ENST00000506884.1

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PART1,a 2495 bp long non-coding RNA, mapping to chromosome 5q12, functions a signature in cancers.

Contents

Annotated Information

Name

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].

Disease

prostate carcinogenesis

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. 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. 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
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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 -
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