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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACAATGGTTGAAAAGAAGTCTTGGACGAGGCCTCCCATTCAGATGGAGTTCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAGgtccgttctctacccctgcctctcgatgtgctaagttttcaatggtatgtgtagatacggtccacagggaattgctcaccttggtgatatttaatttatctag

Basic information

species Physcomitrella patens
transcript PP1S54_156V6.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S54_156V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: Vv02s0012g00910.t01 (Vitis vinifera), 5'ss of exon 11
---------------------------------------------AACAATGGTTGAAAAGAAGTCTTGGACGAGGCCTCCCATTCAGATGGAGTTCCAGGTTCCCATGTTTAC-TGCATCCGGCCTACGGGTTCGCTTTTTG-AAGgtccgttctctacccc--tgcctctcgatgtgctaagttttcaatggtatgtgtagatacggtccacagggaattgctcaccttggtgatatttaatttatctag
                                              || ||||  ||||||||||||||||| ||||| || ||||||||||| |||||||| || |     |  |   || |  |  | |  | ||||| |   |      || |||||     ||| |   |||| | | | |     |    | |                                                      
TGGACAAACTGAGCCAACAATGAGTGCAGAAGTAGAGTTGATTTCCACGATGGCAGAAAAGAAGTCTTGGACCAGGCCACCGATTCAGATGGAATTCCAGgtacctaaaaaaatatttttctgtacatcagagtggctttatatgataatgtttttctactataatgcattctgatgaggttaatgccagaattcaggaa----------------------------------------------------
















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|208351914|gb|DC917961.1|DC917961
EST:     TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGCTCGCTTTTTGAAG                         GTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
genomic: TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAGgtccgttctc ... atttatctagGTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
EST: gi|37823101|gb|BJ581167.1|BJ581167
EST:     TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAG                         GTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
genomic: TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAGgtccgttctc ... atttatctagGTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
EST: gi|162280314|gb|FC456331.1|FC456331
EST:     TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAG                         GTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
genomic: TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAGgtccgttctc ... atttatctagGTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
EST: gi|18341242|gb|BJ173275.1|BJ173275
EST:     TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAG                         GTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
genomic: TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAGgtccgttctc ... atttatctagGTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
EST: gi|162233607|gb|FC409366.1|FC409366
EST:     TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAG                         GTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
genomic: TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAGgtccgttctc ... atttatctagGTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
EST: gi|67701419|gb|BJ961652.1|BJ961652
EST:     TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAG                         GTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
genomic: TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAGgtccgttctc ... atttatctagGTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
EST: gi|208354116|gb|DC957378.1|DC957378
EST:     TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAG                         GTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
genomic: TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAGgtccgttctc ... atttatctagGTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
EST: gi|18336390|gb|BJ168412.1|BJ168412
EST:     TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAG                         GTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
genomic: TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAGgtccgttctc ... atttatctagGTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
EST: gi|162178166|gb|FC354884.1|FC354884
EST:     TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAG                         GTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
genomic: TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAGgtccgttctc ... atttatctagGTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
EST: gi|18334361|gb|BJ166378.1|BJ166378
EST:     TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAG                         GTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
genomic: TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAGgtccgttctc ... atttatctagGTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
EST: gi|208387404|gb|DC949189.1|DC949189
EST:     TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAG                         GTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
genomic: TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAGgtccgttctc ... atttatctagGTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
EST: gi|37840969|gb|BJ598977.1|BJ598977
EST:     TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAG                         GTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
genomic: TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAGgtccgttctc ... atttatctagGTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
EST: gi|162229888|gb|FC404341.1|FC404341
EST:     TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAG                         GTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
genomic: TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAGgtccgttctc ... atttatctagGTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
EST: gi|37821184|gb|BJ579250.1|BJ579250
EST:     TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAG                         GTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
genomic: TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAGgtccgttctc ... atttatctagGTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
EST: gi|67694036|gb|BJ954269.1|BJ954269
EST:     TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAG                         GTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
genomic: TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAGgtccgttctc ... atttatctagGTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
EST: gi|37849854|gb|BJ607862.1|BJ607862
EST:     TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAG                         GTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
genomic: TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAGgtccgttctc ... atttatctagGTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
EST: gi|162223091|gb|FC399982.1|FC399982
EST:     TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAG                         GTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
genomic: TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAGgtccgttctc ... atttatctagGTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
EST: gi|37836430|gb|BJ594438.1|BJ594438
EST:     TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAG                         GTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
genomic: TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAGgtccgttctc ... atttatctagGTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
EST: gi|18334031|gb|BJ166047.1|BJ166047
EST:     TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAG                         GTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
genomic: TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAGgtccgttctc ... atttatctagGTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
EST: gi|67695977|gb|BJ956210.1|BJ956210
EST:     TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAG                         GTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
genomic: TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAGgtccgttctc ... atttatctagGTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
EST: gi|162229889|gb|FC404342.1|FC404342
EST:     TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAG                         GTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA
genomic: TCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAGgtccgttctc ... atttatctagGTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACA

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: 29 (upstream exon), 32 (downstream exon)
Score: 10

AACAATGGTTGAAAAGAAGTCTTGGACGAGGCCTCCCATTCAGATGGAGTTCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAGgtccgttctc ... atttatctagGTATGGGAGAAAAGTGGTTACAGCACTGTTGAATGGGTGCGCTACATCACAAGAGCCGGTTCATACGAAATTCGGTGCTAATTTGGAACATTTGCCCATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACAATGGTTGAAAAGAAGTCTTGGACGAGGCCTCCCATTCAGATGGAGTTCCAGGTTCCCATGTTTACTGCATCCGGCCTACGGGTTCGCTTTTTGAAGgtccgttctctacccctgcctctcgatgtgctaagttttcaatggtatgtgtagatacggtccacagggaattgctcaccttggtgatatttaatttatctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG