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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACGAATTTCATGTCAGACATAGCTGATGAGTTCAAGATTGTGGTTGTGGAGGCCATCCGCTCTTTGTGTCTCAAGTTCCCTCAAAAATATCGCTCATTgtgagctccatgttgatacacctttatttctttacaatatcttctgcatggactacatgttatatgtcacggctcttaaaatgctagttgcttaagtcagaataatacttgcttgattgatgatactggtacttacgttctggcatgacgagcgtcctgctcctttttttcag

Basic information

species Physcomitrella patens
transcript PP1S41_154V6.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S41_154V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: LOC_Os03g12590.1 (Oryza sativa), 5'ss of exon 9
TCACGAATTTCATGTCAGACATAGCTGATGAGTTCAAGATTGTGGTTGTGGAGGCCATCCGCTCTTTGTGTCTCAAGTTCCCTCAAAAATATCGCTCATTgtgagctccatgttgatacacctttatttctttacaatatcttctgcatggactacatgttatatgtcacggctcttaaa-atgctagttgcttaagtcagaataatacttgcttgattgatgatactggtacttacgttctggcatgacgagcgtcctgctcctttttttcag
| || |||||||||||||||||||| ||||| |||||||| || ||||| || || || || ||| | || || ||||| || |  || ||||| ||| |||  |           || | ||| |||   |    ||  | | | |||    |   ||   |||||   | || | |       | | ||   ||  |    | ||  ||  ||  |  ||                                                    
TTACCAATTTCATGTCAGACATAGCAGATGAATTCAAGATAGTTGTTGTTGAAGCTATACGATCTCTATGCCTTAAGTTTCCCCTGAAGTATCGTTCAATgtatg-----------taaatcttaattcggtgttgatgacatttacattcttttagtgccgtatgttttgactatcagttgcatttggtgtccaatgctct-tcatttttttttcttctatag--------------------------------------------------

upper sequence: PP1S41_154V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GRMZM2G012501_T02 (Zea mays), 5'ss of exon 7
TCACGAATTTCATGTCAGACATAGCTGATGAGTTCAAGATTGTGGTTGTGGAGGCCATCCGCTCTTTGTGTCTCAAGTTCCCTCAAAAATATCGCTCATTgtgagctccatgttgatacacctttatttctttacaata---tcttctgcatggactacatgttatatgtcacggctcttaaaatgctagttgcttaagtcagaataatacttgcttgattgatgatactggtacttacgttctggcatgacgagcgtcctgctcctttttttcag
| ||   ||||||||| |||||||| ||||| |||||||| || ||||| || || || || |||||||| || |||||||| | ||||||||||||| |||  |        ||| | |   ||  |||||| |  |    ||| |||| | |||||  | || | | |  | |                                                                                                     
TTACCCTTTTCATGTCTGACATAGCAGATGAATTCAAGATAGTTGTTGTTGAAGCTATACGGTCTTTGTGCCTGAAGTTCCCACTAAAATATCGCTCAATgtatgtgaacaactgaaagagtgttgattctttgccttcaattctactgctttgactatgtcttctgtctttcag-----------------------------------------------------------------------------------------------------

upper sequence: PP1S41_154V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GRMZM2G036034_T01 (Zea mays), 5'ss of exon 9
TCACGAATTTCATGTCAGACATAGCTGATGAGTTCAAGATTGTGGTTGTGGAGGCCATCCGCTCTTTGTGTCTCAAGTTCCCTCAAAAATATCGCTCATTgtgagctccatgttgatacacctttatttctttacaatatcttctg-catggactacatgttatatgtcacggctcttaaaatgctagttgcttaagtcagaataatacttgcttgattgatgatactggtacttacgttctggcatgacgagcgtcctgctcctttttttcag
| || || || ||||||||||||||||||||||| |||||||| ||||| || || ||  | ||| ||||  | ||||||||||  ||||||||||||||||  | |  ||      |   |||  |    |     | |    |  |||  ||||| | ||  || |    ||  |  || | | | ||   |   | ||                                                                         
TGACCAACTTTATGTCAGACATAGCTGATGAGTTTAAGATTGTTGTTGTTGAAGCAATAAGATCTCTGTGCTTGAAGTTCCCTCTGAAATATCGCTCATTgtatg-tatatagaagcatgtcttcttgcgctagtcttgttaaatatcataaactacctttttcatctataagcatt--aatttccatttatctgttttag-------------------------------------------------------------------------

upper sequence: PP1S41_154V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 9
TCACGAATTTCATGTCAGACATAGCTGATGAGTTCAAGATTGTGGTTGTGGAGGCCATCCGCTCTTTGTGTCTCAAGTTCCCTCAAAAATATCGCTCATTgtgagctccatgttgatacacctttatttctttacaatatcttctgcatggactacatgttatatgtcacggctcttaaaatgctagttgcttaagtcagaataatacttgcttgattgatgatactggtacttacgttctggcatgacgagcgtcctgctcctttttttcag
| || || || ||||||||||||||||||||||| |||||||| ||||| || || ||  | ||  ||||  | ||||||||||  ||||||||||||||||  |    || | ||  |   |||      ||    | |   |  | |  ||||| | ||  || |    ||  |  || |   | ||   |    |||                                                                         
TGACCAACTTTATGTCAGACATAGCTGATGAGTTTAAGATTGTTGTTGTTGAAGCAATAAGATCCCTGTGCTTGAAGTTCCCTCTGAAATATCGCTCATTgtatgt---atatagaagcgtgtttgcactattcttgt-taaacatcgtaaactacctttttcatctataagcatt--aattttcatttatctgttccag-------------------------------------------------------------------------

upper sequence: PP1S41_154V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: AT4G34450.1 (Arabidopsis thaliana), 5'ss of exon 8
TCACGAATTTCATGTCAGACATAGCTGATGAGTTCAAGATTGTGGTTGTGGAGGCCATCCGCTCTTTGTGTCTCAAGTTCCCTCAAAAATATCGCTCATTgtgagctccatgttgatacacctttatttctttacaatatcttctgcatggactacatgttatatgtcacggctcttaaaatgctagttgcttaagtcagaataatacttgcttgattgatgatactggtacttacgttctggcatgacgagcgtcctgctcctttttttcag
| || ||||| |||||||| || |||||||||||||| |||||||| ||||| || ||  | || |||||| | || ||||| |  |||||  | || |||| ||     | ||        ||| ||  ||     ||  ||  |  | ||  |  | |  | | |        | || ||| ||     |    | || ||    |||   ||||||||  ||       ||   || | |                              
TAACTAATTTTATGTCAGATATTGCTGATGAGTTCAAAATTGTGGTCGTGGACGCAATAAGATCGTTGTGTGTGAAATTCCCACTGAAATACAGATCCTTgtaagtaaagttttaggg----tttgttattt----gtagttttggtctcgagcatttctatttttttgaatgattaaatatgttatggtatctttttagcatttggctta--tgattgatc-tatcaccttttcatttgtag------------------------------

upper sequence: PP1S41_154V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 5'ss of exon 9
TCACGAATTTCATGTCAGACATAGCTGATGAGTTCAAGATTGTGGTTGTGGAGGCCATCCGCTCTTTGTGTCTCAAGTTCCCTCAAAAATATCGCTCATTgtgagctccatgttgatacacctttatttctttacaatatcttctgcatggactacatgttatatgtcacggctcttaaaatgctagttgcttaagtcagaataatacttgcttgattgatgatactggtacttacgttctggcatgacgagcgtcctgctcctttttttcag
| || |||||||||||||| || |||||||| ||||| ||||| || ||||| |||||| | || |||||  | ||||| |||   || ||| |  | |||| ||    ||  || |     || || || | |  | | | | ||    |  |  || || ||||||     | |||||     |||     | ||     | ||      | || | |   |  |    ||| | ||   |                              
TTACAAATTTCATGTCAGATATTGCTGATGAATTCAAAATTGTTGTAGTGGAAGCCATCAGATCATTGTGCTTGAAGTTTCCTTTGAAGTATAGAGCCTTgtaagtgatatcctgtt----tttgatgtcatcattaaaacatttg----ggttttatttt-tatgtctt---ttttaaatgaacagtgtaaaatgtttccgtcatgtgaaatagaataaccctttttcc-cttgcttttcag------------------------------

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|162210688|gb|FC386584.1|FC386584
EST:     GAGGCCATCCGCTCTTTGTGTCTCAAGTTCCCTCAAAAATATCGCTCATT                         GATGAATTTTCTGAGCAACATATTAAGAGAGGAAGGAGGGTTTGATTACAA
genomic: GAGGCCATCCGCTCTTTGTGTCTCAAGTTCCCTCAAAAATATCGCTCATTgtgagctcca ... tttttttcagGATGAATTTTCTGAGCAACATATTAAGAGAGGAAGGAGGGTTTGATTACAA