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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaagcaaagagattgttgcttttggctctatcgtccccgttatatatcagaggttgacgcttatataaataagttgatagttttagtttgtttctgcagTACGATGAAGCAGAGCGGAGGAGGGAAATGGCTAAGAACTCTCTTGAACGCTACACACATTACTATGAACGTTGGGCTACAAATGAGTCT

Basic information

species Physcomitrella patens
transcript PP1S178_72V6.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S178_72V6.2 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GRMZM5G876621_T02 (Zea mays), 3'ss of exon 9
tcaagcaaagagattgttgcttttggctctatcgtccccgttatatat-cagaggttgacgcttatataaa------taagttgata---gttttagtttgttt---ctgcagTACGATGAAGCAGAGCGGAGGAGGGAAATGGCTAAGAACTCTCTTGAACGCTACACACATTACTATGAACGTTGGGCTACAAATGAGTCT
       | ||| |  | ||||        ||       ||   |  | || || |||   | | ||  |       | | || ||    ||||| |||||||    || ||||| |||||| | ||  |||| || |||||||| |||||||| |||||  | ||||||||||| |||||||| |||||  | ||| |||| 
-----gtaggagttcttcgcttccaatctaatatcttttgtctgacctgcaaagtttgggtcatgtactagatcttctcaatttatttatgttttggtttgttgtgactacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCG

upper sequence: PP1S178_72V6.2 (Physcomitrella patens), 3'ss of exon 10
lower sequence: EFJ08409 (Selaginella moellendorffii), 3'ss of exon 9
tcaagcaaagagattgttgcttttggctctatcgtccccgttatatatcagaggttgacgcttatataaataagttgatagttttagtttgtttctg---cagTACGATGAAGCAGAGCGGAGGAGGGAAATGGCTAAGAACTCTCTTGAACGCTACACACATTACTATGAACGTTGGGCTACAAATGAGTCT
                                             || ||    ||||   |||  |   |   || |  |  | |   ||||| ||   |||||||||||||| ||| |||||||||||||||||||||||||  | ||  | || ||||||||||| || || ||||| || || || || 
--------------------------------------------gtacca---attgatatttacgtt--tcccttcacggactcatcctgtttgtgtaacagTACGATGAAGCTGAGAGGAGGAGGGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCA

upper sequence: PP1S178_72V6.2 (Physcomitrella patens), 3'ss of exon 10
lower sequence: EFJ15174 (Selaginella moellendorffii), 3'ss of exon 9
tcaagcaaagagattgttgcttttggctctatcgtccccgttatatatcagaggttgacgcttatataaataagttgatagttttagtttgtttctg---cagTACGATGAAGCAGAGCGGAGGAGGGAAATGGCTAAGAACTCTCTTGAACGCTACACACATTACTATGAACGTTGGGCTACAAATGAGTCT
                                             || ||    ||||   |||  |   |   || |  |  | |   ||||| ||   |||||||||||||| ||| ||||||| |||||||||||||||||  | ||  | || ||||||||||| || || ||||| || || || || 
--------------------------------------------gtacca---attgatatttacgtt--tcccttcacggactcatcctgtttgtgtaacagTACGATGAAGCTGAGAGGAGGAGAGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCA

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|22132083|gb|BQ826972.1|BQ826972
EST:     GAGGTTTCTATGCATGTAACCGTTATGAAACTGCCAAGCAAGAAGGCGTG                         TACGATGAAGCAGAGCGGAGGAGGGAAATGGCTAAGAACTCTCTTGAACGC
genomic: GAGGTTTCTATGCATGTAACCGTTATGAAACTGCCAAGCAAGAAGGCGTGgtaagtggac ... gtttctgcagTACGATGAAGCAGAGCGGAGGAGGGAAATGGCTAAGAACTCTCTTGAACGC
EST: gi|162175945|gb|FC352351.1|FC352351
EST:     GAGGTTTCTATGCATGTAACCGTTATGAAACTGCCAAGCAAGAAGGCGTG                         TACGATGAAGCAGAGCGGAGGAGGGAAATGGCTAAGAACTCTCTTGAACGC
genomic: GAGGTTTCTATGCATGTAACCGTTATGAAACTGCCAAGCAAGAAGGCGTGgtaagtggac ... gtttctgcagTACGATGAAGCAGAGCGGAGGAGGGAAATGGCTAAGAACTCTCTTGAACGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcagaggttgacgcttatataaataagttgatagttttagtttgtttctgcagTACGATGAAGCAGAGCGGAGGAGGGAAATGGCTAAGAACTCTCTTGAACGCTACACACATTACTATGAACGTTGGGCTACAAATGAGTCT
                                          tttgtttct  CT-rich tract
                ttatataaataagttg  TA-rich tract