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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttttttgtttttttcttattctttttaattttatttattaatttatttattttattatctcccatgtagttatttctttttacaagcttgaattcttaaacatgatcattgtgatatatctatatttaatgattatctaacaagtggtgaaaataaaattagGTTCAAGTGTGTGGATTTAGATTGTGATGGGGTGATCACTGCAAATGAAATGCATTATTTTTATGAGGAGCAATTACATCGAATGGAATGTATGGCACAA

Basic information

species Physcomitrella patens
transcript PP1S191_94V6.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S191_94V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GRMZM2G104254_T01 (Zea mays), 3'ss of exon 5
gtaatttttttgtttttttcttattctttttaattttatttattaatttatttattttattatctcccatgtagttatttctttttacaagcttgaattcttaaacatgatcattgtgatatatctatatttaatgattatctaacaagtggtgaaaataaaattagGTTCAAGTGTGTGGATTTAGATTGTGATGGGGTGATCACTGCAAATGAAATGCATTATTTTTATGAGGAGCAATTACATCGAATGGAATGTATGGCACAA
                                                              | | |  | |   |  | | | ||  |    | |  |  ||       |   | | | |||| | || ||  |  ||||  || |  || | ||| |      ||||| |||||  | ||| | ||| || ||||  |  | |||   ||||||||||| | ||| |||||||||||||| || |||||||| || |||||||| 
--------------------------------------------------------------tattctgtatttgttgtacatattgtataactcagcttgtagttgcattttctttaaaatat-tgtaattgtttgttattgaa-atatgttaaaatttg---cagGTTTAAGTGCATCGATCTTGATGGTAATGGTATTTTAACTTACAATGAAATGCAATTTTTCTATGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAG

upper sequence: PP1S191_94V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 9
gtaatttttttgtttttttcttattctttttaattttatttattaatttatttattttattatctcccatgtagttatttctttttacaagcttgaattcttaaacatgatcattgtgatatatctatatttaatgattatctaac--aagtggtgaaaataaaatt---agGTTCAAGTGTGTGGATTTAGATTGTGATGGGGTGATCACTGCAAATGAAATGCATTATTTTTATGAGGAGCAATTACATCGAATGGAATGTATGGCACAA
                                                                      || ||| |    | ||||    ||  ||  ||    ||   |||||| |||| ||    |  | |  |  | | |   || |   | ||| ||  ||   ||||| |||||  | ||| | ||| || ||||  |  | |||   ||||||||||| | ||| || ||||||||||| || |||||||| || |||||||||
----------------------------------------------------------------------gttgttgtgatctattaccttattctatctttgc-tatacacattgt-atatctcaggttacagttgtatttttattgaaatatgggaaacaactttcgcagGTTTAAGTGCATCGATCTTGATGGTAATGGTATTTTAACTTTCAATGAAATGCAATTTTTCTACGAGGAGCAATTGCACCGAATGGAGTGCATGGCACAA

upper sequence: PP1S191_94V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 9
gtaatttttttgtttttttcttattctttttaattttatttattaatttatttattttattatctcccatgtagttatttctttttacaagcttgaattcttaaacatgatcattgtgatatatctatatttaatgattatcta---acaagtgg---tgaaaat---aaaattagGTTCAAGTGTGTGGATTTAGATTGTGATGGGGTGATCACTGCAAATGAAATGCATTATTTTTATGAGGAGCAATTACATCGAATGGAATGTATGGCACAA
                                                                            ||    |||   || |      | ||  ||||  |  |||   | | |     |||     | ||| |   || ||  |   |||||||   |  ||||||||||||||  | ||||| ||| |  |||| ||  | ||    |||||| |||| | |||||||||||||||||| ||||| |||||||| ||||| |||
----------------------------------------------------------------------------atgctatttggtaaacagtggatatttgacatcgtggttgacttgttttctggtttttaagtcatcaaagtacgagctgacttgaaaatgtcactattagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTAACAAGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGGATGGAATGCATGGCCCAA

upper sequence: PP1S191_94V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 9
gtaatttttttgtttttttcttattctttttaattttatttattaatttatttattttattatctcccatgtagttatttctttttacaagcttgaattcttaaacatgatcattgtgatatatctatatttaatgattatctaacaagtggtgaaaataaaattagGTTCAAGTGTGTGGATTTAGATTGTGATGGGGTGATCACTGCAAATGAAATGCATTATTTTTATGAGGAGCAATTACATCGAATGGAATGTATGGCACAA
                                                      ||||      | ||   ||  ||     ||   | | | |        ||   ||||| ||||| |  |    ||  || |  | || | ||  ||  |||        |||||||||||||  | ||||| ||| |  |||| ||  | ||    |||||| |||| | |||||||||||||||||| ||||||||||| || ||||| |||
------------------------------------------------------ttttccaccttgcctcctaagtacactcttaggcgaacattgg-----aagtttgatctttgtggttgactattagctatttgtgatttgacgtgtcatga--------ttagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA

upper sequence: PP1S191_94V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 9
gtaatttttttgtttttttcttattctttttaattttatttattaatttatttattttattatctcccatgtagttatttctttttacaagcttgaattcttaaacatgatcattgtgatatatctatatttaatgattatctaacaagtggtgaaaataaaattagGTTCAAGTGTGTGGATTTAGATTGTGATGGGGTGATCACTGCAAATGAAATGCATTATTTTTATGAGGAGCAATTACATCGAATGGAATGTATGGCACAA
                                                         |      | ||   ||  ||     ||   | | | |        ||   ||| | ||||| |  |    | ||       ||| |   |  || ||     |  ||||||||||||||  | ||||| ||| |  |||| ||  | ||    |||||| |||| | |||||||||||||||||| ||||||||||| || ||||| |||
---------------------------------------------------------tccaccttgcctcctaagtacactcttaggcgaacattgg-----aagtttgacctttgtggttgactcttgtt----agctatttgtgatttgatgtgt-catgattagGTTCAAGTGCATTGATTTGGATGGAAATGGAGTTCTGACACGGAATGAACTGCAATTTTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAA

upper sequence: PP1S191_94V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv07s0005g03730.t01 (Vitis vinifera), 3'ss of exon 10
gtaatttttttgtttttttcttattctttttaattttatttattaatttatttattttattatctcccatgtagttatttctttttacaagcttgaattcttaaacatgatcattgtgatatatctatatttaatgattatctaacaagtggtgaaaataaaattagGTTCAAGTGTGTGGATTTAGATTGTGATGGGGTGATCACTGCAAATGAAATGCATTATTTTTATGAGGAGCAATTACATCGAATGGAATGTATGGCACAA
                                                    |||   ||||  |   | | |||   ||         |  ||||     ||||  |  |  || || || ||| || |  |    | |  |    | |  | |   |      |||||||||||  | ||||| ||| |  |||| ||| | ||    ||||||||||| |  ||||||||||||||||| |||||||||||||| ||||| |||
----------------------------------------------------tatgggattaggtttgaggcagtagctt---------aatttgatgctctaaatttatttgttatg-ta-atcaatgtgcatcactcactttgtgaatttttatttt----ccagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTGCTTACACTGAATGAAATGCAGTTCTTTTATGAGGAGCAATTGCATCGAATGGAATGCATGGCCCAA

upper sequence: PP1S191_94V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv14s0036g00750.t01 (Vitis vinifera), 3'ss of exon 6
gtaatttttttgtttttttcttattctttttaattttatttattaatttatttattttattatctcccatgtagttatttctttttacaagcttgaattcttaaacatgatcattgtgatatatctatatttaatgattatctaacaagtggtgaaaataaaattagGTTCAAGTGTGTGGATTTAGATTGTGATGGGGTGATCACTGCAAATGAAATGCATTATTTTTATGAGGAGCAATTACATCGAATGGAATGTATGGCACAA
                                                                  |  || |    ||| || | | |   ||       | |  ||    |||    ||||   | |  |    | ||  |   |  |        |   ||||||||||||||  | ||||| ||| |  |||| ||  | ||    ||||||||||| |  |||||||||||||| || |||||||||||||| ||||| |||
-----------------------------------------------------------------tctttggatggctttattatgaaatatttttgcatctcattatag--atttcattatacaaacaactgtatactacttgtgacattaacttgttttcattagGTTCAAGTGCATAGATTTGGATGGAAATGGAGTTCTGACAAGGAATGAAATGCAATTCTTTTATGAGGAGCAGTTGCATCGAATGGAATGCATGGCCCAA

upper sequence: PP1S191_94V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: EFJ32791 (Selaginella moellendorffii), 3'ss of exon 9
gtaatttttttgtttttttcttattctttttaattttatttattaatttatttattttattatctcccatgtagttatttctttttacaagcttgaattcttaaacatgatcattgtgatatatctatatttaatgattatctaacaagtggtgaaaataaaattagGTTCAAGTGTGTGGATTTAGATTGTGATGGGGTGATCACTGCAAATGAAATGCATTATTTTTATGAGGAGCAATTACATCGAATGGAATGTATGGCACAA
                                                                                                        |   || | |  |||    ||| ||   |  |||    | |||  | | ||          |||||||| ||| | ||| | |||||||| || ||| | ||| |||| || ||||| || ||||||||||||||||| ||||| ||||| ||  | || |||
------------------------------------------------------------------------------------------------------gtaagcga-cgtcttgaatcttctgtaag-atcgatcgattgacagatcgcgacttc-----cagGTTCAAATGTATCGATCTGGATTGTGACGGAGTGGTGACTCCAAACGAGATGCAGTACTTTTATGAGGAGCAATTGCATCGCATGGAGTGCCTAGCTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtgatatatctatatttaatgattatctaacaagtggtgaaaataaaattagGTTCAAGTGTGTGGATTTAGATTGTGATGGGGTGATCACTGCAAATGAAATGCATTATTTTTATGAGGAGCAATTACATCGAATGGAATGTATGGCACAA
                           atctaac  putative branch site (score: 2)
      atatatctatatttaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttttttgtttttttcttattctttttaattttatttattaatttatttattttattatctcccatgtagttatttctttttacaagcttgaattcttaaacatgatcattgtgatatatctatatttaatgattatctaacaagtggtgaaaataaaattagGTTCAAGTGTGTGGATTTAGATTGTGATGGGGTGATCACTGCAAATGAAATGCATTATTTTTATGAGGAGCAATTACATCGAATGGAATGTATGGCACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA