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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCGAATCTTTATTGTATTGGTGACGCCAATGGGAAAATGATGTTAGCACATGCAGCTAGTGCCCAAGGCATCTCTGgtatgtcaattggctctaagacaaataaatgaagtatttatttatatatttattgatttttatcctcaatgctccaatgcttcaaagctattcgatggttccacgcaattgataaattttatgatattttagtttgaagtccttaccgagttaatgactttcttttacag

Basic information

species Physcomitrella patens
transcript PP1S352_68V6.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S352_68V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: AT3G16950.2 (Arabidopsis thaliana), 5'ss of exon 10
GTTCCGAATCTTTATTGTATTGGTGACGCCAATGGGAAAATGATGTTAGCACATGCAGCTAGTGCCCAAGGCATCTCTGgtatgtcaattggctctaagacaa-ataaatgaagtatttatttatatatttattgatttttatcctcaatgctccaatgcttcaaagctattcgatggttccacgcaattgataaattttatgatattttagtttgaagtccttaccgagttaatgactttcttttacag
||||||||  | || || |||||||| |||||||| ||| ||||| | ||||||||||| ||||||||||| || |||||||  |   ||  |  || ||    |  ||  | | | | || | |    || ||  || ||   |    |  |  ||  ||       || ||  ||| |                                                                      
GTTCCGAACTTGTACTGCATTGGTGATGCCAATGGTAAATTGATGCTTGCACATGCAGCCAGTGCCCAAGGAATTTCTGgtaaatggcttatcagtaggaggctactaacaatgcaataatattttcccttttttcttcttgagccttgtatta-aactctgagctcttactctgtggctag--------------------------------------------------------------------

upper sequence: PP1S352_68V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 5'ss of exon 10
GTTCCGAATCTTTATTGTATTGGTGACGCCAATGGGAAAATGATGTTAGCACATGCAGCTAGTGCCCAAGGCATCTCTGgtatgtcaattggctctaagacaaataaatgaagtatttatttatatatttattgatttttatcctcaatgctccaatgcttcaaagctattcgatggttccacgcaattgataaattttatgatattttagtttgaagtccttaccgagttaatgactttcttttacag
|||||  |  | || || || ||||| |||||||| ||| ||||| | || |||||||||||||| ||||| || |||||||     | ||| | ||     ||||  | |  |    ||  || | | | ||| ||||  |  || |  ||  ||| | | | |   |     |  ||  || | ||  ||  | ||  || |   |                                         
GTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTGgta-----aatggtttta---tcaatatttcac-tccaaatgcatctttcttttgtttttccttttctacactg-aatacgttagattgacct--ttattaaactctatgcatctactt-gtgttggctag---------------------------------------

upper sequence: PP1S352_68V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 5'ss of exon 10
GTTCCGAATCTTTATTGTATTGGTGACGCCAATGGGAAAATGATGTTAGCACATGCAGCTAGTGCCCAAGGCATCTCTGgtatgtcaattggctctaagacaaataaatgaagtatttatttatatatttattgatttttatcctcaatgctccaatgcttcaaagctattcgatggttccacgcaattgataaattttatgatattttagtttgaagtccttaccgagttaatgactttcttttacag
|||||  |  | ||||| |||||||| || ||||| ||||||||| | || ||||| || ||||||||||| ||||||||||  | |  | | |    | ||           | | || | | ||  || |||   || |   | |||       | ||| ||| ||      |  ||   ||  || |                                                           
GTTCCTCACTTGTATTGCATTGGTGATGCAAATGGAAAAATGATGCTTGCTCATGCTGCAAGTGCCCAAGGAATCTCTGgta-attaccttgtttgttgccactctc------tctctact-acatggtttttgtcattcagttttaatatc----tacttgaaacctgacttttcttttgtcgacatag-----------------------------------------------------------

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|162191185|gb|FC367863.1|FC367863
EST:     CAATGGGAAAATGATGTTAGCACATGCAGCTAGTGCCCAAGGCATCTCTG                         TCATTGAGCAGATTGCTGGGCGAGATAATGTTCTGAATCATAACAGCGTTC
genomic: CAATGGGAAAATGATGTTAGCACATGCAGCTAGTGCCCAAGGCATCTCTGgtatgtcaat ... tcttttacagTCATTGAGCAGATTGCTGGGCGAGATAATGTTCTGAATCATAACAGCGTTC
EST: gi|37832281|gb|BJ590293.1|BJ590293
EST:     CAATGGGAAAATGATGTTAGCACATGCAGCTAGTGCCCAAGGCATCTCTG                         TCATTGAGCAGATTGCTGGGCGAGATAATGTTNTGAATCATAACAGCGTTC
genomic: CAATGGGAAAATGATGTTAGCACATGCAGCTAGTGCCCAAGGCATCTCTGgtatgtcaat ... tcttttacagTCATTGAGCAGATTGCTGGGCGAGATAATGTTCTGAATCATAACAGCGTTC
EST: gi|162246422|gb|FC421089.1|FC421089
EST:     CAATGGGAAAATGATGTTAGCACATGCAGCTAGTGCCCAAGGCATCTCTG                         TCATTGAGCAGATTGCTGGGCGAGATAATGTTCTGAATCATAACAGCGTTC
genomic: CAATGGGAAAATGATGTTAGCACATGCAGCTAGTGCCCAAGGCATCTCTGgtatgtcaat ... tcttttacagTCATTGAGCAGATTGCTGGGCGAGATAATGTTCTGAATCATAACAGCGTTC
EST: gi|162183079|gb|FC360645.1|FC360645
EST:     CAATGGGAAAATGATGTTAGCACATGCAGCTAGTGCCCAAGGCATCTCTG                         TCATTGAGCAGATTGCTGGGCGAGATAATGTTCTGAATCATAACAGCGTTC
genomic: CAATGGGAAAATGATGTTAGCACATGCAGCTAGTGCCCAAGGCATCTCTGgtatgtcaat ... tcttttacagTCATTGAGCAGATTGCTGGGCGAGATAATGTTCTGAATCATAACAGCGTTC
EST: gi|162186605|gb|FC363577.1|FC363577
EST:     CAATGGGAAAATGATGTTAGCACATGCAGCTAGTGCCCAAGGCATCTCTG                         TCATTGAGCAGATTGCTGGGCGAGATAATGTTCTGAATCATAACAGCGTTC
genomic: CAATGGGAAAATGATGTTAGCACATGCAGCTAGTGCCCAAGGCATCTCTGgtatgtcaat ... tcttttacagTCATTGAGCAGATTGCTGGGCGAGATAATGTTCTGAATCATAACAGCGTTC
EST: gi|162191186|gb|FC367864.1|FC367864
EST:     CAATGGGAAAATGATGTTAGCACATGCAGCTAGTGCCCAAGGCATCTCTG                         TCATTGAGCAGATTGCTGGGCGAGATAATGTTCTGAATCATAACAGCGTTC
genomic: CAATGGGAAAATGATGTTAGCACATGCAGCTAGTGCCCAAGGCATCTCTGgtatgtcaat ... tcttttacagTCATTGAGCAGATTGCTGGGCGAGATAATGTTCTGAATCATAACAGCGTTC
EST: gi|162166471|gb|FC343168.1|FC343168
EST:     GCAGCTAGTGCCCAAGGCATCTCTG                         TCATTGAGCAGATTGCTGGGCGAGATAATGTTCTGAATCATAACAGCGTTC
genomic: GCAGCTAGTGCCCAAGGCATCTCTGgtatgtcaat ... tcttttacagTCATTGAGCAGATTGCTGGGCGAGATAATGTTCTGAATCATAACAGCGTTC
EST: gi|162186604|gb|FC363576.1|FC363576
EST:     CAATGGGAAAATGATGTTAGCACATGCAGCTAGTGCCCAAGGCATCTCTG                         TCATTGAGCAGATTGCTGGGCGAGATAATGTTCTGAATCATAACAGCGTTC
genomic: CAATGGGAAAATGATGTTAGCACATGCAGCTAGTGCCCAAGGCATCTCTGgtatgtcaat ... tcttttacagTCATTGAGCAGATTGCTGGGCGAGATAATGTTCTGAATCATAACAGCGTTC
EST: gi|208368657|gb|DC947932.1|DC947932
EST:     CAATGGGAAAATGATGTTAGCACATGCAGCTAGTGCCCAAGGCATCTCTG                         TCATTGAGCAGATTGCTGGGCGAGATAATGTTCTGAATCATAACAGCGTTC
genomic: CAATGGGAAAATGATGTTAGCACATGCAGCTAGTGCCCAAGGCATCTCTGgtatgtcaat ... tcttttacagTCATTGAGCAGATTGCTGGGCGAGATAATGTTCTGAATCATAACAGCGTTC
EST: gi|67700043|gb|BJ960276.1|BJ960276
EST:     CAATGGGAAAATGATGTTAGCACATGCAGCTAGTGCCCAAGGCATCTCTG                         TCATTGAGCAGATTGCTGGGCGAGATAATGTTCTGAATCATAACAGCGTTC
genomic: CAATGGGAAAATGATGTTAGCACATGCAGCTAGTGCCCAAGGCATCTCTGgtatgtcaat ... tcttttacagTCATTGAGCAGATTGCTGGGCGAGATAATGTTCTGAATCATAACAGCGTTC

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), 32 (downstream exon)
Score: 3

GTTCCGAATCTTTATTGTATTGGTGACGCCAATGGGAAAATGATGTTAGCACATGCAGCTAGTGCCCAAGGCATCTCTGgtatgtcaat ... tcttttacagTCATTGAGCAGATTGCTGGGCGAGATAATGTTCTGAATCATAACAGCGTTCCAGCAGCTTGTTTCACACACCCTGAAATCAGCATGGTTGGACTTACTGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCCGAATCTTTATTGTATTGGTGACGCCAATGGGAAAATGATGTTAGCACATGCAGCTAGTGCCCAAGGCATCTCTGgtatgtcaattggctctaagacaaataaatgaagtatttatttatatatttattgatttttatcctcaatgctccaatgcttcaaagctattcgatggttccacgcaattgataaattttatgatattttagtttgaagtccttaccgagttaatgactttcttttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT