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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttgaaactggagatgattcatcaatcccatttgtgcaacttctctttgaggtttgaaaactaaatgtttcatattcttcctctactgcgtctgaacagCCGCTGTTTCTGTCGGAAGTGAATCAACATTGTCTCAGGTCGTGGACTTTAAGAAACTGCAGAATGGCAG

Basic information

species Physcomitrella patens
transcript PP1S152_87V6.2
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|18326190|gb|BJ158189.1|BJ158189
EST:     TTCGACTTACTTACTATCTCGTCGACCAGGAACGGCAATGGAGACTCGAG                         CCGCTGTTTCTGTCGGAAGTGAATCAACATTGTCTCAGGTCGTGGACTTTA
genomic: TTCGACTTACTTACTATCTCGTCGACCAGGAACGGCAATGGAGACTCGAGgtacgttctt ... gtctgaacagCCGCTGTTTCTGTCGGAAGTGAATCAACATTGTCTCAGGTCGTGGACTTTA
EST: gi|162244981|gb|FC424939.1|FC424939
EST:     TTCGACTTACTTACTATCTCGTCGACCAGGAACGGCAATGGAGACTCGAG                         CCGCTGTTTCTGTCGGAAGTGAATCAACATTGTCTCAGGTCGTGGACTTTA
genomic: TTCGACTTACTTACTATCTCGTCGACCAGGAACGGCAATGGAGACTCGAGgtacgttctt ... gtctgaacagCCGCTGTTTCTGTCGGAAGTGAATCAACATTGTCTCAGGTCGTGGACTTTA
EST: gi|100419828|gb|BY957728.1|BY957728
EST:     TTCGACTTACTTACTATCTCGTCGACCAGGAACGGCAATGGAGACTCGAG                         CCGCTGTTTCTGTCGGAAGTGAATCAACATTGTCTCAGGTCGTGGACTTTA
genomic: TTCGACTTACTTACTATCTCGTCGACCAGGAACGGCAATGGAGACTCGAGgtacgttctt ... gtctgaacagCCGCTGTTTCTGTCGGAAGTGAATCAACATTGTCTCAGGTCGTGGACTTTA
EST: gi|162159476|gb|FC336265.1|FC336265
EST:     CCAGGAACGGCAATGGAGACTCGAG                         CCGCTGTTTCTGTCGGAAGTGAATCAACATTGTCTCAGGTCGTGGACTTTA
genomic: CCAGGAACGGCAATGGAGACTCGAGgtacgttctt ... gtctgaacagCCGCTGTTTCTGTCGGAAGTGAATCAACATTGTCTCAGGTCGTGGACTTTA
EST: gi|100397210|gb|BY972385.1|BY972385
EST:     TTCGACTTACTTACTATCTCGTCGACCAGGAACGGCAATGGAGACTCGAG                         CCGCTGTTTCTGTCGGAAGTGAATCAACATTGTCTCAGGTCGTGGACTTTA
genomic: TTCGACTTACTTACTATCTCGTCGACCAGGAACGGCAATGGAGACTCGAGgtacgttctt ... gtctgaacagCCGCTGTTTCTGTCGGAAGTGAATCAACATTGTCTCAGGTCGTGGACTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgaggtttgaaaactaaatgtttcatattcttcctctactgcgtctgaacagCCGCTGTTTCTGTCGGAAGTGAATCAACATTGTCTCAGGTCGTGGACTTTAAGAAACTGCAGAATGGCAG
              aactaaa  putative branch site (score: 2)
 taaatgtttcatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttgaaactggagatgattcatcaatcccatttgtgcaacttctctttgaggtttgaaaactaaatgtttcatattcttcctctactgcgtctgaacagCCGCTGTTTCTGTCGGAAGTGAATCAACATTGTCTCAGGTCGTGGACTTTAAGAAACTGCAGAATGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG