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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagaaatttacaattgagaaggtcagagagtagctatggcttcaattcatattggcctgattcaaatgtggtattgctattgtcgtgttcatcttaacagGTAGGGCACGATGGTGAGAATCAGTGTGTTGAACGATGCGTTGAAGAACATGTTCAATGCAGAGAAGCGTGGAAAGCGTCAAGTGTTGATTAGGCCTTCG

Basic information

species Physcomitrella patens
transcript PP1S41_94V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S41_94V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv08s0040g02460.t01 (Vitis vinifera), 3'ss of exon 1
------------tagaaatttacaattgagaaggtcagagagt---agctatggcttcaattcatattggcctgattcaaatgtggtattgctattgtcgt-gttcatcttaacagGTAGGGCACGATGGTGAGAATCAGTGTGTTGAACGATGCGTTGAAGAACATGTTCAATGCAGAGAAGCGTGGAAAGCGTCAAGTGTTGATTAGGCCTTCG
              || | ||| |  |       ||      |   |  |||| ||| ||  |||  |   |   |  |  | | |  || |  |||  |  |    ||||  || |        |||||||||| ||||||| ||||| |||||  | |||| |||||  |||||||||||||| |||||||| || ||  |||| |        
catctgtgttggctgatagttatatctccctccctccctccctctgaaatatgtcttgaagacatggttttcaattgaacttcttgctttacctttgcagCAGCCTTTCTTTGCAAG--------GATGGTGAGAGTCAGTGTCTTGAATGATGCTCTAAAGAGCATGTATAATGCAGAGAAGCGGGGAAAGCGACAGGTTATGATCA--------

upper sequence: PP1S41_94V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv13s0019g00530.t01 (Vitis vinifera), 3'ss of exon 2
----tagaaatttacaattgagaaggtcagagagtagctatggcttcaattcatattggcctgattcaaatgtggtattgctattgtcgtgttcatcttaacagG-----TAGGGCACGATGGTGAGAATCAGTGTGTTGAACGATGCGTTGAAGAACATGTTCAATGCAGAGAAGCGTGGAAAGCGTCAAGTGTTGATTAGGCCTTCG
      |   |     |||   |   |     | |    |||     | ||||| |     |  |    | || || |  | |   |  | |   |  || | |      |  |  | |||||||||| | |||||  |||| |||||  | |||| ||||| |||||||||||||||||| ||||| || ||| |||| |        
gtttctgttctgcttgatttctattttttcttatttatcatg-tgggatttcatgtcaaagttttgtgcaagtagtttgacaacccttttatattttgtagCGGCCTTGTTTAGTGAAGATGGTGAGAGTTAGTGTCCTGAATGATGCTCTCAAGAGCATGTACAATGCAGAGAAGCGTGGGAAGCGACAGGTGATGATCA--------
















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|162269234|gb|FC444764.1|FC444764
EST:     AGCTCCTCCCCTTCCTCGCCTTCACACCTCGGCTTGCTTGGCTCCTCAAG                         GTAGGGCACGATGGTGAGAATCAGTGTGTTGAACGATGCGTTGAAGAACAT
genomic: AGCTCCTCCCCTTCCTCGCCTTCACACCTCGGCTTGCTTGGCTCCTCAAGgtgtgttggc ... atcttaacagGTAGGGCACGATGGTGAGAATCAGTGTGTTGAACGATGCGTTGAAGAACAT
EST: gi|18374857|gb|BJ206435.1|BJ206435
EST:     AGCTCCTCCCCTTCCTCGCCTTCACACCTCGGCTTGCTTGGCTCCTCAAG                         GTAGGGCACGATGGTGAGAATCAGTGTGTTGAACGATGCGTTGAAGAACAT
genomic: AGCTCCTCCCCTTCCTCGCCTTCACACCTCGGCTTGCTTGGCTCCTCAAGgtgtgttggc ... atcttaacagGTAGGGCACGATGGTGAGAATCAGTGTGTTGAACGATGCGTTGAAGAACAT
EST: gi|37848628|gb|BJ606636.1|BJ606636
EST:     AGCTCCTCCCCTTCCTCGCCTTCACACCTCGGCTTGCTTGGCTCCTCAAG                         GTAGGGCACGATGGTGAGAATCAGTGTGTTGAACGATGCGTTGAAGAACAT
genomic: AGCTCCTCCCCTTCCTCGCCTTCACACCTCGGCTTGCTTGGCTCCTCAAGgtgtgttggc ... atcttaacagGTAGGGCACGATGGTGAGAATCAGTGTGTTGAACGATGCGTTGAAGAACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatattggcctgattcaaatgtggtattgctattgtcgtgttcatcttaacagGTAGGGCACGATGGTGAGAATCAGTGTGTTGAACGATGCGTTGAAGAACATGTTCAATGCAGAGAAGCGTGGAAAGCGTCAAGTGTTGATTAGGCCTTCG
         gcctgat  putative branch site (score: 4)
                                          ttcatctt  putative PPT
              attcaaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagaaatttacaattgagaaggtcagagagtagctatggcttcaattcatattggcctgattcaaatgtggtattgctattgtcgtgttcatcttaacagGTAGGGCACGATGGTGAGAATCAGTGTGTTGAACGATGCGTTGAAGAACATGTTCAATGCAGAGAAGCGTGGAAAGCGTCAAGTGTTGATTAGGCCTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC