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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgattgattcatttatctaatacaagacactaccaaattcttccactccagactttaaccatcgcaattccacttcacgtgatcatttctatacagggtcttaagtagtgtttatgtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGGACAATGGTTGCTGGAGGTGGTGCCAGTGTCATTTACGCTGATACT

Basic information

species Physcomitrella patens
transcript PP1S63_54V6.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S63_54V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os11g47330.1 (Oryza sativa), 3'ss of exon 6
-------------------------------------------------------gtgtgattgattcatttatctaata----caagacactaccaaattcttccactccagactttaaccatcgcaattccacttcacgtgatcatttctata-----cagggtcttaagtagtgtttatgtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGGACAATGGTTGCTGGAGGTGGTGCCAGTGTCATTTACGCTGATACT
                                                        |  |  ||| |    | | |||||    ||  |   |  || ||   | ||     || |     ||       ||      |  || |  |||  ||      |    | | |  |  |||   | |   | |||||  |||| |||||||| || ||  |  |||| || ||||| ||||| ||||||||||||||||||||||||||||||||||| || |||||||| 
gtatccacatctcaaattacacgtttcacatttcaagcctcctccccaatcttatttaagtatgagttgcctgtataatatcatcagtaggtttgcacatgaattcagataggagtgctggcagtctggctcagtactatatgtttttttgaattattttctaaatgtgatatgatgtccttattctttcagACAAGTGCATCTCTGAAGTTCACCGTTTTGAACCCAAAGGGGCGCATCTGGACAATGGTTGCTGGAGGTGGTGCCAGTGTCATATATGCTGATACA

upper sequence: PP1S63_54V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os12g37870.1 (Oryza sativa), 3'ss of exon 6
--------gtgtgattgattcatttatctaatacaagacactaccaaattcttccactccagactttaa--ccatcgcaattccacttcacgtgatcatttctatacagggtcttaagtagtgttt-atgtggctg--cagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGGACAATGGTTGCTGGAGGTGGTGCCAGTGTCATTTACGCTGATACT
         | |   |   |      ||| |     |   |     | | | |       | | ||  |  | |    |||| |||| |   ||         |||  |  |||| | | | | || ||||   |   |||||  |  | || || ||||| ||  | ||||| ||||| || |||||||||||||||||||| || |||||||| |||||||| || |||||||||
gtaacctcatatttctttctttcccctctgaagtctgctgcctgttagtacatatcacttaaatttggatacaaattgaatttcactgcctctgcatgcaaa-atattgaatcttgaattgaggttgatgtaatttttcagACAAGCTCATCGCTCAAATTCACAGTCCTGAACCCGAAAGGGCGCATTTGGACAATGGTTGCAGGTGGTGGTGCTAGTGTCATATATGCTGATACT

upper sequence: PP1S63_54V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os11g47120.1 (Oryza sativa), 3'ss of exon 6
-------------------------------------------------------gtgtgattgattcatttatctaata----caagacactaccaaattcttccactccagactttaaccatcgcaattccacttcacgtgatcattt-----ctatacagggtcttaagtagtgtttatgtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGGACAATGGTTGCTGGAGGTGGTGCCAGTGTCATTTACGCTGATACT
                                                        |  |  ||| |    | | |||||    ||  |   |  || ||   | ||     || |     ||       ||  |   |  || |  |||      | | |    | | |  || ||    | |   | |||||  |||| |||||||| || ||  |  |||| || ||||| ||||| ||||||||||||||||||||||                          
gtatccacatctcaaattacacgtttcacatttcaagcctcctccccaatcttttttaagtatgagttgcctgtataatatcatcagtaggtttgcacatgaattcagataggagtgctggcagtctggctcagcactatatgtttttttgaattatttgctaaatgtgatataatgaccttattctttcagACAAGTGCATCTCTGAAGTTCACCGTTTTGAACCCAAAGGGGCGCATCTGGACAATGGTTGCTGGAGGTG--------------------------

upper sequence: PP1S63_54V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G034083_T01 (Zea mays), 3'ss of exon 6
-------------------------gtgtgattgattc--atttatctaatacaagacactaccaaattcttccac-tccagactt-taaccatcgcaattccacttcacgtgatcatttctatacagggtcttaagtagtg-----tttatgtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGGACAATGGTTGCTGGAGGTGGTGCCAGTGTCATTTACGCTGATACT
                          |    | |||||  |  | |||  |  |||  | ||    ||| | |    |  | | || ||        || |    || ||       | | |       |  ||||||||||      || | |   |||||||  |||||||||||||||| ||| ||||||| || || || ||||| |||||||||||||| || |||||||| |||||||| ||||| || |||
gtatgttcatgtaaaagtggacaacttacattcgattccaacctttctccttgaagtaattatttcattttccagtgtttacatttctatttggattaacttttattgacagttctgtatgttccactagatttaagtagtgaaccacttctcttcttgcagACAAGTGCTTCTCTGAAATTCACGGTACTGAACCCAAAAGGACGCATCTGGACAATGGTTGCAGGTGGTGGTGCTAGTGTCATATACGCAGACACT

upper sequence: PP1S63_54V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G107082_T01 (Zea mays), 3'ss of exon 6
---------------gtgtgattgattcatttatctaatacaagacactaccaaattcttccactccagactttaaccatcgcaattccacttcacgtgatcatttctatacagggtcttaagtagt-gtttatgtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGGACAATGGTTGCTGGAGGTGGTGCCAGTGTCATTTACGCTGATACT
                | || ||   || ||||| |  |   ||   ||| ||  |          |||  |  |    | | ||| | |  ||  | |   |||    |   | || |||| | |       |||   | |||||  |||| |||||||| || ||| |  |||| ||||| || ||||| ||||| ||||| ||||| |||||||| ||||||||||| |||||||| 
gtattgatctcagggctatgtttttatcttttattttttctgaggt-ctatcatgtataaaataatcagtttccat---tagaaatactagatctggagtgtattctgttgacgtgtgttaattcgccaaccttgttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGGACCATGGTCGCTGGTGGTGGTGCTAGTGTCATTTATGCTGATACA

upper sequence: PP1S63_54V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA03G38810.3 (Glycine max), 3'ss of exon 7
gtgtgattgattcatttatctaatacaagacactaccaaattcttccactccagactttaaccatcgcaattccacttcacgtgatcatttc-tatacagggtcttaag---tagtgtttatgtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGGACAATGGTTGCTGGAGGTGGTGCCAGTGTCATTTACGCTGATACT
                               ||    |  ||  |  | | || ||||     ||   |||   |    | | |||  ||   | |||||  || |||    || | ||| |||   |||||||  |||| ||  ||||||| || ||| |||||||||| || ||||| ||||||||||| || ||||||||||| ||||| ||||| |||||||| 
-----------------------------gtacc-ttagttttgtaaaattcatacttcc-ttattttaatagtaacaaatgggatttttctgtgtacagattcctaaaatatactctttttgta-ttgcagACAAGTGCATCATTGAAATTTACTATATTGAATCCGAAAGGACGCATATGGACAATGGTAGCAGGAGGTGGTGCAAGTGTAATTTATGCTGATACG

upper sequence: PP1S63_54V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA01G03530.1 (Glycine max), 3'ss of exon 8
gtgtgattgattcatttatctaatacaagacactaccaaattcttccactccagactttaaccatcgcaattccacttcacgtgatcatttctatacagggtcttaagtagtgtttatgtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGGACAATGGTTGCTGGAGGTGGTGCCAGTGTCATTTACGCTGATACT
                   |||| |   | ||  |  ||     |  | |   || |  ||  ||   | |    |||   ||  | ||||  |||     | |       | ||||  |   |||||||  |||| ||  | ||||| ||  |  |||| || |||||||| |||||||||||||| ||||| || ||||| ||||||||||| |||||||| 
-------------------ctaacagctgtcatcagtaa-----tgtattgatgaatgcaataat---actattgcttatagttgtaattttgataattaatttgtttgtttatttac-tatttgcagACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCAAAGGGCCGAATTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTCATTTATGCTGATACG

upper sequence: PP1S63_54V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA08G17010.2 (Glycine max), 3'ss of exon 8
gtgtgattgattcatttatctaatacaagacactaccaaattcttccactccagactttaaccatcgcaattccacttcacgtgatcatttctatacagggtcttaagtagtgtttatgtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGGACAATGGTTGCTGGAGGTGGTGCCAGTGTCATTTACGCTGATACT
                 ||||  ||  |  |||     |||| |    || |      ||| ||| ||  |   | |||   |    ||     ||    || |   ||  |  || | ||    |||||  |||| ||| ||||||| ||  || | || || | |||||| |||||||||||||| ||||| || ||||| |||||||| || |||||||| 
-----------------atctcttatcaatcac-----aattttattgcttctag---taatcatggcgctataaattcttttacatatacgcttatgatgttt---gtgtttattttctgttcccagACAAGTGCATCTTTGAAATTCACAGTATTAAACCCAATGGGCCGAATTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTCATCTATGCTGATACG

upper sequence: PP1S63_54V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA15G42140.2 (Glycine max), 3'ss of exon 7
gtgtgattgattcatttatctaatacaagacactaccaaatt-cttccactccagactttaaccatcgcaattccacttcacgtgatcatttctatacagggtcttaagtagtgtttatgtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGGACAATGGTTGCTGGAGGTGGTGCCAGTGTCATTTACGCTGATACT
                   ||  ||  |  ||  |    ||| |||| | |    |   |     |   |||||   || || | | || || |     |    ||   |  |  || | ||    |||||  |||| ||| ||||||| ||  || | || || | |||||| |||||||||||||||||||| || ||||| ||||| || || |||||||| 
-------------------ctcttattaatcataattttattgcttctagt---aatcatggtgctataaattct--tttacataaacacttat-----gatgtttgtttgtttgttttctgttcccagACAAGTGCATCTTTGAAATTCACAGTATTAAACCCAATGGGCCGAATTTGGACAATGGTTGCTGGGGGAGGTGCTAGTGTTATCTATGCTGATACG

upper sequence: PP1S63_54V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA02G04120.2 (Glycine max), 3'ss of exon 8
gtgtgattgattcatttatctaatacaagacactaccaaattcttccactccagactttaaccatcgcaattccacttcacgtgatcatttctatacagggtcttaagtagtgtttatgtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGGACAATGGTTGCTGGAGGTGGTGCCAGTGTCATTTACGCTGATACT
                   |||| |  || ||  |  ||     |  | |  |||    ||  ||   | |    |||   ||  | ||||  ||||    | |       | ||||  |   |||||||  |||| ||  | ||||| ||  |  |||| || |||||||| |||||||||||||| ||||| || ||||| ||||| || || |||||||| 
-------------------ctaacagcagtcatcagtaa-----tgtattgaagaacgcaataat---actattgcttatagttgtaattttgatacttaatttgtttgtttatttac-tatttgcagACAAGTGCATCCTTAAAATTCACAGTGTTGAACCCTAAGGGCCGAATTTGGACAATGGTAGCTGGGGGAGGTGCTAGTGTTATCTATGCTGATACG

upper sequence: PP1S63_54V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: AT1G09430.1 (Arabidopsis thaliana), 3'ss of exon 7
gtgtgattgattcatttatctaatacaagacactaccaaattcttccactccagactttaaccatcgcaattccacttcacgtgatcatttctatacagggtcttaagtagtgtttatg--tggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGGACAATGGTTGCTGGAGGTGGTGCCAGTGTCATTTACGCTGATACT
|| | |         || |||||    | |||| ||     | ||      |||||   ||  |    ||    |  | || ||| ||||  | |    |    |  || |||||| |   |   |||||||  |||||||| |||| || ||  |  ||||||| || |||||||||||||| ||||| |||||||||||||| || ||||| || |||||||| 
gtttaagcatccagcttttctaa----aaacaccac-----ttttgtgactcagacaggaaagacttgaaagtaatgttac-tgaccattcatgtctgtgtgtgtgtgt-gtgtttgttacttattgcagACAAGTGCTTCTTTGAAGTTCACTGTTTTGAATCCTAAAGGCCGCATTTGGACGATGGTAGCTGGAGGTGGTGCTAGCGTCATATATGCTGATACA

upper sequence: PP1S63_54V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: EFJ27687 (Selaginella moellendorffii), 3'ss of exon 7
gtgtgattgattcatttatctaatacaagacactaccaaattcttccactccagactttaaccatcgcaattccacttcacgtgatcatttctatacagggtcttaagtagtgtttatgtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGGACAATGGTTGCTGGAGGTGGTGCCAGTGTCATTTACGCTGATACT
                                                                      |   |||||      || || ||        |  | | | |  ||| | | | | ||||| ||||| ||| | ||  |||| ||||| |||||||| || ||||||||||||||||| ||||| ||||| || ||||| || || || || || 
---------------------------------------------------------------------gtcagacttcttcctctctttcctcagtcttctgatgactcgaatttgttttgtt-cagACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAGGTCGCATTTGGACAATGGTCGCTGGCGGTGGCGCGAGTGTGATCTATGCCGACACA

upper sequence: PP1S63_54V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: EFJ37257 (Selaginella moellendorffii), 3'ss of exon 7
gtgtgattgattcatttatctaatacaagacactaccaaattcttccactccagactttaaccatcgcaattccacttcacgtgatcatttctatacagggtcttaagtagtgtttatgtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGGACAATGGTTGCTGGAGGTGGTGCCAGTGTCATTTACGCTGATACT
                                                                      |   |||||      || || ||        |  | | | |  ||| | | | | ||||| ||||| ||| | ||  |||| ||||| |||||||| || ||||||||||||||||| ||||| ||||| || ||||| || || || || || 
---------------------------------------------------------------------gtcagacttcttcctctctttccttagtcttctgatgactcgaatttgttttgtt-cagACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAGGTCGCATTTGGACAATGGTCGCTGGCGGTGGCGCGAGTGTGATCTATGCCGACACA

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|208365149|gb|DC946778.1|DC946778
EST:     GAAGAACCATGACTCCAGCCGAGGAGAGTATTCACAGGATGGACGAGAAG                         ACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGG
genomic: GAAGAACCATGACTCCAGCCGAGGAGAGTATTCACAGGATGGACGAGAAGgtgtgattga ... gtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGG
EST: gi|162235867|gb|FC412418.1|FC412418
EST:     GAACCATGACTCCAGCCGAGGAGAGTATTCACAGGATGGACGAGAAG                         ACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGG
genomic: GAACCATGACTCCAGCCGAGGAGAGTATTCACAGGATGGACGAGAAGgtgtgattga ... gtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGG
EST: gi|208364467|gb|DC958036.1|DC958036
EST:     GAAGAACCATGACTCCAGCCGAGGAGAGTATTCACAGGATGGACGAGAAG                         ACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGG
genomic: GAAGAACCATGACTCCAGCCGAGGAGAGTATTCACAGGATGGACGAGAAGgtgtgattga ... gtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGG
EST: gi|37846736|gb|BJ604744.1|BJ604744
EST:     ATGACTCCAGCCGAGGAGAGTATTCACAGGATGGACGAGAAG                         ACCCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTG
genomic: ATGACTCCAGCCGAGGAGAGTATTCACAGGATGGACGAGAAGgtgtgattga ... gtggctgcagA-CCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTG
EST: gi|67697641|gb|BJ957874.1|BJ957874
EST:     GAACCATGACTCCAGCCGAGGAGAGTATTCACAGGATGGACGAGAAG                         ACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGG
genomic: GAACCATGACTCCAGCCGAGGAGAGTATTCACAGGATGGACGAGAAGgtgtgattga ... gtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGG
EST: gi|208385420|gb|DC956632.1|DC956632
EST:     GAAGAACCATGACTCCAGCCGAGGAGAGTATTCACAGGATGGACGAGAAG                         ACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGG
genomic: GAAGAACCATGACTCCAGCCGAGGAGAGTATTCACAGGATGGACGAGAAGgtgtgattga ... gtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGG
EST: gi|37845681|gb|BJ603689.1|BJ603689
EST:     CCATGACTCCAGCCGAGGAGAGTATTCACAGGATGGACGAGAAG                         ACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGG
genomic: CCATGACTCCAGCCGAGGAGAGTATTCACAGGATGGACGAGAAGgtgtgattga ... gtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGG

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: 33 (upstream exon), 29 (downstream exon)
Score: 12

GTGGGGCAATGTGGAGTTTCCATTACCCTTTGGAAGAACCATGACTCCAGCCGAGGAGAGTATTCACAGGATGGACGAGAAGgtgtgattga ... gtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGGACAATGGTTGCTGGAGGTGGTGCCAGTGTCATTTACGCTGATACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacttcacgtgatcatttctatacagggtcttaagtagtgtttatgtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGGACAATGGTTGCTGGAGGTGGTGCCAGTGTCATTTACGCTGATACT
              atttctata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgattgattcatttatctaatacaagacactaccaaattcttccactccagactttaaccatcgcaattccacttcacgtgatcatttctatacagggtcttaagtagtgtttatgtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGGACAATGGTTGCTGGAGGTGGTGCCAGTGTCATTTACGCTGATACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT