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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgaataagggtatatttcctgcggttgcccaggtggtcacagcaaattcgtggagattgtagaactcatcctctttatccagagttgtcatacatatacgtgttgtcgtttcagGGATTGGCCTGTGGAGAAGTTGAAGGAGGTTAAAGTAGCAGATGCTTTGAAGCATCCCAACTGGAGCATGGGCCGCAAAATTACGGTTGATTCTGCCACG

Basic information

species Physcomitrella patens
transcript PP1S62_157V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S62_157V6.4 (Physcomitrella patens), 3'ss of exon 9
lower sequence: AT5G62790.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatatgaataagggtatatttcctgcggttgcccaggtggtcacagcaaattcgtggagattgtagaactcatcctctttatccagagttgtcatacatatacgtgttgtcgtttcagGGATTGGCCTGTGGAGAAGTTGAAGGAGGTTAAAGTAGCAGATGCTTTGAAGCATCCCAACTGGAGCATGGGCCGCAAAATTACGGTTGATTCTGCCACG
                   |||  | || |   |       ||     | | |  |     |   |   ||| |    || ||  | | || |||        |  | | | |    |||||||||||||| || ||| | ||||| ||||||||||| ||||| ||||||||||| ||||||| ||||||    ||||| || || || ||||| |||
------------------gtttgtttcgatattcttctctctctgcatagactttttttcttctcaattctcgtttggttaatggaaacttttca--------ctggattttgaaaaagGGATTGGCCTGTCGAAAAGCTAAAGGAAGTTAAAGTAGCGGATGCGTTGAAGCATCCAAACTGGAACATGGGAAAGAAAATCACTGTGGACTCTGCTACG

upper sequence: PP1S62_157V6.4 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv17s0000g08390.t01 (Vitis vinifera), 3'ss of exon 7
gtatatgaataagggtatatttcctgcggttgcccaggtggtcacagcaaattcgtgga-gattgtagaactcatcctctttatccagagttgtcatacatatacgtgttgtcgttt-cagGGATTGGCCTGTGGAGAAGTTGAAGGAGGTTAAAGTAGCAGATGCTTTGAAGCATCCCAACTGGAGCATGGGCCGCAAAATTACGGTTGATTCTGCCACG
                 | |||  ||   ||   |   |||   | |||| ||       |||||| |      | ||    | |  |  ||  | |    || |   |||||     |||||||||||| || || || ||||| || | ||||||  ||||||||||||||||||| |||||||  |||||    || || |||||||| || || || 
-----------------tgttttttgtttttattc---tggcttctgcaatttaacatctgattgttggtgcattacttaggacctggttttaac-tgttcattcactttgtcaccaacagGGATTGGCCCGTTGATAAATTGAAAGAAGCTAAAGTTTCAGATGCTTTGAAGCATCCTAACTGGAATATGGGGAAAAAGATCACGGTTGACTCAGCTACC
















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|162185513|gb|FC361237.1|FC361237
EST:     CGGATTATCCTCACAGCATCCGGAGGTGCATTCAG                         GGATTGGCCTGTGGAGAAGTTGAAGGAGGTTAAAGTAGCAGATGCTTTGAA
genomic: CGGATTATCCTCACAGCATCCGGAGGTGCATTCAGgtatatgaat ... gtcgtttcagGGATTGGCCTGTGGAGAAGTTGAAGGAGGTTAAAGTAGCAGATGCTTTGAA
EST: gi|162250938|gb|FC425760.1|FC425760
EST:     GAAGGTGGATTGAGGCGGATTATCCTCACAGCATCCGGAGGTGCATTCAG                         GGATTGGCCTGTGGAGAAGTTGAAGGAGGTTAAAGTAGCAGATGCTTTGAA
genomic: GAAGGTGGATTGAGGCGGATTATCCTCACAGCATCCGGAGGTGCATTCAGgtatatgaat ... gtcgtttcagGGATTGGCCTGTGGAGAAGTTGAAGGAGGTTAAAGTAGCAGATGCTTTGAA
EST: gi|100442899|gb|BY963394.1|BY963394
EST:     GAAGGTGGATTGAGGCGGATTATCCTCACAGCATCCGGAGGTGCATTCAG                         GGATTGGCCTGTGGAGAAGTTGAAGGAGGTTAAAGTAGCAGATGCTTTGAA
genomic: GAAGGTGGATTGAGGCGGATTATCCTCACAGCATCCGGAGGTGCATTCAGgtatatgaat ... gtcgtttcagGGATTGGCCTGTGGAGAAGTTGAAGGAGGTTAAAGTAGCAGATGCTTTGAA
EST: gi|162272851|gb|FC448007.1|FC448007
EST:     GAAGGTGGATTGAGGCGGATTATCCTCACAGCATCCGGAGGTGCATTCAG                         GGATTGGCCTGTGGAGAAGTTGAAGGAGGTTAAAGTAGCAGATGCTTTGAA
genomic: GAAGGTGGATTGAGGCGGATTATCCTCACAGCATCCGGAGGTGCATTCAGgtatatgaat ... gtcgtttcagGGATTGGCCTGTGGAGAAGTTGAAGGAGGTTAAAGTAGCAGATGCTTTGAA
EST: gi|162163958|gb|FC339868.1|FC339868
EST:     GAAGGTGGATTGAGGCGGATTATCCTCACAGCATCCGGAGGTGCATTCAG                         GGATTGGCCTGTGGAGAAGTTGAAGGAGGTTAAAGTAGCAGATGCTTTGAA
genomic: GAAGGTGGATTGAGGCGGATTATCCTCACAGCATCCGGAGGTGCATTCAGgtatatgaat ... gtcgtttcagGGATTGGCCTGTGGAGAAGTTGAAGGAGGTTAAAGTAGCAGATGCTTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagaactcatcctctttatccagagttgtcatacatatacgtgttgtcgtttcagGGATTGGCCTGTGGAGAAGTTGAAGGAGGTTAAAGTAGCAGATGCTTTGAAGCATCCCAACTGGAGCATGGGCCGCAAAATTACGGTTGATTCTGCCACG
                                              tcgtttc  CT-rich tract
                              atacatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatgaataagggtatatttcctgcggttgcccaggtggtcacagcaaattcgtggagattgtagaactcatcctctttatccagagttgtcatacatatacgtgttgtcgtttcagGGATTGGCCTGTGGAGAAGTTGAAGGAGGTTAAAGTAGCAGATGCTTTGAAGCATCCCAACTGGAGCATGGGCCGCAAAATTACGGTTGATTCTGCCACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA