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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcaagcctctctattcgccacccatttgttgttgaagttctttctcgtgatgtacaacaaatgctcaataaatctattcgtatcctcactttccttgctccaaacctcccttctcggtggacgactgttctaattatgtttatgcctgtcactgcagGGTGGTGGTACGGTGTAGTGGGACATTCTGAGGGTTGCGAAGGGAGCTCTCGACATTGCCGTTGCTATTCGCTTG

Basic information

species Physcomitrella patens
transcript PP1S194_4V6.4
intron # 3
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|162197958|gb|FC373674.1|FC373674
EST:     AGGCGATTGCGTTGAGGTGCAATGGCGTAGGAACAAAGATTTCCCTTACG                         GGTGGTGGTACGGTGTAGTGGGACATTCTGAGGGTTGCGAAGGGAGCTCTC
genomic: AGGCGATTGCGTTGAGGTGCAATGGCGTAGGAACAAAGATTTCCCTTACGgtaagttcaa ... gtcactgcagGGTGGTGGTACGGTGTAGTGGGACATTCTGAGGGTTGCGAAGGGAGCTCTC
EST: gi|37840557|gb|BJ598565.1|BJ598565
EST:     AGGCGATTGCGTTGAGGTGCAATGGCGTAGGAACAAAGATTTCCCTTACG                         GGTGGTGGTACGGTGTAGTGGGACATTCTGAGGGTTGCGAAGGGAGCTCTC
genomic: AGGCGATTGCGTTGAGGTGCAATGGCGTAGGAACAAAGATTTCCCTTACGgtaagttcaa ... gtcactgcagGGTGGTGGTACGGTGTAGTGGGACATTCTGAGGGTTGCGAAGGGAGCTCTC
EST: gi|162213128|gb|FC389552.1|FC389552
EST:     AGGCGATTGCGTTGAGGTGCAATGGCGTAGGAACAAAGATTTCCCTTACG                         GGTGGTGGTACGGTGTAGTGGGACATTCTGAGGGTTGCGAAGGGAGCTCTC
genomic: AGGCGATTGCGTTGAGGTGCAATGGCGTAGGAACAAAGATTTCCCTTACGgtaagttcaa ... gtcactgcagGGTGGTGGTACGGTGTAGTGGGACATTCTGAGGGTTGCGAAGGGAGCTCTC
EST: gi|162171360|gb|FC347259.1|FC347259
EST:     AGGCGATTGCGTTGAGGTGCAATGGCGTAGGAACAAAGATTTCCCTTACG                         GGTGGTGGTACGGTGTAGTGGGACATTCTGAGGGTTGCGAAGGGAGCTCTC
genomic: AGGCGATTGCGTTGAGGTGCAATGGCGTAGGAACAAAGATTTCCCTTACGgtaagttcaa ... gtcactgcagGGTGGTGGTACGGTGTAGTGGGACATTCTGAGGGTTGCGAAGGGAGCTCTC
EST: gi|162197957|gb|FC373673.1|FC373673
EST:     AGGCGATTGCGTTGAGGTGCAATGGCGTAGGAACAAAGATTTCCCTTACG                         GGTGGTGGTACGGTGTAGTGGGACATTCTGAGGGTTGCGAAGGGAGCTCTC
genomic: AGGCGATTGCGTTGAGGTGCAATGGCGTAGGAACAAAGATTTCCCTTACGgtaagttcaa ... gtcactgcagGGTGGTGGTACGGTGTAGTGGGACATTCTGAGGGTTGCGAAGGGAGCTCTC
EST: gi|37838675|gb|BJ596683.1|BJ596683
EST:     AGGCGATTGCGTTGAGGTGCAATGGCGTAGGAACAAAGATTTCCCTTACG                         GGTGGTGGTACGGTGTAGTGGGACATTCTGAGGGTTGCGAAGGGAGCTCTC
genomic: AGGCGATTGCGTTGAGGTGCAATGGCGTAGGAACAAAGATTTCCCTTACGgtaagttcaa ... gtcactgcagGGTGGTGGTACGGTGTAGTGGGACATTCTGAGGGTTGCGAAGGGAGCTCTC
EST: gi|67692780|gb|BJ953013.1|BJ953013
EST:     AGGCGATTGCGTTGAGGTGCAATGGCGTAGGAACAAAGATTTCCCTTACG                         GGTGGTGGTACGGTGTAGTGGGACATTCTGAGGGTTGCGAAGGGAGCTCTC
genomic: AGGCGATTGCGTTGAGGTGCAATGGCGTAGGAACAAAGATTTCCCTTACGgtaagttcaa ... gtcactgcagGGTGGTGGTACGGTGTAGTGGGACATTCTGAGGGTTGCGAAGGGAGCTCTC
EST: gi|67695299|gb|BJ955532.1|BJ955532
EST:     AGGCGATTGCGTTGAGGTGCAATGGCGTAGGAACAAAGATTTCCCTTACG                         GGTGGTGGTACGGTGTAGTGGGACATTCTGAGGGTTGCGAAGGGAGCTCTC
genomic: AGGCGATTGCGTTGAGGTGCAATGGCGTAGGAACAAAGATTTCCCTTACGgtaagttcaa ... gtcactgcagGGTGGTGGTACGGTGTAGTGGGACATTCTGAGGGTTGCGAAGGGAGCTCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacctcccttctcggtggacgactgttctaattatgtttatgcctgtcactgcagGGTGGTGGTACGGTGTAGTGGGACATTCTGAGGGTTGCGAAGGGAGCTCTCGACATTGCCGTTGCTATTCGCTTG
                         ttctaat  putative branch site (score: 2)
                         ttctaattatgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcaagcctctctattcgccacccatttgttgttgaagttctttctcgtgatgtacaacaaatgctcaataaatctattcgtatcctcactttccttgctccaaacctcccttctcggtggacgactgttctaattatgtttatgcctgtcactgcagGGTGGTGGTACGGTGTAGTGGGACATTCTGAGGGTTGCGAAGGGAGCTCTCGACATTGCCGTTGCTATTCGCTTG

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