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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtatacaagaccctacttttaatgtgggctatggttattgtgggctgtagtacgctgaaagagcgctcaacacactaacagttgtggatccgtttggcagATCCAACTTACATGATTCGAGCTGTACCGAGTATTGCATCTGATAATGTTTACTGCACCTTGTTGGCGCATAGTGCCATCCATGGTGCTATGGCTGGTTT

Basic information

species Physcomitrella patens
transcript PP1S69_13V6.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S69_13V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 12
-----------------------------------gtatacaagaccctacttttaatgtgggctatggttattgtgggctgtagtacg--ctgaaagagcgctcaacacactaacagt-tgtggatccgtttggcagATCCAACTTACATGATTCGAGCTGTACCGAGTATTGCATCTGATAATGTTTACTGCACCTTGTTGGCGCATAGTGCCATCCATGGTGCTATGGCTGGTTT
                                     || |      ||| ||| ||   |  |||   ||  | ||      ||||    |  |  ||  | |     || ||||||  |||   | |   ||||||||||||| |||||||| || ||  | || || | |||||| || ||||| ||||||||  || ||||||| |||||||| ||||| || |||||||| | 
gtaaagatcttgtttttatgttcaattctcgatgcacatgcggagtgctagtttgaa---gtactactttttatatgtatctgagtatctccctatggaatgtt----gcaataacagcctgttatttctaatggcagATCCAACCTACATGATCCGTGCAATTCCAAGCAATGCATCAGACAATGTCTACTGCACACTGCTGGCGCACAGTGCCATTCATGGGGCAATGGCTGGATA

upper sequence: PP1S69_13V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 12
gtatacaagaccctactt--ttaatgtgggctatggttatt-gtgggctgtagtacgctgaaagagcgctcaacacactaacagttgtggatccgtttggcagATCCAACTTACATGATTCGAGCTGTACCGAGTATTGCATCTGATAATGTTTACTGCACCTTGTTGGCGCATAGTGCCATCCATGGTGCTATGGCTGGTTT
|||  |     | |  ||  ||  ||   ||  || |  || ||    | ||| | |   |   | |     |   | |  | |   |   |   ||  | |||||||||||||||||| || ||| | || || | |||||| || ||||| || |||||| || | || ||||||||||| |||||||| ||||| || | 
gtaatcgtcttcttttttacttggtgaacgcagtgttagtttgtaatttatagcatgtcaaggaatc---tgatgaagtgcctgccat---ttttttatgtagATCCAACTTACATGATCCGTGCTATTCCAAGCAATGCATCAGACAATGTCTATTGCACCCTGCTCGCACATAGTGCCATTCATGGTGCAATGGCGGGATA

upper sequence: PP1S69_13V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA08G21370.1 (Glycine max), 3'ss of exon 10
gtatacaagaccctacttttaatgtgggctatggttattgtgggctgtagtacgctgaaagagcgctcaacacactaacagttgtggatccgtttggcagATCCAACTTACATGATTCGAGCTGTACCGAGTATTGCATCTGATAATGTTTACTGCACCTTGTTGGCGCATAGTGCCATCCATGGTGCTATGGCTGGTTT
       || | ||| | ||  |   ||      | |  |||     | |||    | ||     || | || | | | |    |   |  || ||  |||||| || |||||||| |||||||| || |||||||||||||||||||| || |||||  |  | || || |||||  | |||||||| |||||||| | 
----gtgag-ctctattctttctactggtgcaaatgagagtgttacct-gtataaagtaaatattctaacca-attgaaaaaaat---tttgtgtgatagATCCCACCTACATGATCCGAGCTGTTCCAAGTATTGCATCTGATAATGTATATTGCACTCTCCTTGCTCAAAGTGCTGTTCATGGTGCAATGGCTGGATA

upper sequence: PP1S69_13V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA15G02400.1 (Glycine max), 3'ss of exon 11
gtatacaagaccctacttttaatgtgggctatggttattgtgggctgtagtacgctgaaagagcgctcaac--acactaacagttgtggatccgtttggcagATCCAACTTACATGATTCGAGCTGTACCGAGTATTGCATCTGATAATGTTTACTGCACCTTGTTGGCGCATAGTGCCATCCATGGTGCTATGGCTGGTTT
                       ||| ||| |  || ||      | || |    | ||||| |    ||   | ||  | |       |   || | |||||||| ||||||||||| || ||| | || |||| ||||||||||||||| ||||||||| |  | || || |||||  | |||||||| ||||| || | 
-----------------------gtgagctctcttttttaaactgtatatttttattaaagaacaaaaaattgataccgataa--aaaaaattgtctcgcagATCCTACTTACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTATACTGCACCCTCCTTGCCCAAAGTGCTGTTCATGGTGCAATGGCAGGATA

upper sequence: PP1S69_13V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA07G01710.1 (Glycine max), 3'ss of exon 10
gtatacaagaccctacttttaatgtgggctatggttattgtgggctgtagtacgctgaaagagcgctcaacacactaacagttgtggatccgtttggcagATCCAACTTACATGATTCGAGCTGTACCGAGTATTGCATCTGATAATGTTTACTGCACCTTGTTGGCGCATAGTGCCATCCATGGTGCTATGGCTGGTTT
       || | ||  | ||  |   ||      |  | ||| | |    ||     |   |  | || |  || |   | || |   || ||  || |||||| || |||||||| || ||||| || ||||||||||||||||||||  | |||||  |  | || || |||||  | |||||||| |||||||| | 
----gtgag-ctctcttctttctactggtgcaaatggtagtgtgttacc-tatataaagtaaatgttctaaccaattgaaattttt--tctgtccggtagATCCCACCTACATGATCCGTGCTGTTCCAAGTATTGCATCTGATAATGTACATTGCACTCTCCTTGCTCAAAGTGCTGTTCATGGTGCAATGGCTGGATA

upper sequence: PP1S69_13V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA13G42990.1 (Glycine max), 3'ss of exon 11
gtatacaagaccctacttttaatgtgggctatggttattgtgggctgtagtacgctgaaagagcgctcaacacactaacagttgtggatccgtttggcagATCCAACTTACATGATTCGAGCTGTACCGAGTATTGCATCTGATAATGTTTACTGCACCTTGTTGGCGCATAGTGCCATCCATGGTGCTATGGCTGGTTT
                 |   | ||| | | |  || ||      | || |    |  |||| |    ||   || | || |     |   || | |||||||| || |||||||| || ||| | || |||| ||||||||||||||| ||||||||| |  | || || |||||  |||||||||| ||||| || | 
----------------gtgagacgtgagatctctttttttaactatatatttttattgaagaacaaaaaattgac-accaataaaaaaattgtctcgcagATCCTACATACATGATCCGTGCTATCCCAAGTAATGCATCTGATAATGTATACTGCACCCTCCTTGCCCAAAGTGCTGTCCATGGTGCAATGGCAGGATA

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|162268582|gb|FC443636.1|FC443636
EST:     GAACATTTTCCCAAAGTTTACAACGATCCTATCACGCTCAAGTACATAG                         ATCCAACTTACATGATTCGAGCTGTACCGAGTATTGCATCTGATAATGTTT
genomic: GAACATTTTCCCAAAGTTTACAACGATCCTATCACGCTCAAGTACATAGgtaattatca ... cgtttggcagATCCAACTTACATGATTCGAGCTGTACCGAGTATTGCATCTGATAATGTTT
EST: gi|162268581|gb|FC443635.1|FC443635
EST:     GAACATTTTCCCAAAGTTTACAACGATCCTATCACGCTCAAGTACATAG                         ATCCAACTTACATGATTCGAGCTGTACCGAGTATTGCATCTGATAATGTTT
genomic: GAACATTTTCCCAAAGTTTACAACGATCCTATCACGCTCAAGTACATAGgtaattatca ... cgtttggcagATCCAACTTACATGATTCGAGCTGTACCGAGTATTGCATCTGATAATGTTT
EST: gi|67700067|gb|BJ960300.1|BJ960300
EST:     GAACATTTTCCCAAAGTTTACAACGATCCTATCACGCTCAAGTACATAG                         ATCCAACTTACATGATTCGAGCTGTACCGAGTATTGCATCNGATAATGTTT
genomic: GAACATTTTCCCAAAGTTTACAACGATCCTATCACGCTCAAGTACATAGgtaattatca ... cgtttggcagATCCAACTTACATGATTCGAGCTGTACCGAGTATTGCATCTGATAATGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtagtacgctgaaagagcgctcaacacactaacagttgtggatccgtttggcagATCCAACTTACATGATTCGAGCTGTACCGAGTATTGCATCTGATAATGTTTACTGCACCTTGTTGGCGCATAGTGCCATCCATGGTGCTATGGCTGGTTT
                           cactaac  putative branch site (score: 1)
                                           tccgttt  putative PPT