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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAAGTGTTGGCAGATTCGGAAACAGTCGAAGGCTCCGCAAGCAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtcgtaaccagcatacccctttcgttttctcccaagatttgtagatgataattaacgagctatcttcttattttacag

Basic information

species Physcomitrella patens
transcript PP1S207_28V6.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S207_28V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GRMZM2G146115_T02 (Zea mays), 5'ss of exon 9
GTGAAGTGTTGGCAGATTCGGAAACAGTCGAAGGCTCCGCAAGCAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgta--cgaagtcgtaaccagcatacccct---ttcgttttctcccaagatttg--tagatgataattaacgag--ctatcttcttattttacag----------------------------------------------------
|| || |||||||||||  |    ||| | || ||||| ||||| |||||||| || ||||| |||||||||||||||||||| || || ||||||  | | |   |    |    ||   |   ||  ||  ||     ||||||  |  ||  ||  | | |||  |  |||| |    ||                                                        
GTAAAATGTTGGCAGATCAGACGCCAGACTAAAGCTCCTCAAGCTGCTGGTGCAATTCACACTGATTTTGAAAGGGGTTTCATATGCGCTGAGgtaacctatgctatttttatgtaactgatatatttattaactattgtgatttggctgtatactagctgatgaggccagtcttttggcattgtttacttggctctatacatgtttcatatatgagtgttacttctttcgtgggtcag
















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|162264592|gb|FC440888.1|FC440888
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|162249698|gb|FC426526.1|FC426526
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|37827125|gb|BJ585137.1|BJ585137
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|162175834|gb|FC352136.1|FC352136
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|18340498|gb|BJ172526.1|BJ172526
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|7287402|gb|AW599889.1|AW599889
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|162217120|gb|FC392484.1|FC392484
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|15261208|gb|BI436518.1|BI436518
EST:     AGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: AGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|162191630|gb|FC367675.1|FC367675
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|162191631|gb|FC367676.1|FC367676
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|37840412|gb|BJ598420.1|BJ598420
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|37826709|gb|BJ584721.1|BJ584721
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|37827937|gb|BJ585949.1|BJ585949
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|37828408|gb|BJ586420.1|BJ586420
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|208374509|gb|DC944979.1|DC944979
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|37839229|gb|BJ597237.1|BJ597237
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|208352669|gb|DC921403.1|DC921403
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|37851612|gb|BJ609620.1|BJ609620
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|7583861|gb|AW699764.1|AW699764
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|67720060|gb|BJ970319.1|BJ970319
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|162217121|gb|FC392485.1|FC392485
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|37837900|gb|BJ595908.1|BJ595908
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|162263697|gb|FC439622.1|FC439622
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|7286362|gb|AW598903.1|AW598903
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|37848687|gb|BJ606695.1|BJ606695
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGNCGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|208353452|gb|DC946316.1|DC946316
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|67697251|gb|BJ957484.1|BJ957484
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|208378223|gb|DC918844.1|DC918844
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|37845126|gb|BJ603134.1|BJ603134
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|37826854|gb|BJ584866.1|BJ584866
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|162272680|gb|FC448306.1|FC448306
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|208365594|gb|DC944092.1|DC944092
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|37831279|gb|BJ589291.1|BJ589291
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|37845996|gb|BJ604004.1|BJ604004
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
EST: gi|37824831|gb|BJ582897.1|BJ582897
EST:     CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAG                         GTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG
genomic: CAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG

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: 35 (upstream exon), 35 (downstream exon)
Score: 40

GTGAAGTGTTGGCAGATTCGGAAACAGTCGAAGGCTCCGCAAGCAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtc ... tattttacagGTCATGAAGTTTGACGACTTGAAGGAGCTCGGAAGTGAGTCAGCGGTGAAG




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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
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGAAGTGTTGGCAGATTCGGAAACAGTCGAAGGCTCCGCAAGCAGCTGGTGCTATACACACAGATTTTGAAAGGGGTTTCATCTGTGCAGAGgtacgaagtcgtaaccagcatacccctttcgttttctcccaagatttgtagatgataattaacgagctatcttcttattttacag

- - - - - - - - - - - - - - - - - - - - -  CAGCTG