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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttctttttaaaaatttaaaaatttaaatttatttgtgaacttcttgctaatacgcatgttattgcatatttgatagtttgctttgatgatatgatcagATACTATGAGCTTGGTCCCGACGATCCCCCTTATGCAGCCAAGTTCTGGGACTGCTGCGGATCAGAAGATCCTGCGTCGGCAGGTTGCAAGACATCTTTT

Basic information

species Physcomitrella patens
transcript PP1S41_200V6.1
intron # 2
splice site 3'
intron type U2

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|162237518|gb|FC413003.1|FC413003
EST:     CGATTTCATCCTACCTATTTTGTCTCTCGTCGTCACGACGATCAGAAAAG                         ATACTATGAGCTTGGTCCCGACGATCCCCCTTATGCAGCCAAGTTCTGGGA
genomic: CGATTTCATCCTACCTATTTTGTCTCTCGTCGTCACGACGATCAGAAAAGgtagtcaaaa ... atatgatcagATACTATGAGCTTGGTCCCGACGATCCCCCTTATGCAGCCAAGTTCTGGGA
EST: gi|162249452|gb|FC424057.1|FC424057
EST:     CGATTTCATCCTACCTATTTTGTCTCTCGTCGTCACGACGATCAGAAAAG                         ATACTATGAGCTTGGTCCCGACGATCCCCCTTATGCAGCCAAGTTCTGGGA
genomic: CGATTTCATCCTACCTATTTTGTCTCTCGTCGTCACGACGATCAGAAAAGgtagtcaaaa ... atatgatcagATACTATGAGCTTGGTCCCGACGATCCCCCTTATGCAGCCAAGTTCTGGGA
EST: gi|67693894|gb|BJ954127.1|BJ954127
EST:     CGATTTCATCCTACCTATTTTGTCTCTCGTCGTCACGACGATCAGAAAAG                         ATACTATGAGCTTGGTCCCGACGATCCCCCTTATGCAGCCAAGTTCTGGGA
genomic: CGATTTCATCCTACCTATTTTGTCTCTCGTCGTCACGACGATCAGAAAAGgtagtcaaaa ... atatgatcagATACTATGAGCTTGGTCCCGACGATCCCCCTTATGCAGCCAAGTTCTGGGA
EST: gi|67570609|gb|BJ943433.1|BJ943433
EST:     CGATTTCATCCTACCTATTTTGTCTCTCGTCGTCACGACGATCAGAAAAG                         ATACTATGAGCTTGGTCCCGACGATCCCCCTTATGCAGCCAAGTTCTGGGA
genomic: CGATTTCATCCTACCTATTTTGTCTCTCGTCGTCACGACGATCAGAAAAGgtagtcaaaa ... atatgatcagATACTATGAGCTTGGTCCCGACGATCCCCCTTATGCAGCCAAGTTCTGGGA
EST: gi|100426000|gb|BY977227.1|BY977227
EST:     CGATTTCATCCTACCTATTTTGTCTCTCGTCGTCACGACGATCAGAAAAG                         ATACTATGAGCTTGGTCCCGACGATCCCCCTTATGCAGCCAAGTTCTGGGA
genomic: CGATTTCATCCTACCTATTTTGTCTCTCGTCGTCACGACGATCAGAAAAGgtagtcaaaa ... atatgatcagATACTATGAGCTTGGTCCCGACGATCCCCCTTATGCAGCCAAGTTCTGGGA
EST: gi|162269315|gb|FC445833.1|FC445833
EST:     CGATTTCATCCTACCTATTTTGTCTCTCGTCGTCACGACGATCAGAAAAG                         ATACTATGAGCTTGGTCCCGACGATCCCCCTTATGCAGCCAAGTTCTGGGA
genomic: CGATTTCATCCTACCTATTTTGTCTCTCGTCGTCACGACGATCAGAAAAGgtagtcaaaa ... atatgatcagATACTATGAGCTTGGTCCCGACGATCCCCCTTATGCAGCCAAGTTCTGGGA
EST: gi|162249451|gb|FC424056.1|FC424056
EST:     CGATTTCATCCTACCTATTTTGTCTCTCGTCGTCACGACGATCAGAAAAG                         ATACTATGAGCTTGGTCCCGACGATCCCCCTTATGCAGCCAAGTTCTGGGA
genomic: CGATTTCATCCTACCTATTTTGTCTCTCGTCGTCACGACGATCAGAAAAGgtagtcaaaa ... atatgatcagATACTATGAGCTTGGTCCCGACGATCCCCCTTATGCAGCCAAGTTCTGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctaatacgcatgttattgcatatttgatagtttgctttgatgatatgatcagATACTATGAGCTTGGTCCCGACGATCCCCCTTATGCAGCCAAGTTCTGGGACTGCTGCGGATCAGAAGATCCTGCGTCGGCAGGTTGCAAGACATCTTTT
                      atatttgatagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttctttttaaaaatttaaaaatttaaatttatttgtgaacttcttgctaatacgcatgttattgcatatttgatagtttgctttgatgatatgatcagATACTATGAGCTTGGTCCCGACGATCCCCCTTATGCAGCCAAGTTCTGGGACTGCTGCGGATCAGAAGATCCTGCGTCGGCAGGTTGCAAGACATCTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA