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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaataaattgtgctgctctgtctgttgttacgtttcagatttttcaagatggagaactaattacagcactattctaattcattgtttgttgcaaaatagGATGTGGGGCAGTCAATTCTCGAAAGCTACTCCAGGGTGCTGGAAAGTCTATCGTTTACCATCATTTCACGCATTGATGATGTCTTGTACGCGGATGATC

Basic information

species Physcomitrella patens
transcript PP1S58_274V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S58_274V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os07g29780.2 (Oryza sativa), 3'ss of exon 7
agaataaattgtgctgctctgtctgttgttacgtttcagatttttcaa-gatggagaactaattacagcactattctaattcattgtttgttgcaaaatagGATGTGGGGCAGTCAATTCTCGAAAGCTACTCCAGGGTGCTGGAAAGTCTATCGTTTACCATCATTTCACGCATTGATGATGTCTTGTACGCGGATGATC
| |  ||  | | |           |||   | | ||   |   |||| ||  |   |  | |   |   ||    |   ||  | |||  |     | ||||  | |||||| |||| || ||||||||||| ||||||||||||||| || | |  |  ||  | ||| | || ||||||||  |    || ||||   
atacaaacatatacgaaataactgattgagccatctcctttggatcaaagaatgttcatcattgctaatgctggcgtgtctccat-tttactttgctacagGACATTGGGCAGGCAATACTTGAAAGCTACTCGAGGGTGCTGGAAAGTTTAGCCTACAATATTGTCTCATGGATAGATGATGTTCTCATTGCAGATGGGA

upper sequence: PP1S58_274V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv18s0001g00550.t01 (Vitis vinifera), 3'ss of exon 4
---agaataaattgtgctgctctgtctgttgttacgtttcagatttttcaagatggagaac-taattacagcact--attctaattcattgtttgttgcaaaatagGATGTGGGGCAGTCAATTCTCGAAAGCTACTCCAGGGTGCTGGAAAGTCTATCGTTTACCATCATTTCACGCATTGATGATGTCTTGTACGCGGATGATC
   || | ||| | |  | |        ||| | | |        ||   |  ||  |||  |   ||    | |  |  | ||| | ||||| ||||||     |||||||||||| ||||| ||||| ||||||||||||||| |||||||  || | || | ||| ||  |  | || |||||| |  | |||   |||||| 
gccaggacaaagtctcttccagccagccttgcttcatccatttcattatgaactgatgaaaatggctatgaaagtgaaagcgaatcccttgtt-gttgca-----gGATGTGGGGCAATCAATCCTCGAGAGCTACTCCAGGGTGATGGAAAGCTTAGCCTTCAACATAATGGCGAGAATAGATGATCTTCTATACATAGATGATG
















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|37832562|gb|BJ590574.1|BJ590574
EST:     CTGGAATGGCGCAGACCGTTTTGGACGCAAATAAGATTCAATTCAACAGG                         GATGTGGGGCAGTCAATTCTCGAAAGCTACTCCAGGGTGCTGGAAAGTCTA
genomic: CTGGAATGGCGCAGACCGTTTTGGACGCAAATAAGATTCAATTCAACAGGgtatgttcaa ... tgcaaaatagGATGTGGGGCAGTCAATTCTCGAAAGCTACTCCAGGGTGCTGGAAAGTCTA
EST: gi|162161815|gb|FC337930.1|FC337930
EST:     CTGGAATGGCGCAGACCGTTTTGGACGCAAATAAGATTCAATTCAACAGG                         GATGTGGGGCAGTCAATTCTCGAAAGCTACTCCAGGGTGCTGGAAAGTCTA
genomic: CTGGAATGGCGCAGACCGTTTTGGACGCAAATAAGATTCAATTCAACAGGgtatgttcaa ... tgcaaaatagGATGTGGGGCAGTCAATTCTCGAAAGCTACTCCAGGGTGCTGGAAAGTCTA
EST: gi|37829564|gb|BJ587576.1|BJ587576
EST:     CTGGAATGGCGCAGACCGTTTTGGACGCAAATAAGATTCAATTCAACAGG                         GATGTGGGGCAGTCAATTCTCGAAAGCTACTCCAGGGTGCTGGAAAGTCTA
genomic: CTGGAATGGCGCAGACCGTTTTGGACGCAAATAAGATTCAATTCAACAGGgtatgttcaa ... tgcaaaatagGATGTGGGGCAGTCAATTCTCGAAAGCTACTCCAGGGTGCTGGAAAGTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagatggagaactaattacagcactattctaattcattgtttgttgcaaaatagGATGTGGGGCAGTCAATTCTCGAAAGCTACTCCAGGGTGCTGGAAAGTCTATCGTTTACCATCATTTCACGCATTGATGATGTCTTGTACGCGGATGATC
                           ttctaat  putative branch site (score: 2)
                         tattctaattcatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaataaattgtgctgctctgtctgttgttacgtttcagatttttcaagatggagaactaattacagcactattctaattcattgtttgttgcaaaatagGATGTGGGGCAGTCAATTCTCGAAAGCTACTCCAGGGTGCTGGAAAGTCTATCGTTTACCATCATTTCACGCATTGATGATGTCTTGTACGCGGATGATC

- - - - - -tgctgct