Difference between revisions of "ENST00000506884.1"
| Line 1: | Line 1: | ||
| − | '' | + | ''PART1'',a 2495 bp long non-coding RNA, mapping to chromosome 5q12, functions a signature in cancers. |
==Annotated Information== | ==Annotated Information== | ||
| Line 8: | Line 8: | ||
===Characteristics=== | ===Characteristics=== | ||
| − | '' | + | ''PART1'',a 2495 bp long non-coding RNA, maps to chromosome 5q12<ref name="ref1" />. |
===Function=== | ===Function=== | ||
| Line 16: | Line 16: | ||
===Regulation=== | ===Regulation=== | ||
| − | + | PART1 is regulated by androgens in human prostate cancer cells<ref name="ref1" />. | |
===Expression=== | ===Expression=== | ||
Revision as of 05:14, 22 June 2016
PART1,a 2495 bp long non-coding RNA, mapping to chromosome 5q12, functions a signature in cancers.
Contents
Annotated Information
Transcriptomic Nomeclature
PART1:prostate androgen-regulated transcript 1 (non-protein coding)(HGNC nomenclature)
DKFZP586D0823, NCRNA00206, "non-protein coding RNA 206"[1]
Characteristics
PART1,a 2495 bp long non-coding RNA, maps to chromosome 5q12[1].
Function
PART1 was found to be significantly down-regulated in gliomas relative to normal brain tissues. PART1 is highly expressed in the human prostate gland . It has been suggested that this gene may play an important role in suppressing prostate carcinogenesis[2].
PART1 signature is a significant determinant of survival in GBM[2].
Regulation
PART1 is regulated by androgens in human prostate cancer cells[1].
Expression
RACE: Nested 5′-RACE reactions were performed with primers as follows,
| 14D7-196 L | 5'-GTGACGGTCTTGGACAGTAAGGG-3'[1] |
| 14D7-85 L | 5'-AGAGTATTGTTGGCTTTGTCTGTC-3'[1] |
Nested 5'-RACE followed by a second reaction using the first reaction product as a template and primers are as follows,
| 14D7RC3 | 5'-CTTTCCCCTCCGACAAGGAAGCTG-3'[1] |
| 14D7RC4 | 5'-CTCATCTGTGTTGTTCCAGTGCAGCC-3'[1] |
Chromosomal Localization of PART-1 by Radiation Hybrid Panel Mapping and by FISH: The G3 Gene bridge radiation hybrid panel was used to map the chromosomal localization of PART-1 with primers as follows,
| 14D7mapR | 5'-TGCTTTGTTAAGATGAGGCAGGC-3'[1] |
| 14D7mapF | 5'-CATTCCAGGTGTCATGGATAAAG-AGC-3'[1] |
Labs working on this lncRNA
- Department of Molecular Biotechnology, University of Washington, Seattle 98195, USA.[1]
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong.[2]
References
- ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 Lin B, White JT, Ferguson C, Bumgarner R, Friedman C, Trask B, et al. PART-1: a novel human prostate-specific, androgen-regulated gene that maps to chromosome 5q12[J]. Cancer research. 2000,60(4):858-63.
- ↑ 2.0 2.1 2.2 Zhang XQ, Sun S, Lam KF, Kiang KM, Pu JK, Ho AS, et al. A long non-coding RNA signature in glioblastoma multiforme predicts survival[J]. Neurobiology of disease. 2013,58:123-31.
Basic Information
| Transcript ID |
ENST00000506884.1 |
| Source |
Gencode19 |
| Same with |
lnc-AC109486.1-1:2,PART1 |
| Classification |
intergenic |
| Length |
2068 nt |
| Genomic location |
chr5+:59783967..59843484 |
| Exon number |
4 |
| Exons |
59783967..59784250,59825231..59825370,59829759..59829846,59841929..59843484 |
| Genome context |
|
| Sequence |
000001 ATAACAAGTC TAACTGGCTC TGGAAAGCTG AAAGGGCTGC ACTGGAACAA CACAGATGAG ATATTCTACA CATTAATCTA 000080
000081 CTTATCTGGA ATCACTTTGC CTCTAAAGGC CAGAGAAAAA TCACAGCTTC CTTGTCGGAG GGGAAAAGGA CAGGTGATCT 000160 000161 GGGGAAAACG CAGCTACACC TGGAGCAAGG TCTCTTCCCG GCTTGGCAAT CTCAGCTGTG CCGGCGCTAC GGGACCCGAG 000240 000241 CCGTCCCAGA AACCAAAGGG CAGGCACGGC AGCAAACGCC TGAGCCTGCC TTGTACTTCA TGCAGGTTGA ACAGAAATGT 000320 000321 TTTCTGAGCA TGTATTGTTA CAGCCCTCTG AGATGGTATA AAAGAATGAA AGAAGACACG ACCTGCCTTC CAGGAGTTTC 000400 000401 ACAAAAAAGA TGGGATGAAC ACAGTGTTCA CTTCCACCTT CCACCCTTTC ACTATGAAGG ACCCTCACCA GATGGTGGCA 000480 000481 CCATGCTCTC GGACTTCCCA GCCTCCAGAA CTGGACGGGT AAATTGAAGC AAAAAGCAGA CAAGTTCTAT GGGATTTGCT 000560 000561 GGCATTGATT TCCCAGGATG GCAAAGTGCT AAGAACTAAA CCTTTAAAGC TAACAAAATG TACTGATGTC TTTGCAAAGT 000640 000641 ATCCAAGACC AACAAGAAAG TAATTTCCCA CCTCACCCTA CCACCACCCA GAAAAGGAGC ACAGAGATGG GGAAGAGAGT 000720 000721 GGCTGCATCT GGCATCCAGC CAGAGGAGTC CGTGCAGGGA TTCTGGATCC CTCTTCCCCC ACCCCACTGC CCTTCCCCCT 000800 000801 CCACCCCAGC GTTTTGGAGA AGCAAGAAAC TGTGATGATG CAGCTCCCTC AAGTATCACA TGAAGATAGT GGAAAGAGCC 000880 000881 TCCTGAGGTA AATATGCCAT GTAGACAGAA ACAAGCAATG GCTCAACAGC AATGTATGAG GTCCAAGGAC CAGGACCAAA 000960 000961 GGGAAAAACA GCCATCTCAC CAGACACCTG CCTACGACCA GATGCGTCAT CTCCAATATT AGCTAACTCC CTGGAACCTG 001040 001041 GACTCAAGGT GTGAAATAAA GGTTAATGGG AAACCGCAGG AGTCAAAAGG AGGGGGCAGG ATTATTGAGG ATTCAGGCTG 001120 001121 TTGAGAAATG AAAGTTTGGA TCACTCCCCA GATAAAGAAC CTTGACCATT TAAGGGCAAT GGAAATACAG AATAGGCAGT 001200 001201 AGAAGAAGGA AGCCATAGAT ACCAACTATG GCCTCTCAAT CAATTACAAA ACTGAGAATT CTGACAGTTT TGTGTATTTC 001280 001281 CTCTTTGCAT GTGATGTATA TGTGTGTATT TGTATATATT AACCATTTTC CTTTTTCTCT CTTCATTATT TTATGAAAGT 001360 001361 TGTTGAATAT AAACTCTACA ATTTAGCCTT TAGGTAAGAG AATATTCAGT GGGACTTTGA TTTGAGGAGT ATTTAAGACA 001440 001441 GCCAGATGAG ACTACGATAA CTGTTGGAAC TGTGTGTCTC CTCATTTGGG GAAAGGGGTG AGAACTCTGC ATTTCTCTGA 001520 001521 AGAACAGAGT TGACTTTGTG TTATACAGAG TTCAAATATA TATATAAAAT GGTGCATGTG GAAGCTAAGA AGCCAAAGGA 001600 001601 GTTCACCAAG ACAGTTATCA ATATATTGCC TCTCCGCTCC AAATCCACCC TTCTTTGCCC TGTTCCACGA TACTAATCTG 001680 001681 GCTCCTCGGT CAGCCAGTGC AATGTCATCT GTTGCTGGTA GAGTGTAGGG GAGACACTAC AAGGTATAGT AAAGGGGTCA 001760 001761 GATGCGGTGT CTCATGCCTG TAATCACAGC CCTTTGGGAG GCAGAGGCAG GAGGATCACC TGAGGCCAGG AGTTTGAGAC 001840 001841 CAGCCTGGAC AACATGGTAA AACCCCATCT CTACTGAAAA TACAAAATTA GCACGCACCT GTAATCCCAG CTACTCGGGA 001920 001921 GGCTGAGGCA GGAGAATCAC TTGAACCTGG GAGGTGGAGG TTGCAGTGAG CCAAGATCGC ATCATTGCAC TCCAGCCAGG 002000 002001 GAAAAAAGGC AAAACTCTGT CTCAAAAAAA TAAATAAATA AAATAAAATA AAACAAGGTA TAGCAAAT |
Predicted Small Protein
| Name | ENST00000506884.1_smProtein_299:526 |
| Length | 76 |
| Molecular weight | 8795.916 |
| Aromaticity | 0.133333333333 |
| Instability index | 77.9146666667 |
| Isoelectric point | 7.76751708984 |
| Runs | 11 |
| Runs residual | 0.0022695035461 |
| Runs probability | 0.0296767355591 |
| Amino acid sequence | MQVEQKCFLSMYCYSPLRWYKRMKEDTTCLPGVSQKRWDEHSVHFHLPPFHYEGPSPDGG TMLSDFPASRTGRVN |
| Secondary structure | LLEEEEEEEEEEELLLHHHHHHLLLLLLLLLLLLEEELLLLEEEELLLLLLLLLLLLLLL LEELLLLLLLLLLLL |
| PRMN | - |
| PiMo | - |
| Name | ENST00000506884.1_smProtein_1052:1261 |
| Length | 69 |
| Molecular weight | 7714.6443 |
| Aromaticity | 0.0724637681159 |
| Instability index | 99.9768115942 |
| Isoelectric point | 9.10076904297 |
| Runs | 11 |
| Runs residual | 0.0200889654183 |
| Runs probability | 0.029443882385 |
| Amino acid sequence | MSLQSIQDQQESNFPPHPTTTQKRSTEMGKRVAASGIQPEESVQGFWIPLPPPHCPSPST PAFWRSKKL |
| Secondary structure | LLHHHHHHHHHLLLLLLLLLLLLLLHHHLLLEEELLLLLLLLLLEEEELLLLLLLLLLLL LLLEEEELL |
| PRMN | - |
| PiMo | - |
