Hi, Shuli! The transcript id identifies a sequence of RNA.
The main reason that you see the same ID in multiple places is because the DNA at those places is highly similar. Sometimes the similar dna is the result of repetitive elements e.g. transposons. Other causes include the duplication of a segment of dna in the genome, for which there are a number of known mechanisms. Another reason you might see the same or similar ID or sequence is due to alternate splicing, which creates similar sequences that align at similar locations. Our lives would all be a lot simpler if there was no repetitive dna or introns in the genome. Alas, we all struggle with this. For some it can become the center of some interesting research. -Galt On 11/22/10 13:27, Shuli Kang wrote: > The method described for this track: > > "Methods > > RefSeq RNAs were aligned against the human genome using blat; those with > an alignment of less than 15% were discarded. When a single RNA aligned > in multiple places, the alignment having the highest base identity was > identified. Only alignments having a base identity level within 0.1% of > the best and at least 96% base identity with the genomic sequence were > kept." > > Hope this helps. > > Shuli > > On 11/22/2010 02:06 AM, zhangpeng2 wrote: >> Dear editor >> I download the file refGene.txt from the website >> :http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ . >> But I found some lines have the same transcript ID but >> differeent coordinates. As far as I know, the transcriptID is the uniq >> identifier of a transcription. would you please tell me why? >> for example: >> >> 1114 NM_000344 chr5 + 69345349 69373418 >> 69345512 69372398 9 >> 69345349,69359241,69361791,69362760,69363120,69365061,69366467,69372347,69372845, >> >> 69345593,69359313,69361911,69362961,69363273,69365157,69366578,69372401,69373418, >> 0 SMN1 cmpl cmpl 0,0,0,0,0,0,0,0,-1, >> 1120 NM_000344 chr5 + 70220767 70248838 >> 70220930 70247818 9 >> 70220767,70234665,70237215,70238184,70238544,70240484,70241892,70247767,70248265, >> >> 70221011,70234737,70237335,70238385,70238697,70240580,70242003,70247821,70248838, >> 0 SMN1 cmpl cmpl 0,0,0,0,0,0,0,0,-1, >> >> my best, >> thanks >> >> 2010-11-22 >> >> >> >> All my best >> zhangpeng >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
