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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGAAAAGAACTCATTAATTGGTGGTGACGACTTCAAGAGCGGTCAAACGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaagtgcaatgtgtagaggaataaatgtaataaagccttctaacttgcgctgaatccaacttagaatgtctattttttttggattcaggtgtgtctagaactgaagtttatgctttgcgaagctggaatgattgctatgaaagctttgcactgaacccacaattgttggtgtgcacag

Basic information

species Physcomitrella patens
transcript PP1S55_204V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S55_204V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GRMZM2G392513_T02 (Zea mays), 5'ss of exon 4
TGTTGAAAAGAACTCATTAATTGGTGGTGACGACTTCAAGAGCGGTCAAACGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaagtgcaatgtgtagaggaataaatgtaataaagccttctaacttgcgctgaatccaacttagaatgtctattttttttggat-tcaggtgtgtctagaactgaagtttatgctttgcgaagctggaatgattgctatgaaagctttgcactgaacccacaattgttggtgtgcacag
| |  | || ||||   | || |||||||||||||||||||| || || || ||||||||||| || ||||| || || |||||||| || ||||| |||||        | |||||      |  ||          ||   || |     |  | | ||   ||||| |||   | ||   | ||    |   | |   ||||                                                                                
TATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCAGTCCTAGTTGAATTCCTAGTTGGTGCTGGAATAAAGgtacaatttat-caatgaaacctgatatccccccttcgaaatgtttttggcag-acggcat---acttacaataattcttgcatatgttcattgagagcacctag--------------------------------------------------------------------------------

upper sequence: PP1S55_204V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GRMZM2G004528_T03 (Zea mays), 5'ss of exon 6
TGTTGAAAAGAACTCATTAATTGGTGGTGACGACTTCAAGAGCGGTCAAACGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaagtgcaatgtgtagaggaataaatgtaataaagc-cttctaacttgcgctgaatccaacttagaatgtctattttttttggattcaggtgtgtctagaactgaagtttatgctttgcgaagctggaatgattgctatgaaagctttgcactgaacccacaattgttggtgtgcacag
| |  | || ||||   | || |||||||||||||||||||| || || || ||||||||||| || || || || ||||| ||||| || ||||| |||||        | |||||      |  ||          ||    || |  |   ||    |   |   ||    || ||| | ||    || |||                                                                                          
TATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCGGTCCTGGTTGATTTTCTTGTTGGTGCTGGAATAAAGgtacaatttat-caatgaaacctgatatccccccttcgaaatgtttttggcagacgacatacttacaataattcgtgtatatgttc---atgcag------------------------------------------------------------------------------------------

upper sequence: PP1S55_204V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: GRMZM2G155242_T01 (Zea mays), 5'ss of exon 6
TGTTGAAAAGAACTCATTAATTGGTGGTGACGACTTCAAGAGCGGTCAAACGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaagtgcaatgtgtagaggaataaatgtaataaagccttctaacttgcgctgaatccaacttagaatgtctattttttttggattcaggtgtgtctagaactgaagtttatgctttgcgaagctggaatgattgctatgaaagctttgcactgaacccacaattgttggtgtgcacag
| |  |||| ||||  || ||||||||||||||||||||||| || || || ||||||||||| ||  | || || || || ||||| || ||||| |||||| |  |  |   || | |     | |||     || |||  || |         |||    |    |  |  |||  | | |||  |||    ||                                                                                       
TATAAAAAACAACTGCTTGATTGGTGGTGACGACTTCAAGAGTGGACAGACCAAGATGAAATCTGTCTTGGTCGATTTCCTTGTTGGTGCTGGAATAAAGgtggga-acctagtatctctcttctattaag----atgaagtgtttttttggcaaatgacgttattgcaataactcttctatattttcattttcatgcag------------------------------------------------------------------------------------

upper sequence: PP1S55_204V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: AT2G22240.1 (Arabidopsis thaliana), 5'ss of exon 4
TGTTGAAAAGAACTCATTAATTGGTGGTGACGACTTCAAGAGCGGTCAAACGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaagtgcaatgtgtagaggaataaatgtaataaagccttctaacttgcgctgaatccaacttagaatgtctattttttttggattcaggtgtgtctagaactgaagtttatgctttgcgaagctggaatgattgctatgaaagctttgcactgaacccacaattgttggtgtgcacag
| |    ||||| |  || |||||||| || || |||||||| ||||| || ||||||||||||||| | || || || || |||||||| || |||||||| |   || |  |   |||  |  ||  ||  |||      |||||    ||      |   |||| ||||||  | || |    |                                                                                                 
TATATCGAAGAATTGTTTGATTGGTGGGGATGATTTCAAGAGTGGTCAGACTAAGATGAAATCCGTTTTGGTTGATTTCCTTGTTGGAGCTGGCATTAAGgtaatagaattaaagcttgtttatcaagtaacctaacttg--cttctcttctgttagtgaaggaactaagaatggattttgtggcag-------------------------------------------------------------------------------------------------

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|40781590|gb|AJ583520.1|AJ583520
EST:     CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAG                         CCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
genomic: CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaag ... gtgtgcacagCCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
EST: gi|162197483|gb|FC372861.1|FC372861
EST:     CTAGTGGACTTTCTAGTNGGAGCGGGAA-TAAG                         C
genomic: CTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaag ... gtgtgcacag-
EST: gi|162197483|gb|FC372861.1|FC372861
EST:     CTAGTGGACTTTCTAGTNGGAGCGGGAA-TAAG                         C
genomic: CTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaag ... gtgtgcacag-
EST: gi|162247857|gb|FC420616.1|FC420616
EST:     CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAG                         CCAACGTCAATTGTTAGCTACAACCATT
genomic: CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaag ... gtgtgcacagCCAACGTCAATTGTTAGCTACAACCATT
EST: gi|162197697|gb|FC374947.1|FC374947
EST:     CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAG                         CCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
genomic: CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaag ... gtgtgcacagCCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
EST: gi|162170409|gb|FC347607.1|FC347607
EST:     CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAG                         CCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
genomic: CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaag ... gtgtgcacagCCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
EST: gi|162194434|gb|FC368539.1|FC368539
EST:     CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAG                         CCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
genomic: CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaag ... gtgtgcacagCCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
EST: gi|162165316|gb|FC340817.1|FC340817
EST:     CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAG                         CCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
genomic: CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaag ... gtgtgcacagCCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
EST: gi|162191433|gb|FC368190.1|FC368190
EST:     CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATAAAG                         CCCACGTCAATTGTTAGCTA
genomic: CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaag ... gtgtgcacagCCAACGTCAATTGTTAGCTA
EST: gi|162186353|gb|FC361661.1|FC361661
EST:     CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAG                         CCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
genomic: CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaag ... gtgtgcacagCCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
EST: gi|162184403|gb|FC359149.1|FC359149
EST:     CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAG                         CCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
genomic: CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaag ... gtgtgcacagCCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
EST: gi|162182475|gb|FC357450.1|FC357450
EST:     CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAG                         CCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
genomic: CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaag ... gtgtgcacagCCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
EST: gi|162175808|gb|FC352110.1|FC352110
EST:     CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAG                         CCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
genomic: CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaag ... gtgtgcacagCCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
EST: gi|162184271|gb|FC359693.1|FC359693
EST:     CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAG                         CCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
genomic: CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaag ... gtgtgcacagCCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
EST: gi|162220955|gb|FC396140.1|FC396140
EST:     CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAG                         CCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
genomic: CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaag ... gtgtgcacagCCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
EST: gi|162151547|gb|FC327260.1|FC327260
EST:     CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAG                         CCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
genomic: CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaag ... gtgtgcacagCCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
EST: gi|162213492|gb|FC389364.1|FC389364
EST:     CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAG                         CCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
genomic: CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaag ... gtgtgcacagCCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
EST: gi|162156175|gb|FC332550.1|FC332550
EST:     CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAG                         CCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
genomic: CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaag ... gtgtgcacagCCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
EST: gi|162182387|gb|FC357986.1|FC357986
EST:     CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAG                         CCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
genomic: CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaag ... gtgtgcacagCCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
EST: gi|162194175|gb|FC369687.1|FC369687
EST:     CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAG                         CCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
genomic: CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaag ... gtgtgcacagCCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
EST: gi|162198718|gb|FC373486.1|FC373486
EST:     CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAG                         CCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
genomic: CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaag ... gtgtgcacagCCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
EST: gi|162246259|gb|FC421966.1|FC421966
EST:     CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAG                         CCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
genomic: CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaag ... gtgtgcacagCCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
EST: gi|162218352|gb|FC394526.1|FC394526
EST:     CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAG                         CCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC
genomic: CGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaag ... gtgtgcacagCCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGAAAAGAACTCATTAATTGGTGGTGACGACTTCAAGAGCGGTCAAACGAAGATGAAATCCGTTCTAGTGGACTTTCTAGTTGGAGCGGGAATTAAGgtgagccaagtgcaatgtgtagaggaataaatgtaataaagccttctaacttgcgctgaatccaacttagaatgtctattttttttggattcaggtgtgtctagaactgaagtttatgctttgcgaagctggaatgattgctatgaaagctttgcactgaacccacaattgttggtgtgcacag

- - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG