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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGAAAATGAGTCCCTTGGTGTCCACTCTTCACCTGTACGATGTTTTCAACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccctatcacgtcatttgatttcacatgttcgaattcgttcagctgtatctgttattttcgcaaaatttcaactatgttttctacctctgtcatgtacttatttcccgtgatagcacttcggtaggataagtaaatattggtcgcttattgattccccaactaatgtgagcacactgctttgtcttttaag

Basic information

species Physcomitrella patens
transcript PP1S39_428V6.1
intron # 2
splice site 5'
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|162164277|gb|FC342092.1|FC342092
EST:     ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTG                         GTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
genomic: ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
EST: gi|208346689|gb|DC913335.1|DC913335
EST:     ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTG                         GTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
genomic: ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
EST: gi|162203310|gb|FC378770.1|FC378770
EST:     ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTG                         GTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
genomic: ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
EST: gi|162199459|gb|FC374073.1|FC374073
EST:     ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTG                         GTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
genomic: ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
EST: gi|208354297|gb|DC902497.1|DC902497
EST:     ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTG                         GTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
genomic: ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
EST: gi|100442034|gb|BY962927.1|BY962927
EST:     ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTG                         GTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
genomic: ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
EST: gi|100441689|gb|BY962780.1|BY962780
EST:     ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTG                         GTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
genomic: ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
EST: gi|100432163|gb|BY960366.1|BY960366
EST:     ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTG                         GTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
genomic: ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
EST: gi|208391219|gb|DC933508.1|DC933508
EST:     ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCCCTGCTGTG                         GTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
genomic: ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
EST: gi|100360562|gb|BY984180.1|BY984180
EST:     ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTG                         GTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
genomic: ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
EST: gi|100411228|gb|BY974533.1|BY974533
EST:     ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTG                         GTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
genomic: ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
EST: gi|100387198|gb|BY970342.1|BY970342
EST:     ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTG                         GCGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
genomic: ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
EST: gi|208362073|gb|DC943500.1|DC943500
EST:     ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTG                         GTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
genomic: ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
EST: gi|162182339|gb|FC357210.1|FC357210
EST:     ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTG                         GTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
genomic: ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
EST: gi|100424028|gb|BY976628.1|BY976628
EST:     ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTG                         GTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
genomic: ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
EST: gi|67577872|gb|BJ950039.1|BJ950039
EST:     ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTG                         GTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
genomic: ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
EST: gi|100370521|gb|BY985450.1|BY985450
EST:     ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTG                         GTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
genomic: ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
EST: gi|208379601|gb|DC927098.1|DC927098
EST:     TGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTG                         GTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
genomic: TGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
EST: gi|100356212|gb|BY946251.1|BY946251
EST:     ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTG                         GTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
genomic: ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
EST: gi|100426335|gb|BY958846.1|BY958846
EST:     ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTG                         GTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
genomic: ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
EST: gi|100357996|gb|BY965419.1|BY965419
EST:     ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTG                         GTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
genomic: ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
EST: gi|100439784|gb|BY962105.1|BY962105
EST:     ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTG                         GTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
genomic: ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
EST: gi|67573834|gb|BJ946658.1|BJ946658
EST:     ACACACCCGGAGNTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTG                         GNGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGNACGGGATG
genomic: ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
EST: gi|100386614|gb|BY970155.1|BY970155
EST:     ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTG                         GTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
genomic: ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
EST: gi|100364527|gb|BY984648.1|BY984648
EST:     ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTG                         GTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
genomic: ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
EST: gi|162253124|gb|FC428956.1|FC428956
EST:     ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTG                         GTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
genomic: ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
EST: gi|100388088|gb|BY988561.1|BY988561
EST:     ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTG                         GTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG
genomic: ACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATG

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: 33 (upstream exon), 35 (downstream exon)
Score: 17

CATGAAAATGAGTCCCTTGGTGTCCACTCTTCACCTGTACGATGTTTTCAACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccc ... gtcttttaagGTGCGAGGATTCCTTGGCAACGACCAATTGGGACCTGCTTTGGACGGGATGGACTTGGTTATTATACCCGCTGGAGTTCCACGAAAGCCAGGCATGACAA




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGAAAATGAGTCCCTTGGTGTCCACTCTTCACCTGTACGATGTTTTCAACACACCCGGAGTTGTTGCTGATTTGAGCCACACAAACACCTCTGCTGTGgtaccctccctatcacgtcatttgatttcacatgttcgaattcgttcagctgtatctgttattttcgcaaaatttcaactatgttttctacctctgtcatgtacttatttcccgtgatagcacttcggtaggataagtaaatattggtcgcttattgattccccaactaatgtgagcacactgctttgtcttttaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT