Difference between revisions of "NONHSAT056039"
Chunlei Yu (talk | contribs) |
Chunlei Yu (talk | contribs) (→Labs working on this lncRNA) |
||
| Line 38: | Line 38: | ||
==Labs working on this lncRNA== | ==Labs working on this lncRNA== | ||
*Division of Biochemistry and Innovative Cancer Therapeutics, Chiba Cancer Center Research Institute, Chiba 260-8717, Japan<ref name="ref1" /> | *Division of Biochemistry and Innovative Cancer Therapeutics, Chiba Cancer Center Research Institute, Chiba 260-8717, Japan<ref name="ref1" /> | ||
| − | + | ||
* Department of Urology, the First affiliated Hospital of China Medical University, China<ref name="ref2" />. | * Department of Urology, the First affiliated Hospital of China Medical University, China<ref name="ref2" />. | ||
Revision as of 10:57, 21 April 2015
SNHG16,shorted forsmall nucleolar RNA host gene 16, which is located on 17q25.1 and has two splice variants, palys significant roles in cancers.
Contents
Annotated Information
Transcriptomic Nomeclature
SNHG16, small nucleolar RNA host gene 16(HGNC nomenclature)
ncRAN, "non-coding RNA expressed in aggressive neuroblastoma"[1]
Characteristics
ncRAN, non-coding RNA expressed in aggressive neuroblastoma (ncRAN), is located on 17q25.1 and has two splice variants, a long form (Nbla10727) and a short form (Nbla12061)[2]
Function
ncRAN may be a novel non-coding RNA mapped to the region of 17q gain and act like an oncogene in aggressive neuroblastomas[1].
ncRAN may play an important role in the pathogenesis of human bladder cancer, and may help in designing effective therapy targeting the ncRAN pathway to control bladder cancer growth and invasion[2]
ncRAN might represent a novel prognostic indicator, a biomarker for the early detection of metastasis and a target for gene therapy in CRC[3].
Expression
ncRAN expression is dramatically up-regulated and associated with poor prognosis in human neuroblastoma[1].
The primers of RT-PCR were as follows,
| primer | Forward | Reverse |
| ncRAN(long-form) | 5'-CAGTCAGCCTCAGTTTCCAA-3' | 5'-AGGCAGGGCTGTGCTGAT-3'[2] |
| ncRAN (short-form) | 5'-ATGTTAGCTCCCAGCGATGC-3' | 5'-CTAACTGCCAAAAGGTTTTCC-3'[2] |
Labs working on this lncRNA
- Division of Biochemistry and Innovative Cancer Therapeutics, Chiba Cancer Center Research Institute, Chiba 260-8717, Japan[1]
- Department of Urology, the First affiliated Hospital of China Medical University, China[2].
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Institute of Pathology, Fudan University, Shanghai, China[3].
References
- ↑ 1.0 1.1 1.2 1.3 Yu M, Ohira M, Li Y, Niizuma H, Oo ML, Zhu Y, et al. High expression of ncRAN, a novel non-coding RNA mapped to chromosome 17q25.1, is associated with poor prognosis in neuroblastoma[J]. International journal of oncology. 2009,34(4):931-8.
- ↑ 2.0 2.1 2.2 2.3 2.4 Zhu Y, Yu M, Li Z, Kong C, Bi J, Li J, et al. ncRAN, a newly identified long noncoding RNA, enhances human bladder tumor growth, invasion, and survival[J]. Urology. 2011,77(2):510 e1-5.
- ↑ 3.0 3.1 Qi P, Xu MD, Ni SJ, Shen XH, Wei P, Huang D, et al. Down-regulation of ncRAN, a long non-coding RNA, contributes to colorectal cancer cell migration and invasion and predicts poor overall survival for colorectal cancer patients[J]. Molecular carcinogenesis. 2014.
Basic Information
| Transcript ID |
NONHSAT056039 |
| Source |
NONCODE4.0 |
| Same with |
SNHG16, ncRAN |
| Classification |
intergenic |
| Length |
2538 nt |
| Genomic location |
chr17+:74553846..74561430 |
| Exon number |
4 |
| Exons |
74553846..74553939,74555027..74555125,74557370..74557484,74559201..74561430 |
| Genome context |
|
| Sequence |
000001 GCGTTCTTTT CGAGGTCGGC CGCGTGGCTG GAAGACATGG CCACTCCAGT CGGTGTTGAG CACGGCGAGC AGTCTCAGGC 000080
000081 CTTTAGTGAT GATGATTAAA GGTGGTGGCT GTGGCCTTGA AAACAGTCAT GTGAAAACTC ATCACCTTAA GGTGTTAAGT 000160 000161 GTAAGGATCT TCATGATGAA ATTTCTGTAA ATGGTGCAGT CAGCCTCAGT TTCCAAAGCC GGAAAAGGAT CCTCTAGTAG 000240 000241 CCACGGTGTG GCAGCTGCTC TGAACCAGGA CCTGGACCCG GACCCAAAGT GCCATGTCTT TAATGTGAGT TAGCTCCCAG 000320 000321 CGATGCCAGA TGGGATCAGC ACAGCCCTGC CTCTGCTGCT AATTGTTCCT CTAAAGTAAT CGCCATGCGT TCTTTGGGCT 000400 000401 TCATCTTTAA AGGAATGAAG CAACTGAGAT TATTCTGGAA AACCTTTTGG CAGTTAGTGA AATTAGAGTA CAACTAAGAA 000480 000481 CATTTTCAGA CCTCCACTGT GGATGACCTG GGTATAATCT CACAAATCGA TGGGACTGCA AGGATTGTAA ACTGAAATGA 000560 000561 ACATGATTAT ACTCTGTTGG AAGAGCCTAA GAGGAAACTG ATGCCATGAG TTTCAGAGAG TAATGCTTAA CCCCAGTTAC 000640 000641 ACAGGATGCC GTCTTGTGTT TCCTCTTGTT TAgttaccca ctacagtgat tttgtgatct gctaatgggt tgccacccac 000720 000721 aACCATTGCT TTAGCACTTT TACTTCAAAT CAATGAAGGA TTGATAAAAG TTCTCCTGGT GTCTCCGCAG AGTGCCTTCC 000800 000801 AGGAACAGAT CTTTGCATAG AATATCAGTG GTTTCCTTTT TTGTTTCAAA TAGTGGTCAG AAAATACCCA GTGTTGACTC 000880 000881 ACCAAGGCAA TCAGCTTCCT TTTTCCCttt ttttgttttt tttttaacat tttatatttt tgctttattt tattttattt 000960 000961 tattttattt tattttattt tattttattt tttgagacgg agttccactc tgtcgccagg ctggagtgaa gtggtacaat 001040 001041 cttggctcac tgcaacctcc acctcccggg ttcaagcaat tctcctggct cagcctcctg agtgctggga ctacaggcgc 001120 001121 gtaccttctt tagtagagac tgggtttcac catgttggcc aggatggtct ctatctcctg accttgtgat ctgcctgcct 001200 001201 cagcttccca aagtgctgag atgacaggtg tgagccatca gacccagcat tttttttttt aatttaaatt taaatttttt 001280 001281 ttcatttttt tgagaggttt tttttgtttt gttttgttgt tgttgttgtt gttgtttttg agacagtctt gctctgtcac 001360 001361 ccaggctggg agtgcagtgg catgatctct gcaacctcta cctcccaggt tcaagcaatt cttgtgcctc agcctcccaa 001440 001441 gtaactggga ctacaggtgc acgctaccac acctggctga ttttttttgt tttagtagag acagggtttc aaccatgttg 001520 001521 cccaggttgg tctcaaactc ctgagctcag gcaatccacc cgccttggcc tcccaaagtg ctaggattac aggtgtgagc 001600 001601 caccacaccc agcTAttttt tctttcgttt tttaatttta aagttggggg ggggtctcaa tttgttaccc tggctggtct 001680 001681 cgaactcccg gacttaagcg atcctcTGGC TCCAAGCCCA CTACCAGTCT CAGGTTTCTT TACTAAAAGA TCACTACCTT 001760 001761 TTTTtctctt atctgctgcc atgtgagatg tggctttcac cttccgccat gattgtgagg ccttcccagc catgtagaac 001840 001841 tgtaagtcca ataaacctct tttgtaaatt aAAAAAAAAA AATCACTATT TAAGATACTA GGATGGATTG TGACTGTTGA 001920 001921 GGAGTACTTA CATATCCTAC ATTTGACTAC ATTATTTCCA AACCAAGTAT TCCATCCAAA GGAACATACT GCTATCATAG 002000 002001 AGACCAAGGA GGGACTGTTT AAGGTTGCCA AGGTGAAGCG AGCTGAGAGG CTTTGTCCTC GTGCCAGTAA CTCTGAAATC 002080 002081 TCTCTTAATT CCTGCTGTCC AGGCAGCAGA ATGCCATGGT TTCCCCAAGT AGGTAGCTGC TTTAGCAGTT AAAGCCCAAA 002160 002161 TGTCTGTTCT GTTGATCAGA GGTCTCTGAA TTTCTGAAGT GGTGTTTCGT TTCTGGTGAC TGAGTTAATC CTTTACAATC 002240 002241 CCTCTTGTAA AGTGTGCTAA TAGAAAGAAT CCACCTTTCA AAGCTGCAGA ACCAGACCGT GCCCTAAATT GACCAACGTA 002320 002321 ACTGATGTGC CTCAGGAAGT CTCTTGCCAG CTGTCCCTGT GAAGACCCCC CTCCTCCCCC CCAGCTGCTG CCTTGCACAC 002400 002401 TGAAGCATCT CAGACTGTGC AAAGCCGTGT AGTCATCAAG ACAGTAAATC CCAGGGCTTG GTTAAGTGCT GTGTGATAAC 002480 002481 TTGTTTGGAT GAGACTTAAC TTAAAACCAC TTACAATAAA CTTGGGAAAC TACCGTCA |
