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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGCGCGGCGAAGCCGGCTCCGCGGCGCGGCCAGGAGAAGCTCGCGACGGTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtagggagcttgtttgtggtcgtgagtttgtggtctgggtgggcttcgcggcgtgattttggcactgagaggcggcgagttgtgtgtttgtatgtttgtgtttggggttttgggtggattgtgtggctgacgtcagtgtgcctccacag

Basic information

species Physcomitrella patens
transcript PP1S61_262V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S61_262V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ33124 (Selaginella moellendorffii), 5'ss of exon 1
AGAGCGCGGCGAAGCCG--GCTCCGCGGCGCGGC-CAGGAGAAGCTCGCGACGGTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtagggagcttg--tttgtggtcgtgagtttgtggtctgggtgggcttcgcggcgtgattttggcactgagaggcggcgagttgtgtgtttgtatgtttgtgtttggggttttgggtggattgtgtggctgacgtcagtgtgcctccacag
    |||   |||||||  || | || |   |   |||||||||||  |  ||||||| |||||||| |||||||| ||||| | ||| || ||||||||||||| |||   |   | |  ||| | |  | |  |   |  |||   |   || ||| |                                                                                                  
---CCGCCAAGAAGCCGCAGCCCAGCAGAAAGATGCAGGAGAAGCTGCCATCGGTGTTTAGCTGCCCGTTCTGCAATCACGAGAGCAGCGTCGAGTGCCGCATgtaagtgccgcattagggtttttagaagcgc-tccctcatctctttcctct-cgcag--------------------------------------------------------------------------------------------------
















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|67726792|gb|BJ977051.1|BJ977051
EST:     GTGTTCA-CTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|18357028|gb|BJ189087.1|BJ189087
EST:     GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|18342257|gb|BJ174292.1|BJ174292
EST:     GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|18358512|gb|BJ190571.1|BJ190571
EST:     GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|37841638|gb|BJ599646.1|BJ599646
EST:     GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|67694213|gb|BJ954446.1|BJ954446
EST:     GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|67570911|gb|BJ943735.1|BJ943735
EST:     GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|162271048|gb|FC446608.1|FC446608
EST:     GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|67704114|gb|BJ964347.1|BJ964347
EST:     GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|162217190|gb|FC392554.1|FC392554
EST:     GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|162217189|gb|FC392553.1|FC392553
EST:     GCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|162279151|gb|FC455490.1|FC455490
EST:     GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|22131587|gb|BQ826691.1|BQ826691
EST:     GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|162219652|gb|FC395648.1|FC395648
EST:     GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|22492043|gb|BU051966.1|BU051966
EST:     GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|162214750|gb|FC391821.1|FC391821
EST:     GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|37851018|gb|BJ609026.1|BJ609026
EST:     TGTTCAGCTGCCCTTTCTGCAACCACGACAACCAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: TGTTCAGCTGCCCTTTCTGCAACCACGACAA-CAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|37837722|gb|BJ595730.1|BJ595730
EST:     TGTTCAGCTGCCCTTTCTGCAACCACGACAACCAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: TGTTCAGCTGCCCTTTCTGCAACCACGACAA-CAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|162279150|gb|FC455489.1|FC455489
EST:     GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|22131404|gb|BQ826597.1|BQ826597
EST:     AGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: AGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|22491946|gb|BU051869.1|BU051869
EST:     GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|67720461|gb|BJ970720.1|BJ970720
EST:     GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|67701971|gb|BJ962204.1|BJ962204
EST:     GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|100422336|gb|BY976324.1|BY976324
EST:     GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|162214749|gb|FC391820.1|FC391820
EST:     GACACCAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATNGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|18358618|gb|BJ190677.1|BJ190677
EST:     GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|162219651|gb|FC395647.1|FC395647
EST:     GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|162251659|gb|FC426065.1|FC426065
EST:     GCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|37840626|gb|BJ598634.1|BJ598634
EST:     GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|162258978|gb|FC435921.1|FC435921
EST:     GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|18370194|gb|BJ201796.1|BJ201796
EST:     GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|67718302|gb|BJ968561.1|BJ968561
EST:     GTGTTCA-CTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|162271047|gb|FC446607.1|FC446607
EST:     GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
EST: gi|18364714|gb|BJ196787.1|BJ196787
EST:     GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCAT                         GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA
genomic: GTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAA

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: 34 (upstream exon), 33 (downstream exon)
Score: 100

AGAGCGCGGCGAAGCCGGCTCCGCGGCGCGGCCAGGAGAAGCTCGCGACGGTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtaggg ... gcctccacagGGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGCGCGGCGAAGCCGGCTCCGCGGCGCGGCCAGGAGAAGCTCGCGACGGTGTTCAGCTGCCCTTTCTGCAACCACGACAACAGTGTGGAGTGCCGCATgtgagtagggagcttgtttgtggtcgtgagtttgtggtctgggtgggcttcgcggcgtgattttggcactgagaggcggcgagttgtgtgtttgtatgtttgtgtttggggttttgggtggattgtgtggctgacgtcagtgtgcctccacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG