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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttatgctggtgagtaaaataggagaaacacgtggaaagtcctagtcgttacctttagttagtcttattatgtaggctgatgtttcagttttcacgcagGTGCTATTACTGGTGCAGTGACTACGCCACTTGATGTTATTAAGACCCGACTTATGACCCAG

Basic information

species Physcomitrella patens
transcript PP1S450_16V6.1
intron # 10
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|208350179|gb|DC926120.1|DC926120
EST:     GAACAGGGATCTTCTAGATCTGGAGACAGCTCTTGTAGGAGCAACCTCTG                         GTGCTATTACTGGTGCAGTGACTACGCCACTTGATGTTATTAAGACCCGAC
genomic: GAACAGGGATCTTCTAGATCTGGAGACAGCTCTTGTAGGAGCAACCTCTGgtacagactc ... tttcacgcagGTGCTATTACTGGTGCAGTGACTACGCCACTTGATGTTATTAAGACCCGAC
EST: gi|162207066|gb|FC382180.1|FC382180
EST:     GAACAGGGATCTTCTAGATCTGGAGACAGCTCTTGTAGGAGCAACCTCTG                         GTGCTATTACTGGTGCAGTGACTACGCCACTTGATGTTATTAAGACCCGAC
genomic: GAACAGGGATCTTCTAGATCTGGAGACAGCTCTTGTAGGAGCAACCTCTGgtacagactc ... tttcacgcagGTGCTATTACTGGTGCAGTGACTACGCCACTTGATGTTATTAAGACCCGAC
EST: gi|162187904|gb|FC364478.1|FC364478
EST:     GAACAGGGATCTTCTAGATCTGGAGACAGCTCTTGTAGGAGCAACCTCTG                         GTGCTATTACTGGTGCAGTGACTACGCCACTTGATGTTATTAAGACCCGAC
genomic: GAACAGGGATCTTCTAGATCTGGAGACAGCTCTTGTAGGAGCAACCTCTGgtacagactc ... tttcacgcagGTGCTATTACTGGTGCAGTGACTACGCCACTTGATGTTATTAAGACCCGAC
EST: gi|37826195|gb|BJ584207.1|BJ584207
EST:     ATCTGGAGACAGCTCTTGTAGGAGCAACCTCTG                         GTGCTATTACTGGTGCAGTGACTACGCCACTTGATGTTATTAAGACCCGAC
genomic: ATCTGGAGACAGCTCTTGTAGGAGCAACCTCTGgtacagactc ... tttcacgcagGTGCTATTACTGGTGCAGTGACTACGCCACTTGATGTTATTAAGACCCGAC
EST: gi|162187903|gb|FC364477.1|FC364477
EST:     GAACAGGGATCTTCTAGATCTGGAGACAGCTCTTGTAGGAGCAACCTCTG                         GTGCTATTACTGGTGCAGTGACTACGCCACTTGATGTTATTAAGACCCGAC
genomic: GAACAGGGATCTTCTAGATCTGGAGACAGCTCTTGTAGGAGCAACCTCTGgtacagactc ... tttcacgcagGTGCTATTACTGGTGCAGTGACTACGCCACTTGATGTTATTAAGACCCGAC
EST: gi|67726554|gb|BJ976813.1|BJ976813
EST:     GAACAGGGATCTTCTAGATCTGGAGACAGCTCTTGTAGGAGCAACCTCTG                         GTGCTATTACTGGTGCAGTGACTACGCCACTTGATGTTATTAAGACCCGAC
genomic: GAACAGGGATCTTCTAGATCTGGAGACAGCTCTTGTAGGAGCAACCTCTGgtacagactc ... tttcacgcagGTGCTATTACTGGTGCAGTGACTACGCCACTTGATGTTATTAAGACCCGAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 24 (upstream exon), 29 (downstream exon)
Score: 5

GTGAACAGGGATCTTCTAGATCTGGAGACAGCTCTTGTAGGAGCAACCTCTGgtacagactc ... tttcacgcagGTGCTATTACTGGTGCAGTGACTACGCCACTTGATGTTATTAAGACCCGACTTATGACCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcgttacctttagttagtcttattatgtaggctgatgtttcagttttcacgcagGTGCTATTACTGGTGCAGTGACTACGCCACTTGATGTTATTAAGACCCGACTTATGACCCAG
                              ggctgat  putative branch site (score: 5)
                                            ttttcac  putative PPT
                    ttattatgta  TA-rich tract