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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTCAAGTGCTGGCAGGTGGTCGAGGGTTAGGTACTTTCAAGAATGGACTTAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctcctttccattttgatagaagctggttctagaggggtagaacaatttggttatgtttttctttattagactaggcatgttgttgattctatc...

Basic information

species Physcomitrella patens
transcript PP1S9_103V6.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S9_103V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT2G20420.1 (Arabidopsis thaliana), 5'ss of exon 3
AGTCAAGTGCTGGCAGGTGGTCGAGGGTTAGGTACTTTCAAGAATGGACTTAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctcctttccattttgatagaagctggttctagaggg-gtagaacaatttggttatgttt-ttctttattagactaggcatgttgttgattctatc
|| ||  |  |||| |||||  ||||  | || || ||||||| ||| ||||||||||||||||||||||| ||  | ||  |||  || ||||| || ||||     | |      | ||| | |  |||  |||| |||   ||       | | ||| |     || || ||     |       || ||  || ||  
AGCCAGATTTTGGCTGGTGGAAGAGGTCTTGGAACATTCAAGAGTGGTCTTAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtat--tgtacaggatttcttgtttgtggct--ttctggagtctgttttttgttgttgttgtacaagttattgatctatttcaaatctttattacttgtag-

upper sequence: PP1S9_103V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 5'ss of exon 3
AGTCAAGTGCTGGCAGGTGGTCGAGGGTTAGGTACTTTCAAGAATGGACTTAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctcctttccattttgatagaagctggttctagaggggtagaacaatttggttatgttttt--ctttattagactaggcatgttgttgattctatc-----
|| ||| | || |||||||| ||||| || || || ||||| | ||| ||||||||||| ||||||||||| ||||  |||||||| |||||| | || ||||         ||  |||||      |  |  || ||      || |    |||  || | |  ||  |||| ||    | |  || |  || ||  | |      
AGCCAAATTCTTGCAGGTGGGCGAGGCTTGGGAACATTCAAAAGTGGTCTTAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTGgtaa--taaggattgtattttat----atttcattttaacaccataaatttttttttttgtttccttagctttgtttcctttga-atctcttttatcatgtaaaggt
















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|208373828|gb|DC936599.1|DC936599
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|100436155|gb|BY979407.1|BY979407
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|100387442|gb|BY988313.1|BY988313
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|100379638|gb|BY949869.1|BY949869
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|100395304|gb|BY953670.1|BY953670
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|67712940|gb|BJ966389.1|BJ966389
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|100438224|gb|BY961716.1|BY961716
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|208369720|gb|DC932618.1|DC932618
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|208390018|gb|DC938073.1|DC938073
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|18326965|gb|BJ158966.1|BJ158966
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|208376441|gb|DC932309.1|DC932309
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|208354269|gb|DC902483.1|DC902483
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|208386847|gb|DC941565.1|DC941565
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|100365282|gb|BY966901.1|BY966901
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|67571747|gb|BJ944571.1|BJ944571
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGC
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGC
EST: gi|100450378|gb|CJ974233.1|CJ974233
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|100379592|gb|BY949846.1|BY949846
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|67704790|gb|BJ965023.1|BJ965023
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|67719429|gb|BJ969688.1|BJ969688
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|208364000|gb|DC939593.1|DC939593
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|208393623|gb|DC904339.1|DC904339
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|100376654|gb|BY949400.1|BY949400
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|100385264|gb|BY950856.1|BY950856
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|100394556|gb|BY989846.1|BY989846
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|100444730|gb|BY982559.1|BY982559
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|18350484|gb|BJ182535.1|BJ182535
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGG
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGG
EST: gi|100369353|gb|BY948059.1|BY948059
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|162189404|gb|FC366562.1|FC366562
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGC
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGC
EST: gi|100356151|gb|BY946222.1|BY946222
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|67508667|gb|BJ941528.1|BJ941528
EST:     TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA
EST: gi|100363621|gb|BY966478.1|BY966478
EST:     TAAGGGTGGTGATCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAG                         GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAG
genomic: TAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctc ... actttggcagGCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTCAAGTGCTGGCAGGTGGTCGAGGGTTAGGTACTTTCAAGAATGGACTTAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctcctttccattttgatagaagctggttctagaggggtagaacaatttggttatgtttttctttattagactaggcatgttgttgattctatc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG