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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaatcacttgctgtaccacgttaacgttccaaatgttcaaaatgacaaaagctttgtggacctttagtttcaacaatagattttgttttctttaaacagGTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGCTATAAAGCTTGTATGGTCGTGTCATCGTGAAATTATCCAAGATGTTGGA

Basic information

species Physcomitrella patens
transcript PP1S41_177V6.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S41_177V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: Vv17s0000g05800.t01 (Vitis vinifera), 3'ss of exon 15
caaatcacttgctgtaccacgttaacgttccaaatgttcaaaatgacaaaagctttgtggacctttagtttcaacaatagattttgttttctttaaacagGTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGCTATAAAGCTTGTATGGTCGTGTCATCGTGAAATTATCCAAGATGTTGGA
  |   |   | |  | ||| |      |       |||| |||||||     |     |  | | | | |       | |   || |||  |    ||||||||| ||||| || || ||  | || || || |||||||| || ||||| ||||||||||| |||||||||||| | ||||| ||  | ||| |||| 
gtatgtagaagatccaacacttcctttcttgcctgcttcacaatgacattg--tcaaaagtacgtcaatatatgtggaaaacaatggttttgt--ggcagGTTTGGACCAGCAGGGGACCCAAGAGGGGCAGGAATTGGGACGCCAGAAGCAATAAAGCTTGTTTGGTCGTGTCATAGAGAAATCATATATGATATTGGT
















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|162249296|gb|FC423979.1|FC423979
EST:     ACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTG                         GTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGC
genomic: ACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTGgtgggttttc ... ctttaaacagGTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGC
EST: gi|37825115|gb|BJ583181.1|BJ583181
EST:     ACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTG                         GTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGC
genomic: ACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTGgtgggttttc ... ctttaaacagGTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGC
EST: gi|162192524|gb|FC368634.1|FC368634
EST:     ACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTG                         GTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGC
genomic: ACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTGgtgggttttc ... ctttaaacagGTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGC
EST: gi|162263738|gb|FC439637.1|FC439637
EST:     ACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTG                         GTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGC
genomic: ACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTGgtgggttttc ... ctttaaacagGTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGC
EST: gi|162278733|gb|FC454843.1|FC454843
EST:     ACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTG                         GTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGC
genomic: ACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTGgtgggttttc ... ctttaaacagGTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGC
EST: gi|18334344|gb|BJ166361.1|BJ166361
EST:     ACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTG                         GTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGC
genomic: ACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTGgtgggttttc ... ctttaaacagGTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGC
EST: gi|208394915|gb|DC924134.1|DC924134
EST:     ACTTATGCTGGCATCCGAGCTCGGACGACTGGGGCACCCCAGAATCATTG                         GTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGC
genomic: ACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTGgtgggttttc ... ctttaaacagGTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGC
EST: gi|162230101|gb|FC406249.1|FC406249
EST:     ACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTG                         GTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGC
genomic: ACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTGgtgggttttc ... ctttaaacagGTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGC
EST: gi|162278732|gb|FC454842.1|FC454842
EST:     ACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTG                         GTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGC
genomic: ACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTGgtgggttttc ... ctttaaacagGTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGC
EST: gi|162214450|gb|FC391209.1|FC391209
EST:     ACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTG                         GTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGC
genomic: ACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTGgtgggttttc ... ctttaaacagGTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGC
EST: gi|37823906|gb|BJ581972.1|BJ581972
EST:     ACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTG                         GTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGC
genomic: ACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTGgtgggttttc ... ctttaaacagGTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGC
EST: gi|67692630|gb|BJ952863.1|BJ952863
EST:     ACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTG                         GTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGC
genomic: ACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTGgtgggttttc ... ctttaaacagGTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGC
EST: gi|208397350|gb|DC916318.1|DC916318
EST:     ACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTG                         GTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGC
genomic: ACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTGgtgggttttc ... ctttaaacagGTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGC

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: 26 (upstream exon), 33 (downstream exon)
Score: 7

GAAGTCTTGAGCAACACTGTTAACGGAACGACTTATGCTGGCATCCGAGCTCGGACAACTGGGGCACCCCAGAATCATTGgtgggttttc ... ctttaaacagGTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGCTATAAAGCTTGTATGGTCGTGTCATCGTGAAATTATCCAAGATGTTGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaaagctttgtggacctttagtttcaacaatagattttgttttctttaaacagGTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGCTATAAAGCTTGTATGGTCGTGTCATCGTGAAATTATCCAAGATGTTGGA
                                    ttttgttttcttt  CT-rich tract
                              aatagattttgttttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaatcacttgctgtaccacgttaacgttccaaatgttcaaaatgacaaaagctttgtggacctttagtttcaacaatagattttgttttctttaaacagGTTTGGGCCAGCTGGAGATCCCCGTGGAGCGGGGATTGGGACACCTGAAGCTATAAAGCTTGTATGGTCGTGTCATCGTGAAATTATCCAAGATGTTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - -tgctgta