGCTCCTGATAGTCACCGTGTAATAGAAGATTAAAAGACAAGCTCAGCTCTTGTTCCAG | ||
| + | TCAGCCTCATTCCTCTGCCTACAATACAAAAGTCACTCAATCATATTCTTGTCTTAAATTGAACAGTCCT | ||
| + | TACATGGTTAAGAAAAGGAGAAATTCATTGTAAGGAATGTTTACATTTTGTTTATAATTCCTGCAAGTGT | ||
| + | AATGTTTCAAAAGGTTTTCCTGTGGCTGAAGTACATTTACCCTGTGTAGCTCTAGAGAAATGAACTTACA | ||
| + | AACTGAAAAATTTCAGCTCAGTATATAAAGAAAAACAGATTTTCACAATTAGATCTATCCCAAAGAGAAT | ||
| + | AAATTTTGAGGTGATAAGCTCACTGCTGGCTTAGATCATCACTTATGGGACCTCTAATGGGGCAGGGATC | ||
| + | AGACTAGATGTGTACAAAGATCTCTTCCAACTGAAGCTGCTACTGTGGAGGACGTTGTTTTCAGTGGACT | ||
| + | CTCTAATCAGATTTATTTTCATACCAAGAAATGAAGAAGGTGAGCTGGGGGATGCAGCTGGGACTCAGAA | ||
| + | GACTGCACGTGATAGACTCATGAGCTGAAGATCTCGTGCTTAGTCTGGAGAAGCTCATCAAGTCTAGCTC | ||
| + | ACTTTGGAGTAAGTTGGTGCTGGAGAATGAATTCATGCTAACCAAATTCACCAAGAGCCTGATTTACAAA | ||
| + | TGAGAGAGCCAAGGCCTTAAGTTTAGAGCAAAAGACAAACTTCCAATGACTTTAGTTTTCTTGTCCAATA | ||
| + | TCTAGGGCACCTTCCCCTCTCCACCTGCTGTGTACACAGGAGAAATAATCACTCCACACCCGACTGAACA | ||
| + | TTTTCTAACCTTATCACTGTGGCAGAAACTGGCTACTCTTCCTCCTGGGTAGACAGCCAGGCTGTATTTC | ||
| + | CCCGCTGCCCCTGCAGTGAGAGGTAGCCATTGGAGCCGGCGCAGGCCAATGGACTCTGCACTGGAGTGAC | ||
| + | ACATGCTGCTTCCAGGCCTGTCCCTCAAACCTCCCACATGTCCTCTGTCTGCTCTTCTCACTTCCAAGGA | ||
| + | GTGTGACCATCGTGGAAGCCCCAGGTTAGCAATGGCAGATTGGGAGGCATCGATGGGAGGAACCTGGGTC | ||
| + | CCTGACTTAAAGCATCATGGATTTGGACTTTCCGTTATTGAGAAATAAACTTCCATTGTGTTTAAGCCTT | ||
| + | T</dnaseq> | ||
===Function=== | ===Function=== | ||
DDX11-AS1 contributes to tumor growth. <ref name="ref1" /> | DDX11-AS1 contributes to tumor growth. <ref name="ref1" /> | ||
| Line 23: | Line 59: | ||
Depletion of DDX11-AS1 causes sister chromatid cohesion defects | Depletion of DDX11-AS1 causes sister chromatid cohesion defects | ||
DDX11-AS1 interacts with DDX11 and regulates its function through enhancing the ATPase activity of DDX11.<ref name="ref1" /> | DDX11-AS1 interacts with DDX11 and regulates its function through enhancing the ATPase activity of DDX11.<ref name="ref1" /> | ||
| + | |||
| + | Depletion of the selected SCATs including SCAT4 in Caki-2 cells altered cell proliferation, inhibited cell cycle progression, and induced apoptosis <ref name="ref2" />. | ||
==Labs working on this lncRNA== | ==Labs working on this lncRNA== | ||
* Center for Applied Medical Research (CIMA), Department of Gene Therapy and Regulation of Gene Expression, University of Navarra, 55 Pio XII Avenue, 31008 Pamplona, Spain; Institute of Health Research of Navarra (IdiSNA), 31008 Pamplona, Spain. <ref name="ref1" /> | * Center for Applied Medical Research (CIMA), Department of Gene Therapy and Regulation of Gene Expression, University of Navarra, 55 Pio XII Avenue, 31008 Pamplona, Spain; Institute of Health Research of Navarra (IdiSNA), 31008 Pamplona, Spain. <ref name="ref1" /> | ||
*Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Boulevard, Baltimore, MD 21224, USA. <ref name="ref1" /> | *Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Boulevard, Baltimore, MD 21224, USA. <ref name="ref1" /> | ||
*Center for Applied Medical Research (CIMA), Department of Gene Therapy and Regulation of Gene Expression, University of Navarra, 55 Pio XII Avenue, 31008 Pamplona, Spain; Institute of Health Research of Navarra (IdiSNA), 31008 Pamplona, Spain. <ref name="ref1" /> | *Center for Applied Medical Research (CIMA), Department of Gene Therapy and Regulation of Gene Expression, University of Navarra, 55 Pio XII Avenue, 31008 Pamplona, Spain; Institute of Health Research of Navarra (IdiSNA), 31008 Pamplona, Spain. <ref name="ref1" /> | ||
| + | |||
==References== | ==References== | ||
<references> | <references> | ||
<ref name="ref1"> Marchese, F.P., et al., A Long Noncoding RNA Regulates Sister Chromatid Cohesion. Mol Cell, 2016. 63(3): p. 397-407. | <ref name="ref1"> Marchese, F.P., et al., A Long Noncoding RNA Regulates Sister Chromatid Cohesion. Mol Cell, 2016. 63(3): p. 397-407. | ||
</ref>(1) | </ref>(1) | ||
| + | <ref name="ref2"> | ||
| + | Ali MM, Akhade VS, Kosalai ST, Subhash S, Statello L, Meryet-Figuiere M, Abrahamsson J, Mondal T, Kanduri C. PAN-cancer analysis of S-phase enriched lncRNAs identifies oncogenic drivers and biomarkers. Nat Commun. 2018 Feb 28;9(1):883. | ||
| + | </ref>(2) | ||
</references> | </references> | ||
Latest revision as of 07:38, 13 August 2019
Contents
Annotated Information
Approved Symbol
DDX11-AS1 (DDX11 antisense RNA 1)
Synonyms
CONCR, SCAT4
DDX11-AS1 is a nuclear lncRNA negatively regulated by p53 and activated by MYC[1]
DDX11-AS1 is upregulated in multiple cancer types[1]
Chromosome
12p11.21
RefSeq(supplied by NCBI)
NR_038927
LncBook transcript ID
HSALNT0288928
Characteristics
DDX11-AS1 is a divergent non-overlapping transcript of the protein-coding gene DDX11, which is a predominant nuclear lncRNA. ChIP-seq data from ENCODE shows that MYC is bound to DDX11-AS1 promoter region in multiple cell types.
Expression
DDX11-AS1 is expressed in a panel of different human cell lines and upregulated in multiple cancer types. [1]
The temporal expression of SCAT4, SCAT5, SCAT7, and SCAT8 elevated during S-phase in serum-starved Caki-2 cells[2].
Regulation
DDX11-AS1 is negatively regulated by p53 and activated by MYC. [1]
Sequence
>NR_038927.2 Homo sapiens DDX11 antisense RNA 1 (DDX11-AS1), long non-coding RNA
000001 GCATGCGCAC TCCGGGACGC GCGCGAACAC GCAGCAGCGA GAATCTACAG GGGCGTGGTT TGCGCACGCG GGAACTGGGA 000080
000081 TCTCAACCCC AGGGCTAGGT GCCTCCTCCC GCTGCTTTCC GCCAGCTGCG GGGTGTGAGA TTAATCCCCG CCGATTAGCG 000160
000161 CCAGGTGTAC TAAGCGCTGG ATGGTTCCCT GACCAGATGA AACATCAGCC GATGTTCTAA TGCCGGTCCC CTGGGCGCTG 000240
000241 TCCCCGAGAG GGAAAACCTG TTTTCTGACC CCGGCTCTAG TCGGCCTCTG GAGGTCTGCA GCTGGGTTAT TTTACCTTTG 000320
000321 AAACGGACGA CACCTGCCCC GTGCACCCCA GCGGCTCCTC CACACGGAGA GATGGTGTCA GTCAAAGGCC GTCTAGATGA 000400
000401 CGAGTTTATG AAATTGTTCC TGGCCCGTGC CGGGCACGAC CTTGCAGAGA GCCCAGAAGA TGAAACCCCA GCCCTGCCAG 000480
000481 GAGCTCACCT GCTAATTAGG AGGACAACGA ATCACCTCAC CTCCCTAGAC TTTGCTTCTC CTTTATTCAG TGAGGGATTG 000560
000561 GACTAGCTGG TCCTTGAGGA CTTTTCAGAA AGTCTGGTTC TGGGAGATGA CCAATGGGAT CATCTTATGC TATGAGCTTT 000640
000641 CCTGGAATGA CAGGTAATGG AGAGTGAGGA GATTTTACCT GATATGGTCC TGTTTGCACC ATCAGCCAGC AACCTTTCTG 000720
000721 GGAAGCGTGC TTATTATGTA CCAACATAAA AGCTTGAATA TAAGGAATCT CACATCTTCT GCCAGCATCC TGAAACTATG 000800
000801 GCAGACTCAC TTGTTAACTT TGCAAATAAG GTCAAATTTC AGAACCTTCA CAGCTCCTGA TAGTCACCGT GTAATAGAAG 000880
000881 ATTAAAAGAC AAGCTCAGCT CTTGTTCCAG TCAGCCTCAT TCCTCTGCCT ACAATACAAA AGTCACTCAA TCATATTCTT 000960
000961 GTCTTAAATT GAACAGTCCT TACATGGTTA AGAAAAGGAG AAATTCATTG TAAGGAATGT TTACATTTTG TTTATAATTC 001040
001041 CTGCAAGTGT AATGTTTCAA AAGGTTTTCC TGTGGCTGAA GTACATTTAC CCTGTGTAGC TCTAGAGAAA TGAACTTACA 001120
001121 AACTGAAAAA TTTCAGCTCA GTATATAAAG AAAAACAGAT TTTCACAATT AGATCTATCC CAAAGAGAAT AAATTTTGAG 001200
001201 GTGATAAGCT CACTGCTGGC TTAGATCATC ACTTATGGGA CCTCTAATGG GGCAGGGATC AGACTAGATG TGTACAAAGA 001280
001281 TCTCTTCCAA CTGAAGCTGC TACTGTGGAG GACGTTGTTT TCAGTGGACT CTCTAATCAG ATTTATTTTC ATACCAAGAA 001360
001361 ATGAAGAAGG TGAGCTGGGG GATGCAGCTG GGACTCAGAA GACTGCACGT GATAGACTCA TGAGCTGAAG ATCTCGTGCT 001440
001441 TAGTCTGGAG AAGCTCATCA AGTCTAGCTC ACTTTGGAGT AAGTTGGTGC TGGAGAATGA ATTCATGCTA ACCAAATTCA 001520
001521 CCAAGAGCCT GATTTACAAA TGAGAGAGCC AAGGCCTTAA GTTTAGAGCA AAAGACAAAC TTCCAATGAC TTTAGTTTTC 001600
001601 TTGTCCAATA TCTAGGGCAC CTTCCCCTCT CCACCTGCTG TGTACACAGG AGAAATAATC ACTCCACACC CGACTGAACA 001680
001681 TTTTCTAACC TTATCACTGT GGCAGAAACT GGCTACTCTT CCTCCTGGGT AGACAGCCAG GCTGTATTTC CCCGCTGCCC 001760
001761 CTGCAGTGAG AGGTAGCCAT TGGAGCCGGC GCAGGCCAAT GGACTCTGCA CTGGAGTGAC ACATGCTGCT TCCAGGCCTG 001840
001841 TCCCTCAAAC CTCCCACATG TCCTCTGTCT GCTCTTCTCA CTTCCAAGGA GTGTGACCAT CGTGGAAGCC CCAGGTTAGC 001920
001921 AATGGCAGAT TGGGAGGCAT CGATGGGAGG AACCTGGGTC CCTGACTTAA AGCATCATGG ATTTGGACTT TCCGTTATTG 002000
002001 AGAAATAAAC TTCCATTGTG TTTAAGCCTT T
000081 TCTCAACCCC AGGGCTAGGT GCCTCCTCCC GCTGCTTTCC GCCAGCTGCG GGGTGTGAGA TTAATCCCCG CCGATTAGCG 000160
000161 CCAGGTGTAC TAAGCGCTGG ATGGTTCCCT GACCAGATGA AACATCAGCC GATGTTCTAA TGCCGGTCCC CTGGGCGCTG 000240
000241 TCCCCGAGAG GGAAAACCTG TTTTCTGACC CCGGCTCTAG TCGGCCTCTG GAGGTCTGCA GCTGGGTTAT TTTACCTTTG 000320
000321 AAACGGACGA CACCTGCCCC GTGCACCCCA GCGGCTCCTC CACACGGAGA GATGGTGTCA GTCAAAGGCC GTCTAGATGA 000400
000401 CGAGTTTATG AAATTGTTCC TGGCCCGTGC CGGGCACGAC CTTGCAGAGA GCCCAGAAGA TGAAACCCCA GCCCTGCCAG 000480
000481 GAGCTCACCT GCTAATTAGG AGGACAACGA ATCACCTCAC CTCCCTAGAC TTTGCTTCTC CTTTATTCAG TGAGGGATTG 000560
000561 GACTAGCTGG TCCTTGAGGA CTTTTCAGAA AGTCTGGTTC TGGGAGATGA CCAATGGGAT CATCTTATGC TATGAGCTTT 000640
000641 CCTGGAATGA CAGGTAATGG AGAGTGAGGA GATTTTACCT GATATGGTCC TGTTTGCACC ATCAGCCAGC AACCTTTCTG 000720
000721 GGAAGCGTGC TTATTATGTA CCAACATAAA AGCTTGAATA TAAGGAATCT CACATCTTCT GCCAGCATCC TGAAACTATG 000800
000801 GCAGACTCAC TTGTTAACTT TGCAAATAAG GTCAAATTTC AGAACCTTCA CAGCTCCTGA TAGTCACCGT GTAATAGAAG 000880
000881 ATTAAAAGAC AAGCTCAGCT CTTGTTCCAG TCAGCCTCAT TCCTCTGCCT ACAATACAAA AGTCACTCAA TCATATTCTT 000960
000961 GTCTTAAATT GAACAGTCCT TACATGGTTA AGAAAAGGAG AAATTCATTG TAAGGAATGT TTACATTTTG TTTATAATTC 001040
001041 CTGCAAGTGT AATGTTTCAA AAGGTTTTCC TGTGGCTGAA GTACATTTAC CCTGTGTAGC TCTAGAGAAA TGAACTTACA 001120
001121 AACTGAAAAA TTTCAGCTCA GTATATAAAG AAAAACAGAT TTTCACAATT AGATCTATCC CAAAGAGAAT AAATTTTGAG 001200
001201 GTGATAAGCT CACTGCTGGC TTAGATCATC ACTTATGGGA CCTCTAATGG GGCAGGGATC AGACTAGATG TGTACAAAGA 001280
001281 TCTCTTCCAA CTGAAGCTGC TACTGTGGAG GACGTTGTTT TCAGTGGACT CTCTAATCAG ATTTATTTTC ATACCAAGAA 001360
001361 ATGAAGAAGG TGAGCTGGGG GATGCAGCTG GGACTCAGAA GACTGCACGT GATAGACTCA TGAGCTGAAG ATCTCGTGCT 001440
001441 TAGTCTGGAG AAGCTCATCA AGTCTAGCTC ACTTTGGAGT AAGTTGGTGC TGGAGAATGA ATTCATGCTA ACCAAATTCA 001520
001521 CCAAGAGCCT GATTTACAAA TGAGAGAGCC AAGGCCTTAA GTTTAGAGCA AAAGACAAAC TTCCAATGAC TTTAGTTTTC 001600
001601 TTGTCCAATA TCTAGGGCAC CTTCCCCTCT CCACCTGCTG TGTACACAGG AGAAATAATC ACTCCACACC CGACTGAACA 001680
001681 TTTTCTAACC TTATCACTGT GGCAGAAACT GGCTACTCTT CCTCCTGGGT AGACAGCCAG GCTGTATTTC CCCGCTGCCC 001760
001761 CTGCAGTGAG AGGTAGCCAT TGGAGCCGGC GCAGGCCAAT GGACTCTGCA CTGGAGTGAC ACATGCTGCT TCCAGGCCTG 001840
001841 TCCCTCAAAC CTCCCACATG TCCTCTGTCT GCTCTTCTCA CTTCCAAGGA GTGTGACCAT CGTGGAAGCC CCAGGTTAGC 001920
001921 AATGGCAGAT TGGGAGGCAT CGATGGGAGG AACCTGGGTC CCTGACTTAA AGCATCATGG ATTTGGACTT TCCGTTATTG 002000
002001 AGAAATAAAC TTCCATTGTG TTTAAGCCTT T
Function
DDX11-AS1 contributes to tumor growth. [1] Expression of DDX11-AS1 is periodic in the cell cycle and its presence is required for efficient G1/S transition and DNA replication.[1] Depletion of DDX11-AS1 causes sister chromatid cohesion defects DDX11-AS1 interacts with DDX11 and regulates its function through enhancing the ATPase activity of DDX11.[1]
Depletion of the selected SCATs including SCAT4 in Caki-2 cells altered cell proliferation, inhibited cell cycle progression, and induced apoptosis [2].
Labs working on this lncRNA
- Center for Applied Medical Research (CIMA), Department of Gene Therapy and Regulation of Gene Expression, University of Navarra, 55 Pio XII Avenue, 31008 Pamplona, Spain; Institute of Health Research of Navarra (IdiSNA), 31008 Pamplona, Spain. [1]
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Boulevard, Baltimore, MD 21224, USA. [1]
- Center for Applied Medical Research (CIMA), Department of Gene Therapy and Regulation of Gene Expression, University of Navarra, 55 Pio XII Avenue, 31008 Pamplona, Spain; Institute of Health Research of Navarra (IdiSNA), 31008 Pamplona, Spain. [1]
References
- ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 Marchese, F.P., et al., A Long Noncoding RNA Regulates Sister Chromatid Cohesion. Mol Cell, 2016. 63(3): p. 397-407.
- ↑ 2.0 2.1 Ali MM, Akhade VS, Kosalai ST, Subhash S, Statello L, Meryet-Figuiere M, Abrahamsson J, Mondal T, Kanduri C. PAN-cancer analysis of S-phase enriched lncRNAs identifies oncogenic drivers and biomarkers. Nat Commun. 2018 Feb 28;9(1):883.
