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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCACACGCAACTTCAACGCTTGTGGGTGATTTAGCTGAAGTCAATGCAATCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAGgtacttatccttgaatatttactgaagatttagtcttggtaatatgaggtgcttgcctcagtttagaaatagttattgtagtctagatttccaaacggtattttttcggaaaaatagaaccttgacgaacggttggactgtgatgtctctaatgcattttaatgatttgttggaatgttttag

Basic information

species Physcomitrella patens
transcript PP1S52_45V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S52_45V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: Vv02s0025g01730.t01 (Vitis vinifera), 5'ss of exon 5
CGCACACGCAACTTCAACGCTTGTGGGTGATTTAGCTGAAGTCAATGCAATCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAGgta------cttatccttgaatatttact--gaagatttagtcttggtaatatgaggtgcttgcctcagtttagaaatagttattgtagtctagatttccaaacggtattttttcgga-aaaatagaaccttgacgaacggttgga--ctgtgatgtctctaatgc----attttaatgatttgttggaatgttttag-
 || || ||||| ||||| || |  || ||||| || || |||||||| ||||||||||||||||| || || || ||||| |||||||| |  ||||||| |      || |  |    | || | ||   | ||  ||      ||  |   |   | || |  ||  |  | |||   ||| |   | | |   |   |  |  |||| ||   | |  ||         |   | | |  ||  ||||||    | | |||     | |  |||  |||| |   ||  |||   
TGCTCATGCAACATCAACTCTGGCAGGGGATTTGGCAGAGGTCAATGCCATCAAGAAGGTCTTCAAGGACACATCTGAGATAAAGATGAACGGGACTAAGgcaagagaactaaatcccatacatatgcttgcatgaaataaatgaagttctgcaatacgatttctccatat--gcaatgactatagacctttgggaatatgacagagatttcttgacatatgattagcttaaaatctaagatgagaacctgtgaatcttatcatgtaataactggaattgtttgctcttattctttcag
















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|208385483|gb|DC956667.1|DC956667
EST:     TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAG                         TCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
genomic: TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAGgtacttatcc ... aatgttttagTCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
EST: gi|67727266|gb|BJ977525.1|BJ977525
EST:     TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAG                         TCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
genomic: TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAGgtacttatcc ... aatgttttagTCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
EST: gi|208363380|gb|DC946978.1|DC946978
EST:     TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAG                         TCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
genomic: TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAGgtacttatcc ... aatgttttagTCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
EST: gi|67724954|gb|BJ975213.1|BJ975213
EST:     TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAG                         TCTATGATTGGGCACTGTCTTGGAGCTGCNGGTGGCTTGGAAGCGATTGCT
genomic: TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAGgtacttatcc ... aatgttttagTCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
EST: gi|208386909|gb|DC956906.1|DC956906
EST:     TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAG                         TCTATGATTGGGCACTGTCTTGGAGCTGCGGGTGGCTTGGAAGCGATTGCT
genomic: TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAGgtacttatcc ... aatgttttagTCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
EST: gi|208386836|gb|DC953503.1|DC953503
EST:     TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAG                         TCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
genomic: TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAGgtacttatcc ... aatgttttagTCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
EST: gi|162183531|gb|FC359629.1|FC359629
EST:     TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAG                         TCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
genomic: TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAGgtacttatcc ... aatgttttagTCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
EST: gi|162226789|gb|FC403822.1|FC403822
EST:     TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAG                         TCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
genomic: TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAGgtacttatcc ... aatgttttagTCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
EST: gi|162254133|gb|FC429657.1|FC429657
EST:     TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAG                         TCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
genomic: TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAGgtacttatcc ... aatgttttagTCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
EST: gi|208399439|gb|DC924869.1|DC924869
EST:     TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAG                         TCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
genomic: TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAGgtacttatcc ... aatgttttagTCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
EST: gi|208394499|gb|DC953538.1|DC953538
EST:     TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAG                         TCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
genomic: TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAGgtacttatcc ... aatgttttagTCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
EST: gi|208387574|gb|DC953316.1|DC953316
EST:     TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAG                         TCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
genomic: TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAGgtacttatcc ... aatgttttagTCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
EST: gi|37851675|gb|BJ609683.1|BJ609683
EST:     TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAG                         TCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
genomic: TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAGgtacttatcc ... aatgttttagTCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
EST: gi|208366252|gb|DC943812.1|DC943812
EST:     TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAG                         TCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
genomic: TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAGgtacttatcc ... aatgttttagTCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
EST: gi|18337911|gb|BJ169935.1|BJ169935
EST:     TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAG                         TCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
genomic: TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAGgtacttatcc ... aatgttttagTCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
EST: gi|162166325|gb|FC342918.1|FC342918
EST:     TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAG                         TCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
genomic: TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAGgtacttatcc ... aatgttttagTCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
EST: gi|67725320|gb|BJ975579.1|BJ975579
EST:     TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAG                         TCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
genomic: TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAGgtacttatcc ... aatgttttagTCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
EST: gi|37850094|gb|BJ608102.1|BJ608102
EST:     TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAG                         TCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT
genomic: TCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAGgtacttatcc ... aatgttttagTCTATGATTGGGCACTGTCTTGGAGCTGCTGGTGGCTTGGAAGCGATTGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCACACGCAACTTCAACGCTTGTGGGTGATTTAGCTGAAGTCAATGCAATCAAGAAGGTCTTCAAAGATACCTCAGAGATCAAGATGAATGCAACTAAGgtacttatccttgaatatttactgaagatttagtcttggtaatatgaggtgcttgcctcagtttagaaatagttattgtagtctagatttccaaacggtattttttcggaaaaatagaaccttgacgaacggttggactgtgatgtctctaatgcattttaatgatttgttggaatgttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG