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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgcactgtcattgtcaacataattatcgggatgcttttatcacgaatatatttatagatttcggcttttactcgttgcctaactatagactgaatacagGCTGAATGGCGCGGAATCGGAGTCCAGCAATCACGCGGGTGGGTGCACTATGCAATTCACCGACCTGAGCCGCACATCATGCTCTTCCGCAGACCCCTCA

Basic information

species Physcomitrella patens
transcript PP1S7_399V6.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S7_399V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os03g05300.1 (Oryza sativa), 3'ss of exon 2
-----atgcactgtcattgtcaacataattatcgggatgcttttatcac-gaatatatttatagatt------tcggcttttactcgttgcctaactatagactgaatacagGCTGAATGGCGCGGAATCGGAGTCCAGCAATCACGCGGGTGGGTGCACTATGCAATTCACCGACCTGAGCCGCACATCATGCTCTTCCGCAGACCCCTCA
      | ||   ||       ||||   | | |    || ||  |    | ||  |||  | ||||      | ||    |    |||       |   |  |   | |||   || |||||||  |||||||| |||||    ||||||||||||||||| || || ||||| || ||||||||||||||||| |||||| | || ||||
gtaaccttcaagatctccaaatacattcgtgtagaatcgcgttcctggttggatcgattcgttgattgtctgattggggaatgggggtttttccgatggggtttatttgcagAACGAGTGGCGCGCGATCGGAGTGCAGCAGAGCCGCGGGTGGGTGCACTACGCGATCCACCGGCCGGAGCCGCACATCATGCTGTTCCGCCGCCCGCTCA

upper sequence: PP1S7_399V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G038485_T02 (Zea mays), 3'ss of exon 2
---------------------atgcactgtcattgtcaacataattatcgggatgcttttatca-cgaatatatt-tatagatttcggcttttactcgttgcctaactatagactgaatacagGCTGAATGGCGCGGAATCGGAGTCCAGCAATCACGCGGGTGGGTGCACTATGCAATTCACCGACCTGAGCCGCACATCATGCTCTTCCGCAGACCCCTCA
                       ||| |   || |    | |  |  ||  | ||||||  |   | |||   |    |   |   || |    | |    ||   |           | |||    | |||||     | || || |||||    ||||||||||||||||| || || ||||| || ||||||||||||||||| |||||| | ||  |||
gtaaaacgcctgcagtttcacccgcattcctatagattgcgttctcgtcctgttgctttggttgtctaatgcctggcctttgtgggggatccccccccccccccccccccctctcctgtgcagAAGCAGTGGCGGTTGGTGGGTGTGCAGCAGAGCCGCGGGTGGGTGCACTACGCGATCCACCGGCCGGAGCCGCACATCATGCTGTTCCGCCGCCCGATCA

upper sequence: PP1S7_399V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AC149818.2_FGT004 (Zea mays), 3'ss of exon 2
--------------------atgcactgtcattgtcaacataattatcgggatgcttttatca-cgaatatatttatagatttcggcttttactcgttgcctaactatagactgaatacagGCTGAATGGCGCGGAATCGGAGTCCAGCAATCACGCGGGTGGGTGCACTATGCAATTCACCGACCTGAGCCGCACATCATGCTCTTCCGCAGACCCCTCA
                     |||| |    |||    | |  ||  |  | || |||  | | |  ||   |  ||  ||||     | |     ||      || |    |   | |||   || |||||||  |||||||| |||||    ||||||||||||||||| || || ||||| || ||||||||||||||||| |||||| | ||  |||
gtaaacgcctgcagttccacctgcatttatgttgattgcgttcttgccctgttggtttggttatctgatgcctggatgaattttttggtgtggggatttttcccct-tctcttctttgcagAACGAGTGGCGCGCGATCGGAGTGCAGCAGAGCCGCGGGTGGGTGCACTACGCGATCCACCGCCCGGAGCCGCACATCATGCTGTTCCGCCGCCCGATCA

upper sequence: PP1S7_399V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv06s0061g00810.t01 (Vitis vinifera), 3'ss of exon 3
atgcactgtcattgtcaacataattatcgggatgcttttatc----acgaatatatttatagatttcggc--ttttactcgttgcctaactatagactgaatacagGCTGAATGGCGCGGAATCGGAGTCCAGCAATCACGCGGGTGGGTGCACTATGCAATTCACCGACCTGAGCCGCACATCATGCTCTTCCGCAGACCCCTCA
     || |   ||     | ||   |  || |  || |||     | ||| | | ||  |   ||| ||     ||    |    |     | |  ||| | |||  ||||||||| |  || || || |||||    || |||||||| |||||||||||||| || |||||||| ||||||||||||||| | || || || |
-----ctctttctgcttcta-aacagtgcggttttttctattgaaaaagaaaaaaatttcaatcttctgcagccctaaagttgatattttgttgggttgatttcagAATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTATGCAATTCATCGCCCTGAGCCACACATCATGCTCTTCAGGAGGCCTCTGA

upper sequence: PP1S7_399V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EDP06083 (Chlamydomonas reinhardtii), 3'ss of exon 2
atgcactgtcattgtcaa-cataattatcg-ggatgcttttatcacgaatatatttatagatttcggcttttactcgttgcctaact-atagactgaatacagGCTGAATGGCGCGGAATCGGAGTCCAGCAATCACGCGGGTGGGTGCACTATGCAATTCACCGACCTGAGCCGCACATCATGCTCTTCCGCAGACCCCTCA
             || |  | |  ||||    || |   ||   | |      |      | |||| |||| |    |  | |  |     |  |   | |||   || |||||||   | || || ||||| || || || ||||||||||| || ||||||||||| ||||| || |||||||| ||| |           
-------------gtgaggcgtgcttatgatagacggcattcctatgcgcccctgcgccaacttcgcctttaaactatctcatcccccgctgctttcctgcagAACGAGTGGCGCGCTCTGGGCGTGCAGCAGTCGCGTGGCTGGGTGCACTACGCGATTCACCGACCAGAGCCACATATCATGCTGTTCAG-----------

upper sequence: PP1S7_399V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ28856 (Selaginella moellendorffii), 3'ss of exon 2
atgcactgtcattgtcaacataattatcgggatgcttttatcacgaatatatttatagatttcggcttttactcgttgcctaactatagactgaatacagGCTGAATGGCGCGGAATCGGAGTCCAGCAATCACGCGGGTGGGTGCACTATGCAATTCACCGACCTGAGCCGCACATCATGCTCTTCCGCAGACCCCTCA
                                || ||   |      | | |  ||   |||  ||||   |   |||  |      | | |   |  ||   |||||| |   ||| ||||| ||||| ||  | || ||||| ||||| || |||||| |||| ||||||||||||||||||||  | || || || |
-------------------------------gtgtttgcgttcttcttctttgcatttgtttttgcttaacccgcttgttttctctcaaatt---tctagAACGAATGGAGGACAATTGGAGTGCAGCAGTCTAGAGGCTGGGTTCACTACGCGATTCACAGACCGGAGCCGCACATCATGCTCTTTAGAAGGCCTCTAA

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|67702808|gb|BJ963041.1|BJ963041
EST:     TCCCTCCCGACATTGCCAAGTTGTTACCCAAGAACCGGCTTCTGTCCGAG                         GCTGAATGGCGCGGAATCGGAGCCCAGCAATCACGCGGGTGGGTGCACTAT
genomic: TCCCTCCCGACATTGCCAAGTTGTTACCCAAGAACCGGCTTCTGTCCGAGgtattacatg ... ctgaatacagGCTGAATGGCGCGGAATCGGAGTCCAGCAATCACGCGGGTGGGTGCACTAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatatatttatagatttcggcttttactcgttgcctaactatagactgaatacagGCTGAATGGCGCGGAATCGGAGTCCAGCAATCACGCGGGTGGGTGCACTATGCAATTCACCGACCTGAGCCGCACATCATGCTCTTCCGCAGACCCCTCA
                                gcctaac  putative branch site (score: 2)
     atttatagattt  TA-rich tract