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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAAATTGATCGATACGCCAGCGAGAACGTAAACAAGCTTCTCGTGGGCAACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaagcgaaaaccgaggcgatgttttccatgcatgggaagatagtgatgttgtaggttggatttagctgtgtgttttccatcgttggtggtgatt...

Basic information

species Physcomitrella patens
transcript PP1S91_243V6.3
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S91_243V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: EDO96600 (Chlamydomonas reinhardtii), 5'ss of exon 7
CGAAATTGATCGATACGCCAGCGAGAACGTAAACAAGCTTCTCGTGGGCAACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaagcgaaa--accgaggcgatgttttccatgcatgggaagatagtga--tgttg--taggttggatttagctgtgtgttttccatcgttggtggtgatt-------------------
||| ||||| || ||||||||||||||||| |||||||| || |||||||||||    || ||  | |||||||||||||| || ||      ||| |||||| |||    | |   || |  | | ||    ||  |  | ||| |  ||  |  |||||   ||   ||    |||| |  |   | |  |||| |   ||  |                   
CGAGATTGACCGGTACGCCAGCGAGAACGTGAACAAGCTGCTGGTGGGCAACAAGAGCGACCTGACGTCGAAGAAGGTGGTTGAGTACTCCGTCGCCAAGgtgcgtgtgctggacgcacgggtggggtgacggcccgggttcggaggccagccaagtgttggccagccgggtgccagcttttggggctgccgcgttcgacctgcatgtcttactactctatgcag

upper sequence: PP1S91_243V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: EFJ23285 (Selaginella moellendorffii), 5'ss of exon 6
CGAAATTGATCGATACGCCAGCGAGAACGTAAACAAGCTTCTCGTGGGCAACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaagcgaaaaccgaggcgatgttttccatgcatgggaagatagtgatgttgtaggttggatttagctgtgtgttttccatcgttggtggtgatt
||| || ||||| ||||| |||||||||||||||||||||||||| |||||||| |  ||| |  || | ||||| || ||||||||| | || || ||||||         | |||    |  ||  ||||  |  |  | |  |     |  |  |   || |    ||                             
CGAGATCGATCGCTACGCGAGCGAGAACGTAAACAAGCTTCTCGTCGGCAACAAGTGCGATTTAACTGCAAAGAAAGTCGTGGATTATCAGACTGCCAAGgtg---------acaacttctgttattctttctttctactgtacaaagtaaaaatcttttcttcgtgacag-----------------------------

upper sequence: PP1S91_243V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: EFJ20286 (Selaginella moellendorffii), 5'ss of exon 6
CGAAATTGATCGATACGCCAGCGAGAACGTAAACAAGCTTCTCGTGGGCAACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaagcgaaaaccgaggcgatgttttccatgcatgggaagatagtgatgttgtaggttggatttagctgtgtgttttccatcgttggtggtgatt
||| || ||||| ||||| |||||||||||||||||||||||||| |||||||| |  |||||  || ||||||| || ||||||||  |||| || ||||||       | ||| |       ||  ||||| |  |  | |  | ||| |   | |   || |    ||                             
CGAGATCGATCGCTACGCGAGCGAGAACGTAAACAAGCTTCTCGTCGGCAACAAGTGCGATCTAACTGCGAAGAAAGTCGTGGATTACCAAACTGCCAAGgtg------acaaaatct---cttattctttccgtctactgtacaa-agtaaaaatctttcttcgtgacag-----------------------------

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|208366025|gb|DC951120.1|DC951120
EST:     ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAG                         GCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
genomic: ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaag ... ttttgggcagGCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
EST: gi|208372871|gb|DC956272.1|DC956272
EST:     ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAG                         GCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
genomic: ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaag ... ttttgggcagGCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
EST: gi|208359445|gb|DC953998.1|DC953998
EST:     ACAAATCAGATCTTGCTTCGNAGNAGGTGGTGGATTATGNAACCGCTAAG                         NCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
genomic: ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaag ... ttttgggcagGCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
EST: gi|208359075|gb|DC957823.1|DC957823
EST:     ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAG                         GCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
genomic: ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaag ... ttttgggcagGCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
EST: gi|162261631|gb|FC438064.1|FC438064
EST:     ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAG                         GCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
genomic: ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaag ... ttttgggcagGCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
EST: gi|208367423|gb|DC951313.1|DC951313
EST:     ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAG                         GCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
genomic: ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaag ... ttttgggcagGCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
EST: gi|208370470|gb|DC952173.1|DC952173
EST:     ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAG                         GCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
genomic: ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaag ... ttttgggcagGCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
EST: gi|67692438|gb|BJ952671.1|BJ952671
EST:     GGTGGATTATGNAACCGCTAAG                         GCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
genomic: GGTGGATTATGAAACCGCTAAGgtgtgtgaag ... ttttgggcagGCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
EST: gi|162242155|gb|FC415820.1|FC415820
EST:     ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAG                         GCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
genomic: ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaag ... ttttgggcagGCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
EST: gi|208381304|gb|DC919194.1|DC919194
EST:     AAGGTGGTGGATTATGAAACCGCTAAG                         GCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
genomic: AAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaag ... ttttgggcagGCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
EST: gi|162150705|gb|FC327601.1|FC327601
EST:     ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAG                         GCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
genomic: ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaag ... ttttgggcagGCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
EST: gi|162279565|gb|FC455850.1|FC455850
EST:     TTCGAAGAAGGTGGTGGATTATTAAACCGCTAAG                         GCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
genomic: TTCGAAGAAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaag ... ttttgggcagGCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
EST: gi|208362953|gb|DC946878.1|DC946878
EST:     ACNAATCAGATCNTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAG                         GCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
genomic: ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaag ... ttttgggcagGCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
EST: gi|162173544|gb|FC350118.1|FC350118
EST:     GAAGGTGGTGGATTATGAAACCGCTAAG                         GCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
genomic: GAAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaag ... ttttgggcagGCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
EST: gi|208354508|gb|DC953872.1|DC953872
EST:     ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAG                         GCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
genomic: ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaag ... ttttgggcagGCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
EST: gi|67728237|gb|BJ978496.1|BJ978496
EST:     ACAAGTCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAG                         GCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
genomic: ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaag ... ttttgggcagGCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
EST: gi|208373179|gb|DC944892.1|DC944892
EST:     ACNANTCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAG                         GCA-TTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
genomic: ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaag ... ttttgggcagGCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
EST: gi|208367873|gb|DC955336.1|DC955336
EST:     ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAG                         GCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
genomic: ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaag ... ttttgggcagGCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
EST: gi|208369487|gb|DC952128.1|DC952128
EST:     GAAGGTGGTGGATTATGNAACCGCTAAG                         GCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
genomic: GAAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaag ... ttttgggcagGCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
EST: gi|67571758|gb|BJ944582.1|BJ944582
EST:     ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAG                         GCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
genomic: ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaag ... ttttgggcagGCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
EST: gi|208395629|gb|DC920247.1|DC920247
EST:     ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAG                         GCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
genomic: ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaag ... ttttgggcagGCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
EST: gi|208386592|gb|DC952773.1|DC952773
EST:     ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAG                         GCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
genomic: ACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaag ... ttttgggcagGCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAAT
EST: gi|208372194|gb|DC947997.1|DC947997
EST:     GAAGGTNGTGGATTATGAAACCCGNTAAG                         GCATTTGCCGATGAGATTGGAATTCCTTTTTTAGAAACAAGTGCAAAGAA
genomic: GAAGGTGGTGGATTATGAAA-CCGCTAAGgtgtgtgaag ... ttttgggcagGCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAAATTGATCGATACGCCAGCGAGAACGTAAACAAGCTTCTCGTGGGCAACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaagcgaaaaccgaggcgatgttttccatgcatgggaagatagtgatgttgtaggttggatttagctgtgtgttttccatcgttggtggtgatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA