Linc Noncoding Rna Annotation

Question

[Honey]

How can I download the list of noncoding RNA and their annotations for human genome. Does any one has Encode link or any other database. Thanks.

[Neilfws]

Do you want lincRNA (as the title suggests) or all non-protein coding RNA (as the rest of the question suggests) ? There are quite a lot of available databases, easily found via a simple Web search.

[kanwarjag]

How about only lin noncoding RNA only

[PoGibas]

For lincRNA please see Ido Tamir and my post.

Answer 1

[Medhat]

• ncRNA Expression Database (NRED)
• ChIPBase
• LNCipedia
• lncRNAdb is a database providing comprehensive annotations of eukaryotic long non-coding RNAs (lncRNAs).
• NONCODE is a database of all kinds of noncoding RNAs (except tRNAs and rRNAs).

to summarize look at this.

Answer 2

[Ido Tamir]

ucsc genome browser

[Honey]

The ucsc browser file ;

#bin    name    chrom    strand    txStart    txEnd    cdsStart    cdsEnd    exonCount    exonStarts    exonEnds
4    TCONS_00000720    chr1    -    209701799    209741018    209741018    209741018    7    209701799,209704591,209714042,209714652,209719401,209740254,209740879,    209702024,209704719,209714133,209714774,209719484,209740331,209741018,
4    TCONS_00000721    chr1    -    209701885    209720925    209720925    209720925    6    209701885,209714042,209714652,209716190,209719357,209720836,    209702024,209714133,209714774,209716263,209719484,209720925,
10    TCONS_l2_00001979    chr1    +    13629937    13635298    13635298    13635298    4    13629937,13632322,13633030,13634720,    13629979,13632634,13633609,13635298,
14    TCONS_l2_00001219    chr1    -    48226249    48260426    48260426    48260426    4    48226249,48240841,48244125,48260257,    48226952,48241111,48244216,48260426,

I believe txStart and txEnd should be the coordinates for linc RNA? Genome browser has no explanation? Am I correct

Thanks

[PoGibas]

Check describe table schema (http://genome.ucsc.edu/cgi-bin/hgTables). Tx start is transcription start position.

[Honey]

I am sorry then which are the coordinates for linc RNA or is it that exons are given anything outside that maybe intergenic?

bin    name    chrom    strand    txStart    txEnd    cdsStart    cdsEnd    exonCount    exonStarts    exonEnds
585    TCONS_l2_00002359    chr1    -    16606    29370    29370    29370    8    16606,16853,17232,17605,17914,18267,24737,2932

[PoGibas]

If you need coordinates then chr1 - 16606 29370 aka chrom strand txStart txEnd should be fine.

[Ido Tamir]

simply switch to a bed output file

Answer 3

[PoGibas]

I am using two annotations: Gencode and Cabili et al..

Still I didn't get what ncRNA you need. Is it only long intergenic ncRNA or you're interested in all long ncRNA (intergenic and antisesense)?

[Honey]

Poe,

I have another issue, excuse me for coming back with difficulties on the same issue-

when I downloaded GTF file of Gencode/ Cabili et al (Broad) it has lot of information how can I match gene annotation with bed file which has unique records.

e.g GTF file :

chr1    HAVANA    exon    139790    139847    .    -    .    gene_id     XLOC_000658    ; transcript_id     TCONS_00000437    ; exon_number     1    ; oId     ENST00000493797    ; linc_name     linc-ZNF692-6    ; tss_id     TSS1017    ; class_code     u    ; gene_name     linc-ZNF692-6    ;
chr1    HAVANA    exon    140075    140339    .    -    .    gene_id     XLOC_000658    ; transcript_id     TCONS_00000437    ; exon_number     2    ; oId     ENST00000493797    ; linc_name     linc-ZNF692-6    ; tss_id     TSS1017    ; class_code     u    ; gene_name     linc-ZNF692-6    ;

while bed file is-

chr1    139789    140339    TCONS_00000437    0    -    139789    140339    0,0,0    2    58,265,    0,285,
chr1    141473    149707    TCONS_00000438    0    -    141473    149707    0,0,0    2    1538,3322,    0,4912,