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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAAGGGTGGGGAATGTACGCCATCGGAGGGAGTGCGTTTCCAACAATCAATAGCGAGGGCAATCGCTTCTTCGCTCCCGATGGCAGCAACATGAAGGAAgtaagctccacatctttcacgacatttcaaccctattctccctcatactgatctttgaaattttaataatgctcagtggaatcaacaatgagacccttacttggtcgtttggtttttttacag

Basic information

species Physcomitrella patens
transcript PP1S563_1V6.1
intron # 3
splice site 5'
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|208399715|gb|DC924913.1|DC924913
EST:     ATAGCGAGGGCAATCGCTTCTTCGCTCCCGATGGCAGCAACATGAAGGAA                         GTGACAAAGCGGCTTGACGACGGAGGGGACAACTGGCGATCAGCTGGTGAC
genomic: ATAGCGAGGGCAATCGCTTCTTCGCTCCCGATGGCAGCAACATGAAGGAAgtaagctcca ... ttttttacagGTGACAAAGCGGCTTGACGACGGAGGGGACAACTGGCGATCAGCTGGTGAC
EST: gi|208394878|gb|DC915643.1|DC915643
EST:     ATAGCGAGGGCAATCGCTTCTTCGCTCCCGATGGCAGCAACATGAAGGAA                         GTGACAAAGCGGCTTGACGACGGAGGGGACAACTGGCGATCAGCTGGTGAC
genomic: ATAGCGAGGGCAATCGCTTCTTCGCTCCCGATGGCAGCAACATGAAGGAAgtaagctcca ... ttttttacagGTGACAAAGCGGCTTGACGACGGAGGGGACAACTGGCGATCAGCTGGTGAC
EST: gi|208381596|gb|DC915462.1|DC915462
EST:     ATAGCGAGGGCAATCGCTTCTTCGCTCCCGATGGCAGCAACATGAAGGAA                         GTGACAAAGCGGCTTGACGACGGAGGGGACAACTGGCGATCAGCTGGTGAC
genomic: ATAGCGAGGGCAATCGCTTCTTCGCTCCCGATGGCAGCAACATGAAGGAAgtaagctcca ... ttttttacagGTGACAAAGCGGCTTGACGACGGAGGGGACAACTGGCGATCAGCTGGTGAC
EST: gi|67720714|gb|BJ970973.1|BJ970973
EST:     CCGATGGCAGCAACATGAAGGAA                         GTGACAAAGCGGCTTGACGACGGAGGGGACAACTGGCGATCAGCTGGTGAC
genomic: CCGATGGCAGCAACATGAAGGAAgtaagctcca ... ttttttacagGTGACAAAGCGGCTTGACGACGGAGGGGACAACTGGCGATCAGCTGGTGAC
EST: gi|67725729|gb|BJ975988.1|BJ975988
EST:     CCGATGGCAGCAACATGAAGGAA                         GTGACAAAGCGGCCTGACGACGGAGGGGACAACTGGCGATCAGCTGGTGAC
genomic: CCGATGGCAGCAACATGAAGGAAgtaagctcca ... ttttttacagGTGACAAAGCGGCTTGACGACGGAGGGGACAACTGGCGATCAGCTGGTGAC
EST: gi|208351163|gb|DC926027.1|DC926027
EST:     ATAGCGAGGGCAATCGCTTNTTCGCTCCCGATGGCAGCAACATGAAGGAA                         GTGACAAAGCGGCTTGACGACGGAGGGGACAACTGGCGATCAGCTGNTGAC
genomic: ATAGCGAGGGCAATCGCTTCTTCGCTCCCGATGGCAGCAACATGAAGGAAgtaagctcca ... ttttttacagGTGACAAAGCGGCTTGACGACGGAGGGGACAACTGGCGATCAGCTGGTGAC
EST: gi|67720772|gb|BJ971031.1|BJ971031
EST:     ATAGCGAGGGCAATCGCTTCTTCGCTCCCGATGGCAGCAACATGAAGGAA                         GTGACAAAGCGGCTTGACGACGGAGGGGACAACTGGCGATCAGCTGGTGAC
genomic: ATAGCGAGGGCAATCGCTTCTTCGCTCCCGATGGCAGCAACATGAAGGAAgtaagctcca ... ttttttacagGTGACAAAGCGGCTTGACGACGGAGGGGACAACTGGCGATCAGCTGGTGAC
EST: gi|208381592|gb|DC915458.1|DC915458
EST:     ATAGCGAGGGCAATCGCTTCTTCGCTCCCGATGGCAGCAACATGAAGGAA                         GTGACAAAGCGGCTTGACGACGGAGGGGACAACTGGCGATCAGCTGGTGAC
genomic: ATAGCGAGGGCAATCGCTTCTTCGCTCCCGATGGCAGCAACATGAAGGAAgtaagctcca ... ttttttacagGTGACAAAGCGGCTTGACGACGGAGGGGACAACTGGCGATCAGCTGGTGAC
EST: gi|67724167|gb|BJ974426.1|BJ974426
EST:     ATAGCGAGGGCAATCGCTTCTTCGCTCCCGATGGCAGCAACATGAAGGAA                         GTGACAAAGCGGCTTGACGACGGAGGGGACAACTGGCGATCAGCTGGTGAC
genomic: ATAGCGAGGGCAATCGCTTCTTCGCTCCCGATGGCAGCAACATGAAGGAAgtaagctcca ... ttttttacagGTGACAAAGCGGCTTGACGACGGAGGGGACAACTGGCGATCAGCTGGTGAC
EST: gi|67724701|gb|BJ974960.1|BJ974960
EST:     ATAGCGAGGGCAATCGCTTCTTCGCTCCCGATGGCAGCAACATGAAGGAA                         GTGACAAAGCGGCTTGACGACGGAGGGGACAACTGGCGATCAGCTGGTGAC
genomic: ATAGCGAGGGCAATCGCTTCTTCGCTCCCGATGGCAGCAACATGAAGGAAgtaagctcca ... ttttttacagGTGACAAAGCGGCTTGACGACGGAGGGGACAACTGGCGATCAGCTGGTGAC
EST: gi|208379611|gb|DC927108.1|DC927108
EST:     ATAGCGAGGGCAATCGCTTCTTCGCTCCCGATGGCAGCAACATGAAGGAA                         GTGACAAAGCGGCTTGACGACGGAGGGGACAACTGGCGATCAGCTGGTGAC
genomic: ATAGCGAGGGCAATCGCTTCTTCGCTCCCGATGGCAGCAACATGAAGGAAgtaagctcca ... ttttttacagGTGACAAAGCGGCTTGACGACGGAGGGGACAACTGGCGATCAGCTGGTGAC
EST: gi|67725973|gb|BJ976232.1|BJ976232
EST:     ATAGCGAGGGCAATCGCTTCTTCGCTCCCGATGGCAGCAACATGAAGGAA                         GTGACAAAGCGGCTTGACGACGGAGGGGACAACTGGCGATCAGCTGGTGAC
genomic: ATAGCGAGGGCAATCGCTTCTTCGCTCCCGATGGCAGCAACATGAAGGAAgtaagctcca ... ttttttacagGTGACAAAGCGGCTTGACGACGGAGGGGACAACTGGCGATCAGCTGGTGAC
EST: gi|67725992|gb|BJ976251.1|BJ976251
EST:     ATAGCGAGGGCAATCGCTTCTTCGCTCCCGATGGCAGCAACATGAAGGAA                         GTGACAAAGCGGCTTGACGACGGAGGGGACAACTGGCGATCAGCTGGTGAC
genomic: ATAGCGAGGGCAATCGCTTCTTCGCTCCCGATGGCAGCAACATGAAGGAAgtaagctcca ... ttttttacagGTGACAAAGCGGCTTGACGACGGAGGGGACAACTGGCGATCAGCTGGTGAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 23 (upstream exon), 34 (downstream exon)
Score: 7

CGAAGGGTGGGGAATGTACGCCATCGGAGGGAGTGCGTTTCCAACAATCAATAGCGAGGGCAATCGCTTCTTCGCTCCCGATGGCAGCAACATGAAGGAAgtaagctcca ... ttttttacagGTGACAAAGCGGCTTGACGACGGAGGGGACAACTGGCGATCAGCTGGTGACATTTTCCTGAACGGTGCTTTCTTTACCGCATCAGGAGTCTCTGGTCAAT




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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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAAGGGTGGGGAATGTACGCCATCGGAGGGAGTGCGTTTCCAACAATCAATAGCGAGGGCAATCGCTTCTTCGCTCCCGATGGCAGCAACATGAAGGAAgtaagctccacatctttcacgacatttcaaccctattctccctcatactgatctttgaaattttaataatgctcagtggaatcaacaatgagacccttacttggtcgtttggtttttttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA