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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgagccccatgatctatagctttaataaatctgagctttctaatttacactcatgatacagagcttttcttgattgacgtcactttcaatgaactctgagatggtcttgttttcctttccagcttccacgctaactaaaaggatcttgtgttttagGAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAACGCTATCATCAATGCTGCGGAGTTGGCCAGTTATGACCAAGTCAAGCAG

Basic information

species Physcomitrella patens
transcript PP1S15_443V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S15_443V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os11g48040.1 (Oryza sativa), 3'ss of exon 4
gtctgagccccatgatctatagctttaataaatctgagctttctaatttacactcatgatacagagcttttcttgattgacgtcactttcaatgaactctgagatggtcttgttttcctttccagcttccacgctaactaaaaggatcttgtgttttagGAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAACGCTATCATCAATGCTGCGGAGTTGGCCAGTTATGACCAAGTCAAGCAG
                                                               || ||| |  |  ||  | || | | |  |   || |   ||         |   |       |  ||   | | || |      || |   | ||||||| ||  |    |||||||||||  |||| || ||||| || || || || |||||||||||||| ||||||||||| ||||| ||||||||||||
------------------------------------------------------------gttgaccttctgcttcttt-cttcgcatgcgcttgcctgttccataccaacacatcattgcttgcttcacatctttattata------ttat-cctcagGAAGGGTTTGCTGCTTTGTGGACTGGCATTGGACCCAATGTTGCGCGCAATGCCATCATCAATGCTGCCGAGTTGGCCAGCTATGATCAAGTCAAGCAG

upper sequence: PP1S15_443V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G000510_T02 (Zea mays), 3'ss of exon 4
gtctgagccccatgatctatagctttaataaatctgagctttc-taatttacactcatgatacag--agcttttcttgattgacgtcactttcaatgaactctgagatggtcttgttttcctttccagcttccacgctaactaaaaggatcttgtgttttagGAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAACGCTATCATCAATGCTGCGGAGTTGGCCAGTTATGACCAAGTCAAGCAG
                                |||| |||  | |  | | | | ||    || |   |||||  ||| ||  |  | |  ||||| || |  |||     ||||  |    ||  |  |   | |    ||      ||| |      ||||||||  |  |     |||||||||| ||||| |||||||| || || || ||||||||||||||||| ||||||||||||||||| ||||||||||||
-------------------------------gtctgtgctggcatgctcttctcccagctaaccgttcgctttctttgttttgctac-caatcaataaaattagag-----cttggctcttattatatgtgtgatgt--gcttggctcatcct------tagGAAGGGGTTGCCGCTCTGTGGACTGGCCTTGGACCAAATGTAGCGCGGAATGCTATCATCAATGCTGCTGAGTTGGCCAGTTATGATCAAGTCAAGCAG

upper sequence: PP1S15_443V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM5G852877_T01 (Zea mays), 3'ss of exon 4
gtctgagccccatgatctatagctttaataaatctgagctttctaatttacactcatgatacagagcttttcttgattgacgtcactttcaatgaactctgagatggtcttgttttcctttccagcttccacgctaactaaaaggatcttgtg-ttttagGAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAACGCTATCATCAATGCTGCGGAGTTGGCCAGTTATGACCAAGTCAAGCAG
                                                                    || ||| |   |  |||    || | |  |     |      | |||   ||| ||   |||        | |||   | |  || ||  |||||||  |   |   ||||||||||| ||||||||||||||||| || || || || || || ||||| ||||||||||| ||||| ||  |||| |||
-------------------------------------------------------------------gttactttaacaa--tcatgggcagtaagttt----acaagactatttcttttttcattgtcc--------ttaaaatctttcatgcttccagGAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAG

upper sequence: PP1S15_443V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G165629_T02 (Zea mays), 3'ss of exon 4
gtctgagccccatgatctatagctttaataaatctgagctttctaatttacactcatgatacagagcttttcttgattgacgtcactttcaatgaactctgagatggtcttgttttcctttccagcttccacgctaactaaaaggatcttgtg-ttttagGAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAACGCTATCATCAATGCTGCGGAGTTGGCCAGTTATGACCAAGTCAAGCAG
                                                                                 || ||||| |      |  |   |    ||      |||||    ||   || |  |   ||   | |  || ||  |||||||  |   |   ||||||||||| ||||||||||||||||| || || || || || || ||||| ||||||||||| ||||| ||  |||| |||
---------------------------------------------------------------------------------gttactttaacaatcatgggcagtaagtttacgagactttct---tttttcgttgtccttaaatctttcatgcttccagGAAGGTATTGGAGCTTTGTGGACTGGCCTTGGTCCAAATGTCGCACGCAATGCCATAATTAACGCTGCCGAGTTGGCCAGCTATGATCAGTTCAAACAG

upper sequence: PP1S15_443V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ24273 (Selaginella moellendorffii), 3'ss of exon 4
gtctgagccccatgatctatagctttaataaatctgagctttctaatttacactcatgatacagagcttttcttgattgacgtcactttcaatgaactctgagatggtcttgttttcctttccagcttccacgctaactaaaaggatcttgtgttttagGAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAACGCTATCATCAATGCTGCGGAGTTGGCCAGTTATGACCAAGTCAAGCAG
                                                                                                   |  |  |  | |  | || ||||    | |||    |     |    || | |  |  ||||||| ||| ||||| | |||||||| || ||||||||||| || ||||||||||||||||| || || ||| | || || ||||| ||||| || |||
--------------------------------------------------------------------------------------------------gtatggcgaacatactgtcttttca---tccca----agtcggactcttcatctcatacagGAAGGTTTCGCAAAACTTTGGACTGGCCTGGGTCCAAATGTGGCCCGTAACGCTATCATCAACGCGGCCGAGCTCGCTAGCTATGATCAAGTAAAACAG

upper sequence: PP1S15_443V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ35536 (Selaginella moellendorffii), 3'ss of exon 4
gtctgagccccatgatctatagctttaataaatctgagctttctaatttacactcatgatacagagcttttcttgattgacgtcactttcaatgaactctgagatggtcttgttttcctttccagcttccacgctaactaaaaggatcttgtgttttagGAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAACGCTATCATCAATGCTGCGGAGTTGGCCAGTTATGACCAAGTCAAGCAG
                                                                                                   |  |  |  | |  | || ||||     || |  |  |||       || | |  |  ||||||| ||| ||||| | |||||||| || ||||||||||| || ||||||||||||||||| || || ||| | || || ||||| ||||| || |||
--------------------------------------------------------------------------------------------------gtatggcgaacatactgtcttttc--atctcaagtccgactc-----ttcatctcatacagGAAGGTTTCGCAAAACTTTGGACTGGCCTGGGTCCAAATGTGGCCCGTAACGCTATCATCAACGCGGCCGAGCTCGCTAGCTATGATCAAGTAAAACAG

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|18334877|gb|BJ166894.1|BJ166894
EST:     CCGCCGCTACAGCGGTGCCATGAATGCTTACTCGACCATTGTCAAGCAG                         GAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAAC
genomic: CCGCCGCTACAGCGGTGCCATGAATGCTTACTCGACCATTGTCAAGCAGgtctgagccc ... tgtgttttagGAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAAC
EST: gi|208396055|gb|DC924521.1|DC924521
EST:     CCCGCCGCTACAGCGGTGCCATGAATGCTTACTCGACCATTGTCAAGCAG                         GAAGGATTCACAAAATTGTNGACTGGGCTTGGTCCAAATGTCGCTCGTAAC
genomic: CCCGCCGCTACAGCGGTGCCATGAATGCTTACTCGACCATTGTCAAGCAGgtctgagccc ... tgtgttttagGAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAAC
EST: gi|100358857|gb|BY946723.1|BY946723
EST:     CCCGCCGCTACAGCGGTGCCATGAATGCTTACTCGACCATTGTCAAGCAG                         GAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAAC
genomic: CCCGCCGCTACAGCGGTGCCATGAATGCTTACTCGACCATTGTCAAGCAGgtctgagccc ... tgtgttttagGAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAAC
EST: gi|162262932|gb|FC439299.1|FC439299
EST:     CCCGCCGCTACAGCGGTGCCATGAATGCTTACTCGACCATTGTCAAGCAG                         GAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAAC
genomic: CCCGCCGCTACAGCGGTGCCATGAATGCTTACTCGACCATTGTCAAGCAGgtctgagccc ... tgtgttttagGAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAAC
EST: gi|162268960|gb|FC445764.1|FC445764
EST:     CCCGCCGCTACAGCGGTGCCATGAATGCTTACTCGACCATTGTCAAGCAG                         GAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAAC
genomic: CCCGCCGCTACAGCGGTGCCATGAATGCTTACTCGACCATTGTCAAGCAGgtctgagccc ... tgtgttttagGAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAAC
EST: gi|37833787|gb|BJ591799.1|BJ591799
EST:     CCCGCCGCTACAGCGGTGCCATGAATGCTTACTCGACCATTGTCAAGCAG                         GAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAAC
genomic: CCCGCCGCTACAGCGGTGCCATGAATGCTTACTCGACCATTGTCAAGCAGgtctgagccc ... tgtgttttagGAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAAC
EST: gi|162262931|gb|FC439298.1|FC439298
EST:     CCCGCCGCTACAGCGGTGCCATGAATGCTTACTCGACCATTGTCAAGCAG                         GAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAAC
genomic: CCCGCCGCTACAGCGGTGCCATGAATGCTTACTCGACCATTGTCAAGCAGgtctgagccc ... tgtgttttagGAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAAC
EST: gi|162268961|gb|FC445765.1|FC445765
EST:     CCCGCCGCTACAGCGGTGCCATGAATGCTTACTCGACCATTGTCAAGCAG                         GAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAAC
genomic: CCCGCCGCTACAGCGGTGCCATGAATGCTTACTCGACCATTGTCAAGCAGgtctgagccc ... tgtgttttagGAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAAC

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: 27 (upstream exon), 28 (downstream exon)
Score: 7

TCTAGTGAAAGTGCGTCTTCAATCCGAGGGCAAGCTCCCTCCTGGTGTTCCCCGCCGCTACAGCGGTGCCATGAATGCTTACTCGACCATTGTCAAGCAGgtctgagccc ... tgtgttttagGAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAACGCTATCATCAATGCTGCGGAGTTGGCCAGTTATGACCAAGTCAAGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtcttgttttcctttccagcttccacgctaactaaaaggatcttgtgttttagGAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAACGCTATCATCAATGCTGCGGAGTTGGCCAGTTATGACCAAGTCAAGCAG
                               aactaaa  putative branch site (score: 7)
                              taactaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgagccccatgatctatagctttaataaatctgagctttctaatttacactcatgatacagagcttttcttgattgacgtcactttcaatgaactctgagatggtcttgttttcctttccagcttccacgctaactaaaaggatcttgtgttttagGAAGGATTCACAAAATTGTGGACTGGGCTTGGTCCAAATGTCGCTCGTAACGCTATCATCAATGCTGCGGAGTTGGCCAGTTATGACCAAGTCAAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC