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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTACGTGGATTTCATTTTCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttttcgtgggtccatttgcatgggactggtttgggttacatctggattggtggcatgtgatgtagtggttaatatttgataatgactagaacatttctcgctgtacatcctgcag

Basic information

species Physcomitrella patens
transcript PP1S74_140V6.1
intron # 10
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|208376489|gb|DC922520.1|DC922520
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|208364850|gb|DC957887.1|DC957887
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|208372243|gb|DC948046.1|DC948046
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|208356591|gb|DC922381.1|DC922381
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCCGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|37839167|gb|BJ597175.1|BJ597175
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|208383807|gb|DC928082.1|DC928082
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|208345159|gb|DC925457.1|DC925457
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|162227965|gb|FC404585.1|FC404585
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|162163035|gb|FC338425.1|FC338425
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|67699393|gb|BJ959626.1|BJ959626
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|37843958|gb|BJ601966.1|BJ601966
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|208362330|gb|DC954576.1|DC954576
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|208347730|gb|DC925603.1|DC925603
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|162160597|gb|FC337172.1|FC337172
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|208394555|gb|DC953594.1|DC953594
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|208374223|gb|DC945269.1|DC945269
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|162184644|gb|FC360842.1|FC360842
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCA-GGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|67720670|gb|BJ970929.1|BJ970929
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|162184643|gb|FC360841.1|FC360841
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|18337850|gb|BJ169874.1|BJ169874
EST:     AGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: AGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|208353070|gb|DC926093.1|DC926093
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|208368488|gb|DC947889.1|DC947889
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|208369247|gb|DC944564.1|DC944564
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|208395850|gb|DC924260.1|DC924260
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|37841119|gb|BJ599127.1|BJ599127
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|67727318|gb|BJ977577.1|BJ977577
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|208365534|gb|DC954775.1|DC954775
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|208347297|gb|DC925321.1|DC925321
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|162175918|gb|FC351596.1|FC351596
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|208394056|gb|DC957137.1|DC957137
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|208346565|gb|DC916831.1|DC916831
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|18340220|gb|BJ172248.1|BJ172248
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|208367374|gb|DC951292.1|DC951292
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|208356213|gb|DC957331.1|DC957331
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|37845825|gb|BJ603833.1|BJ603833
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|208374190|gb|DC945236.1|DC945236
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
EST: gi|37840264|gb|BJ598272.1|BJ598272
EST:     CAGAGCATTTGGCGCAAGTTCAAGGGNTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGGCTGCGTTACCGAAAG
genomic: CAGAGCATTT-GCGCAAGTTCAA-GGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTT-GGCTGCGTTACCGAAAG
EST: gi|162209215|gb|FC385434.1|FC385434
EST:     TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAG                         ACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT
genomic: TCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCT

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: 31 (upstream exon), 34 (downstream exon)
Score: 21

TTACGTGGATTTCATTTTCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttt ... catcctgcagACAGAGGACACCAAGGTGATAGCCGTAAAGTTGGCTGCGTTACCGAAAGCTGGCGGCACCCACAAGCGTGTCGCTGTCATCACCCAGGGAACTGACCCCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTACGTGGATTTCATTTTCGGCAACGAGAGCGAGGCCAGAGCATTTGCGCAAGTTCAAGGCTGGGAGgtaagacttttcgtgggtccatttgcatgggactggtttgggttacatctggattggtggcatgtgatgtagtggttaatatttgataatgactagaacatttctcgctgtacatcctgcag

- - - - - - - - - - - - - - - - - -  AGAGCA